FANTOM5 analysis call: Difference between revisions

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'''FANTOM5 Analysis Call has been reincarnated as RNA analysis call.'''
Weekly telephone calls open to all collaborators are held every '''Thursday 17:00 -18:00 JST'''. In case of Japanese holidays or special events, no call will be held. In such cases, information will be sent out to the FANTOM5 mailing list.


For the time-being the call will be held intermittently at the Thursday teleconference time-slot. Notifications will be sent through FANTOM 5 mailing list as usual.
The agenda is decided by the FANTOM5 Management group at RIKEN. Suggestions can be sent to Piero Carninci. Agenda will be announced to the FANTOM5 mailing list every Wednesday. Presentation materials will be available on this page before each meeting.


The agenda is decided by the FANTOM5 Management group at RIKEN. Suggestions can be sent to Michiel de Hoon. Agenda will be announced to the FANTOM5 mailing list every Wednesday. Presentation materials will be available on this page before each meeting.
The meetings will be recorded and saved here for later reference.


The meetings will be recorded and saved here for later reference.


Phone numbers:
<br> Phone numbers:


From outside of Japan: +81-3-4333-4000
From outside of Japan: +81-3-4333-4000


From anywhere in Japan: 050-3786-6666 (in Japanese) or 0570-03-4444 (in English)
From anywhere in Japan: 050-3786-6666 (in Japanese) or 0570-03-4444 (in English)


From the Tokyo Area: 03-4333-4444 (in Japanese) or 03-4333-4000 (in English)
From the Tokyo Area: 03-4333-4444 (in Japanese) or 03-4333-4000 (in English)


From the Osaka Area: 06-7637-2222
From the Osaka Area: 06-7637-2222


<br> You will be asked to enter conference ID followed by # and guest password followed by # to join the conference. Please find them below:


Conference id: 24711
You will be asked to enter conference ID and guest password for the conference. Please find them below:


Guest password: 3502
Conference id: 24711


You will also be asked to state your name and press the # key.
Guest password: 3502


<br> TIPS ON USAGE:
=April 5th=


We recommend putting your line in "listen-only" mode during presentation sessions of the call to avoid noise and other interferences.
Chair: Piero Carninci


To enable "listen-only" mode press 97.


To disable "listen-only" mode press 96.
'''AGENDA'''


<br> [http://www.clearconference.jp/guide/download/clearconference_sheet_guest_e.pdf Call In Instructions for guest users (English)]
1. Progress report for this week by RIKEN OSC(Hideya KAWAJI and Alistair FORREST)


[http://www.clearconference.jp/guide/download/clearconference_sheet_guest.pdf Call In Instructions for guest users (Japanese)]
2. Work in progress(Albin SANDELIN, University of Copenhagen)


= July 2nd -- FANTOM5 lncRNA Analysis Call =
'''Audio File'''
The audio file from the call on April 5th (uploaded after the call): [[File:120405_F5_Telecon.zip]]


'''Topic: FANTOM5 lncRNA Analysis'''


*Presentation file:


*1. Benchmarking the accuracy of 5'end of FANTOM CAT lncRNA by Chung [[File:FANTOM5_lncRNA_teleconference_20150702_chung.pdf‎]]
=March 29th=


Audio File: The audio file from the call (uploaded after the call): [[File:150702_002.MP3.zip]]
'''CANCELLED'''


= June 10th -- FANTOM5 lncRNA Analysis Call =
Chair: Piero Carninci


'''Topic: FANTOM5 lncRNA Analysis'''


*Presentation file:
'''AGENDA'''


*1. Histone marks and RNA processing motifs of promoter- & enhancer-derived lncRNA by Chung, Tanvir, Haitham [[File:FANTOM5_lncRNA_teleconference_20150610_chung.pdf‎]]
1. Progress reports for this week by RIKEN OSC
*2. Tissue specificity of lncRNA (by Martin & Thomas) [[File:Thomaspres11062015.pdf]]

Audio File: The audio file from the call (uploaded after the call): [recording missed]

= May 28th -- FANTOM5 lncRNA Analysis Call =

'''Topic: FANTOM5 lncRNA Analysis'''

*Presentation file:

*1. Recap: Defining promoter- and enhancer-derived lncRNA using ROADMAP data (by Chung) [[File:FANTOM5_lncRNA_teleconference_20150528_chung.pptx]]
*2. GWAS SNP enrichment in lncRNA (by Sebastian & Elena) [[File:FANTOM5_lncRNA_teleconference_20150528_sebastian.pptx]]
*3. Tissue specificity of lncRNA (by Martin & Thomas) [[File:FANTOM5_lncRNA_teleconference_20150528_thomas.pdf]]


Audio File: The audio file from the call: [recording missed]

= May 7th -- FANTOM5 lncRNA Analysis Call =

'''Topic: FANTOM5 lncRNA Analysis (Chung Chau HON)'''

*Presentation file:
*by Chung [[File:FANTOM5 lncRNA teleconference 20150507.pptx]]
*by Phil Kapranov [[File:Kapranov FANTOM-2015 v4.pptx]]

Audio File: The audio file from the call (uploaded after the call): [[]]

= April 9nd -- FANTOM5 lncRNA Analysis Call =

'''Topic: FANTOM5 lncRNA Analysis (Chung Chau HON)'''

*Presentation file: [[File:FANTOM5_lncRNA_teleconference_20150409.pdf]]

Audio File: The audio file from the call (uploaded after the call): [[File:150409_001.mp3.zip]]

= April 2nd -- FANTOM5 short RNA Analysis Call =

'''Topic: FANTOM5 short RNA Analysis (Michiel de Hoon)'''

*Presentation file: [[File:Telecon_20150402.pptx‎]]

Audio File: The audio file from the call (uploaded after the call): [[Image:150402 F5 Telecon.MP3.zip]]

= March 26th -- FANTOM5 lncRNA Analysis Call =

'''Topic: FANTOM5 lncRNA Analysis (Chung)'''

*Presentation file: [[Image:FANTOM5_lncRNA_teleconference_20150326.pdf]]

Audio File: The audio file from the call (uploaded after the call): [[Image:150326_F5_Telecon.MP3.zip]]

= March 19th -- FANTOM5 short RNA Analysis Call =

'''Topic: FANTOM5 short RNA Analysis (Tanvir Alam)'''

*Presentation file: [[Image:F5shortRNA_2015_03_19_KAUST.pdf]]

Audio File: The audio file from the call (uploaded after the call): [[Image:150319 F5 Telecon.MP3.zip]]

= March 12th -- FANTOM5 RNA Analysis Call =

'''Topic: FANTOM5 lncRNA Analysis: FANTOM CAT: p_lncRNA vs e_lncRNA'''

*Sarah's slides: [[Image:F5 CAT vs histmarks SD march2015.pdf]]
*Chung's slides: [[Image:FANTOM5_lncRNA_teleconference_20150312_Chung.pdf‎]]

Audio File : The audio file from the call (uploaded after the call): [[Image:150312_F5_Telecon.MP3.zip]]

= March 5th -- FANTOM5 short RNA Analysis Call =

'''Topic: FANTOM5 short RNA Analysis (Michiel de Hoon)'''

*Presentation file: [[Image:Telecon 20150305.pptx]]

Audio File&nbsp;: The audio file from the call (uploaded after the call): [[Image:150305 F5 Telecon.MP3.zip]]

= February 26th -- FANTOM5 lncRNA Analysis Call =

'''Topic: FANTOM5 lncRNA Analysis (Chung Chau HON)'''

*Presentation file: [[Image:FANTOM5 lncRNA teleconference 20150226.pdf]]

= February 19th -- FANTOM5 short RNA Analysis Call =

'''Topic: FANTOM5 short RNA Analysis (Michiel de Hoon)'''

*Presentation file: [[Image:Telecon 20150219.pptx]]

Audio File&nbsp;: The audio file from the call (uploaded after the call): [[Image:150219 F5 Telecon.zip]]

= February 12th -- FANTOM5 lncRNA Analysis Call =

'''Topic: FANTOM5 lncRNA Analysis (Chung Chau Hon)'''

*Presentation file: [[Image:FANTOM5 lncRNA teleconference 20150112.pdf]]

Audio File&nbsp;: The audio file from the call (uploaded after the call): [[Image:150212 F5 Telecon.zip]]

= February 5th -- FANTOM5 short RNA Analysis Call =

'''Topic: FANTOM5 short RNA Analysis (Michiel de Hoon)'''

*Presentation file: [[Image:Telecon 20150205.pptx]]

Audio File&nbsp;: The audio file from the call (uploaded after the call): [[Image:150205 001.MP3.zip]]

= January 22nd -- FANTOM5 short RNA Analysis Call =

'''Topic: FANTOM5 short RNA Analysis (Michiel de Hoon)'''

*Presentation file: [[Image:Telecon 20150122.pptx]]

Audio File&nbsp;: The audio file from the call (uploaded after the call): [[Image:150122 F5 Telecon.zip]]

= October 23rd -- FANTOM5 short RNA Analysis Call =

'''Topic: Update on the FANTOM5 short RNA main paper (Michiel de Hoon)'''

*Presentation file: [[Image:Telecon 20141023.pptx]]

Audio File&nbsp;: The audio file from the call (uploaded after the call): No recording

= October 2nd -- FANTOM5 lncRNA Analysis Call =

'''Topic: FANTOM5 RNA-seq lncRNA catalog and some on-going analyses on lncRNA properties; plan on analysing lncRNA expression patterns, sub-classifying lncRNAs and intersecting lncRNA catalog with ENCODE data by Hon Chung Chau (RIKEN DGT)'''

*Presentation file: [[Image:FANTOM5 lncRNAome teleconference 02102014.pdf]]

Audio File&nbsp;: The audio file from the call (uploaded after the call): [[Image:141002 F5 Telecon.zip]]

= April 10th -- FANTOM5 short RNA Analysis Call =

'''Topic: Update on the FANTOM5 short RNA main paper (Michiel de Hoon)'''

*Presentation file: [[Image:Telecon 20140410.pptx]]

Audio File&nbsp;: The audio file from the call (uploaded after the call): [[Image:140410 F5 Telecon.zip]]

= September 5th -- FANTOM5 short RNA &amp; lncRNA Analysis Call =

'''Topic: Identifying promoters of primary microRNA transcripts by Michiel de Hoon'''

*Presentation file: [[Image:Telecon 20130905.pptx]]

Audio File&nbsp;: The audio file from the call (uploaded after the call): [[Image:130905 F5 Telecon.zip]]

= May 30th -- FANTOM5 short RNA &amp; lncRNA Analysis Call =

'''Topic: Presentation on lncRNA Freeze2 Overview &amp; Data availability (Nicolas Bertin)'''

*Presentation file: [[Image:TC.lncRNAome build2.30May13b.pdf]]

Audio File&nbsp;: The audio file from the call (uploaded after the call): [[Image:130530 F5 Telecon.zip]]

= May 9th -- FANTOM5 short RNA &amp; lncRNA Analysis Call =

'''Topic&nbsp;: FANTOM5 short RNA analysis''' [Michiel de Hoon]

*Presentation file&nbsp;: https://fantom5-collaboration.gsc.riken.jp/webdav/home/mdehoon/sRNA/Presentations/telecon_20130509.pdf

'''Topic&nbsp;: Update of the lncRNA analysis''' [Nicolas Bertin]

*Presentation file&nbsp;: https://fantom5-collaboration.gsc.riken.jp/webdav/home/nbertin/

Audio File&nbsp;: The audio file from the call (uploaded after the call): [[Image:130509 F5 Telecon.zip]]

= April 18th -- FANTOM5 lncRNAome Analysis Call =

'''Topic&nbsp;: Overview of the lncRNAome build 1 and call for help on specific topics / figures'''

*Presentation file&nbsp;: https://fantom5-collaboration.gsc.riken.jp/webdav/home/nbertin/F5_lncRNAome_CC.18apr13.pdf
*Overview of the lncRNAome build 1&nbsp;: https://fantom5-collaboration.gsc.riken.jp/webdav/home/nbertin/lncRNAome-RNAseq_Freeze1_27Mar13/lncRNAome_build1.16april13.overview_diagram.pdf
*Associated ZENBU view&nbsp;: https://fantom5-collaboration.gsc.riken.jp/zenbu/gLyphs/#config=f_78BiZ0IZbgU_yutrJLhB;loc=hg19::chr5:96407353..96479621
*Further details of the construction of the lncRNAome build 1&nbsp;:
**readme https://fantom5-collaboration.gsc.riken.jp/webdav/home/nbertin/lncRNAome-RNAseq_Freeze1_27Mar13/lncRNAome_freeze1.27mar13.readme.pdf
**data files (beds, gtfs, fa)&nbsp;: https://fantom5-collaboration.gsc.riken.jp/webdav/home/nbertin/lncRNAome-RNAseq_Freeze1_27Mar13/

Audio File The audio file from the call (uploaded after the call): [[Image:130418 F5 lcnRNAome telecon.zip]]

= FANTOM5 Promoterome Analysis Call has been discontinued (posted Jan-10-13) =

= December 13th =

'''CANCELLED'''

<br>

= December 7th =

'''CANCELLED'''

This week's telecon will not be held.

<br>

= November 8th =

'''CANCELLED'''

This week's telecon will not be held.

<br>

= November 1st =

'''CANCELLED'''

This week's telecon will not be held due to the FANTOM5 Time-courses meeting being held at RIKEN OSC.

<br>

= October 25th =

Chair: Piero Carninci

<br> CANCELLED

= October 18th =

Chair: Piero Carninci

<br> '''AGENDA'''

1. Progress report by OSC

Some analysis on Motifs and first results of a F3/4/5 comparison. [[Image:TalkOct18lassmann.pdf]]

2. Other topics, if any

<br>

Analysis Call Tip:

If concerned about the noise, we recommend putting your line in "listen-only" mode during presentation sessions of the call.

To enable "listen-only" mode press 97.

To disable "listen-only" mode press 96.

<br> '''Audio File''' The audio file from the call on October 18th (uploaded after the call): [[Image:121018 F5 Telecon.zip]]

<br>

= October 11th =

Chair: Piero Carninci

<br> '''AGENDA'''

1. Macroape results summary - VIGG (questions from Al [[Image:Motifs check 2 seva.pdf]]), presentation files: 1. [[Image:Cluster structure.zip]], 2. [[Image:BH distance distributions Kn Dn^Lx.xls]], 3. [[Image:BestHits between databases IK.ppt]], 4. [[Image:Annotation vs SelfAnnotation.xls]]

2. TomTom results summary - Michiel (Ohmiya) [[Image:Fantom5 20121011 michiel.pptx]]

3. PWM scanning Michiel

4. Any other updates from collaborators

<br>

Analysis Call Tip:

If concerned about the noise, we recommend putting your line in "listen-only" mode during presentation sessions of the call.

To enable "listen-only" mode press 97.

To disable "listen-only" mode press 96.

<br> '''Audio File''' The audio file from the call on October 11th (uploaded after the call): [[Image:121011 F5 Telecon.zip]]

= October 4th =

Chair: Piero Carninci

<br> '''AGENDA'''

1. Progress report by OSC

2. Other topics

<br> Analysis Call Tip:

If concerned about the noise, we recommend putting your line in "listen-only" mode during presentation sessions of the call.

To enable "listen-only" mode press 97.

To disable "listen-only" mode press 96.

<br> '''Audio File''' The audio file from the call on October 4th (uploaded after the call): [[Image:121004 F5 Telecon.zip]]

= September 27th =

Chair: Piero Carninci

<br> '''AGENDA'''

1. Progress report by OSC

2. Presentation by VIGG [[Image:VIGG Clustering 27 09 from dropbox.ppt]] (an old file - [[Image:VIGG Clustering 27 09.ppt]] )

3. Other topics

<br> Analysis Call Tip:

If concerned about the noise, we recommend putting your line in "listen-only" mode during presentation sessions of the call.

To enable "listen-only" mode press 97.

To disable "listen-only" mode press 96.

<br> '''Audio File''' The audio file from the call on September 27th (uploaded after the call): [[Image:120927 F5 Telecon.zip]]

= September 20th =

Chair: Piero Carninci

<br> '''AGENDA'''

1. Progress report by OSC

2. Presentation by Lenhard group - temporary link: [https://dl.dropbox.com/u/9244938/Sequence_and_chromatin_landscape_sharp_vs_broad_promoters.pdf Sequence_and_chromatin_landscape_sharp_vs_broad_promoters.pdf]

3. Other topics

<br> Analysis Call Tip:

If concerned about the noise, we recommend putting your line in "listen-only" mode during presentation sessions of the call.

To enable "listen-only" mode press 97.

To disable "listen-only" mode press 96.

<br> '''Audio File''' The audio file from the call on September 20th (uploaded after the call): [[Image:120920 F5 Telecon.zip]]

= September 13th =

Chair: Piero Carninci

<br> '''AGENDA'''

1. Main paper updates (Al)

2. ENCODE- implications for FANTOM5 Project

3. Other topics

<br> Analysis Call Tip:

If concerned about the noise, we recommend putting your line in "listen-only" mode during presentation sessions of the call.

To enable "listen-only" mode press 97.

To disable "listen-only" mode press 96.

<br> '''Audio File''' The audio file from the call on September 13th (uploaded after the call): [[Image:120913 F5 Telecon.zip]]

<br>

= September 6th =

Chair: Piero Carninci

<br> '''AGENDA'''

1. Progress report by OSC


2.
2.


<br> Analysis Call Tip:
'''Audio File'''
The audio file from the call on March 29th (uploaded after the call): [[File:120329_F5_Telecon.zip]]


If concerned about the noise, we recommend putting your line in "listen-only" mode during presentation sessions of the call.


To enable "listen-only" mode press 97.
=March 22nd=


To disable "listen-only" mode press 96.
Chair: Piero Carninci


<br> '''Audio File''' The audio file from the call on September 6th (uploaded after the call): [[Image:120906 F5 Telecon.zip]]


= August 30th =
'''AGENDA'''


Chair: Piero Carninci
1. Progress reports for this week by RIKEN OSC


<br> '''AGENDA'''
2. Presentation by Boris Lenhard and Vanja Haberle (Imperial College London/University of Bergen): "Distribution and enrichment of TF motifs and ChIPseq binding sites in cell-type specific promoters from ENCODE cell lines". [[Media:Distribution_of_TF_binding_sites_ENCODE_cell_lines.pdf]]


1. Progress report by OSC
3. Presentation by Ryota Mori from Asai-Lab: "Analyzing the secondary structures of human lncRNAome". [[Media:LncRNA_2ndarystructure_080322.pdf]]


2.
'''Audio File'''
The audio file from the call on March 22nd (uploaded after the call): [[File:120322_F5_Telecon.zip]]


<br> Analysis Call Tip:
=March 15th=


If concerned about the noise, we recommend putting your line in "listen-only" mode during presentation sessions of the call.
Chair: Piero Carninci


To enable "listen-only" mode press 97.


To disable "listen-only" mode press 96.
'''AGENDA'''


<br> '''Audio File''' The audio file from the call on August 30th (uploaded after the call): [[Image:120830 F5 Telecon.zip]]
1. Progress reports for this week by RIKEN OSC


= August 23th =
2. Presentation by group of Albin Sandelin, University of Copenhagen


CANCELLED
'''Audio File'''
The audio file from the call on March 15th (uploaded after the call): [[File:120315_F5_Telecon.zip]]


The Analysis Call will not be held due to OSC summer break.
=March 8th=


= August 16th =
Chair: Piero Carninci


CANCELLED


'''AGENDA'''
'''AGENDA'''


1. Progress reports for this week by RIKEN OSC(Timo Lassmann)
1. Progress report by OSC


2.
2. gencode10 lncRNA set by Andrea Tanzer (CRG) [[Media:atanzer_lncRNA_gen10_120308.pdf | lncRNA classification in gen10]]


<br> Analysis Call Tip:
'''Audio File'''
The audio file from the call on March 1st (uploaded after the call): [[File:120308_F5_Telecon.zip]]


If concerned about the noise, we recommend putting your line in "listen-only" mode during presentation sessions of the call.
3. Motif discussion points - Continued analysis from Michael and Christian's effect of background and length (minor interpretation from Al).
[[Media:Length_and_background_effects.pdf]]


To enable "listen-only" mode press 97.
=March 1st=


To disable "listen-only" mode press 96.
Chair: Piero Carninci


<br> '''Audio File''' The audio file from the call on August 16th (uploaded after the call): [[Image:120816 F5 Telecon.zip]]


= August 9th =
'''AGENDA'''


Chair: Piero Carninci
1. Progress reports for this week
Deadlines and milestones for the promoterome and lncRNAome papers [[Media:Deadlines_UPDATE_March1_2012.xls]]


<br> '''AGENDA'''
2. Brief Presentation on RNA analysis by Cedric Notredame [[Media:RNAmapping_01032012.ppt]]


1. Progress report by OSC
3. Motif discussion points
- Link to Michael's comparative analysis - effect of background and length.
https://fantom5-collaboration.gsc.riken.jp/webdav/home/rehli/ab%20initio%20motifs.pptx


2.
- Motif finding vs Motif scoring - target vs background discussion


<br> Analysis Call Tip:
- CpG island promoters - tissue specificity in the CpG or the flanking sequences?


If concerned about the noise, we recommend putting your line in "listen-only" mode during presentation sessions of the call.


To enable "listen-only" mode press 97.
'''Audio File'''
The audio file from the call on March 1st (uploaded after the call): [[File:120301_F5_Telecon.zip]]


To disable "listen-only" mode press 96.
=February 23rd=


<br> '''Audio File''' The audio file from the call on August 9th (uploaded after the call): [[Image:120809 F5 Telecon.zip]]
Chair: Piero Carninci


= August 2nd =


Chair: Piero Carninci
'''AGENDA'''


<br> '''AGENDA'''
1. Progress reports for this week
Deadlines and milestones for the promoterome and lncRNAome papers [[Media:Deadlines_UPDATE_Feb23_2012.xls]]


1.
'''Audio File'''
The audio file from the call on February 23rd (uploaded after the call): [[File:120223_F5_Telecon.zip]]


2.


<br> Analysis Call Tip:
=February 16th=


If concerned about the noise, we recommend putting your line in "listen-only" mode during presentation sessions of the call.
Chair: Piero Carninci


To enable "listen-only" mode press 97.


To disable "listen-only" mode press 96.
'''AGENDA'''


<br> '''Audio File''' The audio file from the call on August 2nd (uploaded after the call): [[Image:120802 F5 Telecon.zip]]
1. Progress reports for this week


= July 26th =
2. Discussion on motifs


Chair: Piero Carninci
3. Discussion on publication timeline ,


<br> '''AGENDA'''


1. Reports by the Promoterome main paper section leaders
Deadlines and milestones for the promoterome and lncRNAome papers [[Media:Deadlines_UPDATE_Feb16_2012.xls]]
Publication timeline [[Media:Deadlines_Feb15_2012_for_distribution.xls]]


2. Update on the motif evaluations (Michiel) [[Image:Teleconference-20120726.pptx]] [https://fantom5-collaboration.gsc.riken.jp/webdav/home/mdehoon/Motifs/MacroAPE_1083/hg19.filtered.pvalues.pdf p-value heatmap]


<br>
'''Audio File'''
The audio file from the call on February 16th (uploaded after the call): [[File:120216_F5_Telecon.zip]]


Analysis Call Tip:
=February 9th=


If concerned about the noise, we recommend putting your line in "listen-only" mode during presentation sessions of the call.
Chair: Piero Carninci


To enable "listen-only" mode press 97.


To disable "listen-only" mode press 96.
'''AGENDA'''
* "Updates", RIKEN OSC, Japan
Deadlines and milestones for the promoterome and lncRNAome papers [[Media:Deadlines_Feb09_2012.xls]]


<br> '''Audio File''' The audio file from the call on July 26th (uploaded after the call): [[Image:120726 F5 Telecon.zip]]
'''Audio File'''
The audio file from the call on February 9th (uploaded after the call): [[File:120209_F5_Telecon.zip]]


= July 19th =


Chair: Piero Carninci


<br> '''AGENDA'''
=February 2nd=


1. Reports by the Promoterome main paper section leaders
Chair: Piero Carninci


2. Update on motif activity calculations (Michiel) [https://fantom5-collaboration.gsc.riken.jp/webdav/home/mdehoon/Motifs/MacroAPE_493/motif_tf_correlation_matrix.pdf Heatmap] [https://fantom5-collaboration.gsc.riken.jp/webdav/home/mdehoon/Motifs/MacroAPE_493/ranks.png Ranks]


3. recent updates and the discussions on the resource browser
'''AGENDA'''
* "Using SUPERFAMILY to track evolutionary milestones in the FANTOM data.", Owen Rackham, University of Bristol, UK. Presentation files: [[File:F5evol.pdf]]
* "Updates", RIKEN OSC, Japan


*pathway enrichment analysis of co-expression module - [https://fantom5-collaboration.gsc.riken.jp/resource_browser/Coexpression_cluster:C3 example:C3]
'''Audio File'''
*synchronize with FF sample ontology [https://fantom5-collaboration.gsc.riken.jp/files/data/shared/contrib/sample_ontology/FF_ontology_v019_01/ v019_01]
The audio file from the call on February 2nd (uploaded after the call): [[File:120202_F5_Telecon.zip]]
*link to the genome browsers - [https://fantom5-collaboration.gsc.riken.jp/resource_browser/index.php/FFCP_PHASE1:Hg19::chr10:101089107..101089141,%2B example:p1@CNNM1] and [https://fantom5-collaboration.gsc.riken.jp/ucsc/cgi-bin/hgc?hgsid=2414&o=101089107&t=101089141&g=ffcp_rblink_hg19_bb&i=p1%40CNNM1 link back]
*under discussion/improvement
**table export as CSV
**sorting function of the expression graph (line chart)
**revision of sample order in the expression graph (line chart)
**default order of tables
**revision of sample enrichment analysis
**revision of side bar content
**interaction with other tools (biomart, bioLayout, Albin's promoter/enhancer selector, bioGPS, FONSE)
**genomic view
**nanopublication


<br> Analysis Call Tip:


If concerned about the noise, we recommend putting your line in "listen-only" mode during presentation sessions of the call.


To enable "listen-only" mode press 97.


To disable "listen-only" mode press 96.
=January 26th=


<br> '''Audio File''' The audio file from the call on July 19th (uploaded after the call): [[Image:120719 F5 Telecon.zip]]
Chair: Piero Carninci


= July 12th =


Chair: Piero Carninci
'''AGENDA'''
* "Analysis update", RIKEN Omics Science Center. Presentation files will be uploaded here before the call
Deadlines and milestones for the promoterome and lncRNAome papers [[Media:Deadlines_Jan26_2012.xls]]


'''Audio File'''
'''AGENDA'''
The audio file from the call on January 12th (uploaded after the call): [[File:120126_F5_Telecon.zip]]


1. Reports by the Promoterome main paper section leaders


*Presentation by Kenneth Baillie [[Image:Coexpression clustering v5.docx]]


*Presentation by Michael Rehli [[Image:MR.pdf.zip]]
=January 19th=


<br>
Chair: Piero Carninci


Analysis Call Tip:


If concerned about the noise, we recommend putting your line in "listen-only" mode during presentation sessions of the call.
'''AGENDA'''
* "Analysis update", RIKEN Omics Science Center. Presentation files will be uploaded here before the call


To enable "listen-only" mode press 97.
'''Audio File'''
The audio file from the call on January 12th (uploaded after the call): [[File:120119_F5_Telecon.zip]]


To disable "listen-only" mode press 96.


<br> '''Audio File''' The audio file from the call on July 12th (uploaded after the call): [[Image:120712 F5 Telecon.zip]]


= July 5th =
=January 12th=


Chair: Alistair Forrest
Chair: Piero Carninci


'''AGENDA'''
'''AGENDA'''
* "Analysis update", Hideya Kawaji, RIKEN Omics Science Center. Presentation files: [[File:120112-telecon-kawaji.pdf‎]]


1. Reports by the Promoterome main paper section leaders
'''Audio File'''
The audio file from the call on January 12th (uploaded after the call): [[File:120112_F5_Telecon.zip]]


<br>
=January 5th=

Analysis Call Tip:

If concerned about the noise, we recommend putting your line in "listen-only" mode during presentation sessions of the call.

To enable "listen-only" mode press 97.

To disable "listen-only" mode press 96.

<br> '''Audio File''' The audio file from the call on July 5th (uploaded after the call): [[Image:120705 F5 Telecon.zip]]

<br>

= June 28th =

Analysis call CANCELLED.

The next analysis call will be held on July 5th.

<br>

= June 21th =

Chair: Piero Carninci

<br> '''AGENDA'''

1. Progress report by RIKEN OSC

[[Image:Promoterome draft figs June20.pdf]]

[[Image:Promoterome draft supp figs June20.pdf]]

<br> Analysis Call Tip:

If concerned about the noise, we recommend putting your line in "listen-only" mode during presentation sessions of the call.

To enable "listen-only" mode press 97.

To disable "listen-only" mode press 96.

<br>

'''Audio File''' The audio file from the call on June 21th (uploaded after the call): [[Image:120621 F5 Telecon.zip]]

= June 14th =

Chair: Piero Carninci

<br> '''AGENDA'''

1. Draft figures and section progress [[Image:Promoterome draft figs June14.pdf]]

<br> Analysis Call Tip:

If concerned about the noise, we recommend putting your line in "listen-only" mode during presentation sessions of the call.

To enable "listen-only" mode press 97.

To disable "listen-only" mode press 96.

<br>

'''Audio File''' The audio file from the call on June 14th (uploaded after the call): [[Image:120614 F5 Telecon.zip]]

= June 7th =

Chair: Piero Carninci

<br> '''AGENDA'''

1. Progress report by RIKEN OSC

2. Mini TSS prediction update (Timo, OSC) [[Image:TSSprediction June7.pdf]]

<br>

Analysis Call Tip:

If concerned about the noise, we recommend putting your line in "listen-only" mode during presentation sessions of the call.

To enable "listen-only" mode press 97.

To disable "listen-only" mode press 96.

<br>

'''Audio File''' The audio file from the call on June 7th (uploaded after the call): [[Image:120607 F5 Telecon.zip]]

= May 31st =

Chair: Piero Carninci

<br> '''AGENDA'''

1. Brief progress report by the paper section leaders

<br>

<br> Analysis Call Tip:

If concerned about the noise, we recommend putting your line in "listen-only" mode during presentation sessions of the call.

To enable "listen-only" mode press 97.

To disable "listen-only" mode press 96.

<br>

'''Audio File''' The audio file from the call on May 31st (uploaded after the call): [[Image:120531 F5 Telecon.zip]]

= May 24th =

Chair: Piero Carninci

<br> '''AGENDA'''

1. Flash report by paper section leaders

<br>

<br> Analysis Call Tip:

If concerned about the noise, we recommend putting your line in "listen-only" mode during presentation sessions of the call.

To enable "listen-only" mode press 97.

To disable "listen-only" mode press 96.

<br>

'''Audio File''' The audio file from the call on May 24th (uploaded after the call): [[Image:120524 F5 Telecon.zip]]

= May 17th =

Chair: Piero Carninci

<br> '''AGENDA'''

1. First draft of the promoterome paper from Al

[[Image:Promoterome May17 2012.doc]] CONFIDENTIAL - NOT FOR DISTRIBUTION OUTSIDE OF F5 [[Image:Promoterome draft figsMay17.pdf]] CONFIDENTIAL - NOT FOR DISTRIBUTION OUTSIDE OF F5

<br>

'''Audio File''' The audio file from the call on May 17th (uploaded after the call): [[Image:120517 F5 Telecon.zip]]

= May 10th =

Chair: Alistair Forrest

<br> '''AGENDA'''

1. Progress report for this week by RIKEN OSC (Al Forrest)

2. MARA update (Michiel De Hoon, OSC) [[Image:Teleconference-20120510.pptx]]

3. Short RNAs update (Max Burroughs, OSC) [[Image:F5 small RNA update.pptx]]

<br> '''Audio File''' The audio file from the call on May 10th (uploaded after the call): [[Image:120510 F5 Telecon.zip]]

= May 3rd =

'''CANCELLED'''

Due to a [http://en.wikipedia.org/wiki/Constitution_Memorial_Day national holiday] in Japan, FANTOM5 Analysis Call will not be held.

<br>

= April 26th =

Chair: Piero Carninci

<br> '''AGENDA'''

1. Progress report for this week by RIKEN OSC (Alistair FORREST) [[Image:F5 Teleconference april26.ppt]]

<br> '''Audio File''' The audio file from the call on April 26th (uploaded after the call): [[Image:120426 F5 Telecon.zip]]

= April 19th =

Chair: Piero Carninci

<br> '''AGENDA'''

1. Progress report for this week by RIKEN OSC

2. Presentation by Tom Freeman, Roslin Institute [https://fantom5-collaboration.gsc.riken.jp/webdav/home/freeman/ Presentation materials]

3. A brief presentation by Kenneth Baillie, Roslin Institute [http://www.altitude.org/fantom5 Presentation materials] (user name and password are the same as for the FANTOM5 Wiki page)

<br>

<br> '''Audio File''' The audio file from the call on April 19th (uploaded after the call): [[Image:120419 F5 Telecon.zip]]

<br>

= April 12th =

Chair: Piero Carninci

<br> '''AGENDA'''

1. Progress report for this week by RIKEN OSC

*Al - [[Satellite submission]]
*Kawaji - [https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/111220-DPI/LRtest/120412-inter-intra-peak.pdf TSS usage inter/intra CAGE peaks]

<br>

'''Audio File''' The audio file from the call on April 12th (uploaded after the call): [[Image:120412 F5 Telecon.zip]]

= April 5th =

Chair: Piero Carninci

<br> '''AGENDA'''

1. Progress report for this week by RIKEN OSC(Hideya KAWAJI and Alistair FORREST) [[Image:120405-f5-telecon-kawaji.pdf]]

2. F5 core promoters(Albin SANDELIN, University of Copenhagen) [[Image:F5 core promoters sandelin.pdf]]

<br> '''Audio File''' The audio file from the call on April 5th (uploaded after the call): [[Image:120405 F5 Telecon.zip]]

= March 29th =

'''CANCELLED'''

Chair: Piero Carninci

<br> '''AGENDA'''

1. Progress reports for this week by RIKEN OSC

2.

<br> '''Audio File''' The audio file from the call on March 29th (uploaded after the call): [[Image:120329 F5 Telecon.zip]]

<br>

= March 22nd =

Chair: Piero Carninci

<br> '''AGENDA'''

1. Progress reports for this week by RIKEN OSC

2. Presentation by Boris Lenhard and Vanja Haberle (Imperial College London/University of Bergen): "Distribution and enrichment of TF motifs and ChIPseq binding sites in cell-type specific promoters from ENCODE cell lines". [[Media:Distribution_of_TF_binding_sites_ENCODE_cell_lines.pdf]]

3. Presentation by Ryota Mori from Asai-Lab: "Analyzing the secondary structures of human lncRNAome". [[Media:LncRNA_2ndarystructure_080322.pdf]]

'''Audio File''' The audio file from the call on March 22nd (uploaded after the call): [[Image:120322 F5 Telecon.zip]]

= March 15th =

Chair: Piero Carninci

<br> '''AGENDA'''

1. Progress reports for this week by RIKEN OSC

2. Presentation by group of Albin Sandelin, University of Copenhagen

'''Audio File''' The audio file from the call on March 15th (uploaded after the call): [[Image:120315 F5 Telecon.zip]]

= March 8th =

Chair: Piero Carninci

<br> '''AGENDA'''

1. Progress reports for this week by RIKEN OSC(Timo Lassmann)

2. gencode10 lncRNA set by Andrea Tanzer (CRG) [[Media:Atanzer_lncRNA_gen10_120308.pdf|lncRNA classification in gen10]]

'''Audio File''' The audio file from the call on March 1st (uploaded after the call): [[Image:120308 F5 Telecon.zip]]

3. Motif discussion points - Continued analysis from Michael and Christian's effect of background and length (minor interpretation from Al). [[Media:Length_and_background_effects.pdf]]

= March 1st =

Chair: Piero Carninci

<br> '''AGENDA'''

1. Progress reports for this week Deadlines and milestones for the promoterome and lncRNAome papers [[Media:Deadlines_UPDATE_March1_2012.xls]]

2. Brief Presentation on RNA analysis by Cedric Notredame [[Media:RNAmapping_01032012.ppt]]

3. Motif discussion points - Link to Michael's comparative analysis - effect of background and length.

https://fantom5-collaboration.gsc.riken.jp/webdav/home/rehli/ab%20initio%20motifs.pptx

- Motif finding vs Motif scoring - target vs background discussion

- CpG island promoters - tissue specificity in the CpG or the flanking sequences?

<br> '''Audio File''' The audio file from the call on March 1st (uploaded after the call): [[Image:120301 F5 Telecon.zip]]

= February 23rd =

Chair: Piero Carninci

<br> '''AGENDA'''

1. Progress reports for this week Deadlines and milestones for the promoterome and lncRNAome papers [[Media:Deadlines_UPDATE_Feb23_2012.xls]]

'''Audio File''' The audio file from the call on February 23rd (uploaded after the call): [[Image:120223 F5 Telecon.zip]]

<br>

= February 16th =

Chair: Piero Carninci

<br> '''AGENDA'''

1. Progress reports for this week

2. Discussion on motifs

3. Discussion on publication timeline ,

<br> Deadlines and milestones for the promoterome and lncRNAome papers [[Media:Deadlines_UPDATE_Feb16_2012.xls]] Publication timeline [[Media:Deadlines_Feb15_2012_for_distribution.xls]]

<br> '''Audio File''' The audio file from the call on February 16th (uploaded after the call): [[Image:120216 F5 Telecon.zip]]

= February 9th =

Chair: Piero Carninci

<br> '''AGENDA'''

*"Updates", RIKEN OSC, Japan

Deadlines and milestones for the promoterome and lncRNAome papers [[Media:Deadlines_Feb09_2012.xls]]

'''Audio File''' The audio file from the call on February 9th (uploaded after the call): [[Image:120209 F5 Telecon.zip]]

<br>

= February 2nd =

Chair: Piero Carninci

<br> '''AGENDA'''

*"Using SUPERFAMILY to track evolutionary milestones in the FANTOM data.", Owen Rackham, University of Bristol, UK. Presentation files: [[Image:F5evol.pdf]]
*"Updates", RIKEN OSC, Japan

'''Audio File''' The audio file from the call on February 2nd (uploaded after the call): [[Image:120202 F5 Telecon.zip]]

<br>

<br>

= January 26th =

Chair: Piero Carninci

<br> '''AGENDA'''

*"Analysis update", RIKEN Omics Science Center. Presentation files will be uploaded here before the call

Deadlines and milestones for the promoterome and lncRNAome papers [[Media:Deadlines_Jan26_2012.xls]]

'''Audio File''' The audio file from the call on January 12th (uploaded after the call): [[Image:120126 F5 Telecon.zip]]

<br>

= January 19th =

Chair: Piero Carninci

<br> '''AGENDA'''

*"Analysis update", RIKEN Omics Science Center. Presentation files will be uploaded here before the call

'''Audio File''' The audio file from the call on January 12th (uploaded after the call): [[Image:120119 F5 Telecon.zip]]

<br>

= January 12th =

Chair: Alistair Forrest

'''AGENDA'''

*"Analysis update", Hideya Kawaji, RIKEN Omics Science Center. Presentation files: [[Image:120112-telecon-kawaji.pdf]]

'''Audio File''' The audio file from the call on January 12th (uploaded after the call): [[Image:120112 F5 Telecon.zip]]

= January 5th =


Analysis call CANCELED!
Analysis call CANCELED!


Next call will be held on January 12th
Next call will be held on January 12th


<br>


= December 22nd =


Chair: Piero Carninci
=December 22nd=


'''AGENDA'''
Chair: Piero Carninci


*"Pervasive divergent transcription identifies enhancers", Robin Andersson, University of Copenhagen, Denmark. PPT: [[Image:Andersson F5 telecon dec 22 2011.ppt]], PDF: [[Image:Andersson F5 telecon dec 22 2011.pdf]]
'''AGENDA'''
*"Analysis update", RIKEN Omics Science Center
* "Pervasive divergent transcription identifies enhancers", Robin Andersson, University of Copenhagen, Denmark. PPT: [[File:Andersson_F5_telecon_dec_22_2011.ppt]], PDF: [[File:Andersson_F5_telecon_dec_22_2011.pdf]]
* "Analysis update", RIKEN Omics Science Center


<br> '''Audio File''' The audio file from the call on December 22nd (uploaded after the call): [[Image:111222 F5 Telecon.zip]]


<br>
'''Audio File'''
The audio file from the call on December 22nd (uploaded after the call): [[File:111222_F5_Telecon.zip]]


= December 15th =


Chair: Piero Carninci
=December 15th=


'''AGENDA'''
Chair: Piero Carninci


*"Time course quality control", Erik Arner, RIKEN Omics Science Center, Japan. Presentation file will be uploaded here before the call
'''AGENDA'''
* "Time course quality control", Erik Arner, RIKEN Omics Science Center, Japan. Presentation file will be uploaded here before the call
[[File:Timecourse_qc_20111215.pptx]]
[[File:Timecourse_qc_20111215.pdf‎]]
* "Analysis update", RIKEN Omics Science Center


[[Image:Timecourse qc 20111215.pptx]] [[Image:Timecourse qc 20111215.pdf]]


*"Analysis update", RIKEN Omics Science Center
'''Audio File'''
The audio file from the call on December 15th (uploaded after the call): [[File:111215_F5_Telecon.zip]]


<br> '''Audio File''' The audio file from the call on December 15th (uploaded after the call): [[Image:111215 F5 Telecon.zip]]
=December 8th=


= December 8th =
Chair: Piero Carninci


Chair: Piero Carninci
'''AGENDA'''
* "lncRNAome and lncRNA main paper update", Leonard Lipovich, Wayne State University, USA [[File:F5_Lipovich_08dec2011AnalysisCall.ppt]] [[File:F5_Lipovich_08dec2011AnalysisCall.pdf]]
* Update on promoterome paper", RIKEN OSC, Japan [[File:111208-telecon-kawaji.pdf‎]]
* [[Sample_QC]]


'''Audio File'''
'''AGENDA'''
The audio file from the call on December 8th (uploaded after the call): [[File:111208_F5_Telecon.zip]]


*"lncRNAome and lncRNA main paper update", Leonard Lipovich, Wayne State University, USA [[Image:F5 Lipovich 08dec2011AnalysisCall.ppt]] [[Image:F5 Lipovich 08dec2011AnalysisCall.pdf]]
=December 1st=
*Update on promoterome paper", RIKEN OSC, Japan [[Image:111208-telecon-kawaji.pdf]]
*[[Sample QC]]


'''Audio File''' The audio file from the call on December 8th (uploaded after the call): [[Image:111208 F5 Telecon.zip]]
Chair: Alistair Forrest


= December 1st =
'''AGENDA'''
* "Status report on the ongoing analysis", Hideya kawaji, RIKEN OSC, Japan. [[File:111131-F5telecon-kawaji.pdf]]


Chair: Alistair Forrest


'''Audio File'''
'''AGENDA'''
The audio file from the call on December 1st: [[File:111201_F5_Telecon.zip]]


*"Status report on the ongoing analysis", Hideya kawaji, RIKEN OSC, Japan. [[Image:111131-F5telecon-kawaji.pdf]]
=November 24th=


<br> '''Audio File''' The audio file from the call on December 1st: [[Image:111201 F5 Telecon.zip]]
Chair: Piero Carninci


= November 24th =
'''AGENDA'''
* "Status report on the ongoing analysis", RIKEN OSC, Japan. Presentation file will be uploaded before the call [[File:111124-f5-telecon-kawaji.pdf]]
* [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/Sample_QC Sample QC] page by Al<br>


Chair: Piero Carninci


'''Audio File'''
'''AGENDA'''
Audio file from the call on November 24th (will be uploaded after the call): [[File:111124_F5_Telecon.zip]]


*"Status report on the ongoing analysis", RIKEN OSC, Japan. Presentation file will be uploaded before the call [[Image:111124-f5-telecon-kawaji.pdf]]
=November 17th=
*[https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/Sample_QC Sample QC] page by Al<br>


<br> '''Audio File''' Audio file from the call on November 24th (will be uploaded after the call): [[Image:111124 F5 Telecon.zip]]
Chair: Alistair Forrest


= November 17th =
'''AGENDA'''
* "Brief Status report on the Promoterome paper", Alistair Forrest, RIKEN OSC, Japan. Promoterome update from Al [[Media:Promoterome_update_Nov17.doc]]


Chair: Alistair Forrest


'''Audio File'''
'''AGENDA'''
Audio file from the call on November 17th: [[File:111117_F5_Telecon.zip]]


*"Brief Status report on the Promoterome paper", Alistair Forrest, RIKEN OSC, Japan. Promoterome update from Al [[Media:Promoterome_update_Nov17.doc]]
=November 10th=


<br> '''Audio File''' Audio file from the call on November 17th: [[Image:111117 F5 Telecon.zip]]
Chair: Piero Carninci


= November 10th =
'''AGENDA'''
* "Update on main paper analysis ", Promoterome update from Al [[File:Promoterome_update_Nov10.doc]]


Chair: Piero Carninci
* "Data analysis using the Fantom Sample Ontology", Chris Mungall, Lawrence Berkeley National Laboratory, USA. Presentation file: [[File:Fantom5-ontology.pptx]]


'''AGENDA'''


*"Update on main paper analysis ", Promoterome update from Al [[Image:Promoterome update Nov10.doc]]
'''Audio File'''
Audio file from the call on November 10th will be uploaded here after the call [[File:111110_F5_Telecon.zip]]


*"Data analysis using the Fantom Sample Ontology", Chris Mungall, Lawrence Berkeley National Laboratory, USA. Presentation file: [[Image:Fantom5-ontology.pptx]]
=November 3rd=

<br> '''Audio File''' Audio file from the call on November 10th will be uploaded here after the call [[Image:111110 F5 Telecon.zip]]

= November 3rd =


On Thursday November 3rd, no FANTOM5 Analysis Call will be held since this day is a Japanese Holiday.
On Thursday November 3rd, no FANTOM5 Analysis Call will be held since this day is a Japanese Holiday.


<br>

= October 27th =

Chair: Piero Carninci

'''AGENDA'''

*"Update on main paper analysis ", Hideya Kawaji, RIKEN OSC, Japan. Presentation file will be uploaded here before the call [[Image:111027-telecon-kawaji.pdf]]

'''Audio File''' Audio file from the call on October 27th: [[Image:111027 F5 Telecon.zip]]

<br>

= October 13th =

The Analysis Call on October 13th has been cancelled. We are looking forward to meeting many of you here for the Koyo meeting!


=October 27th=
= October 7th =


Chair: Piero Carninci
Chair: Piero Carninci


'''AGENDA'''
'''AGENDA'''
* "Update on main paper analysis ", Hideya Kawaji, RIKEN OSC, Japan. Presentation file will be uploaded here before the call [[File:111027-telecon-kawaji.pdf‎ ]]


*"Homo sapiens complex motif collection (HoCoMoCo) and homotypic clusters of transcription factor binding sites", Ivan Kulakovskiy, Russian Academy of Sciences, Vavilov Institute of General Genetics, Russia. [[Image:HOCOMOCO and homotypic clusters Kulakovskiy et al.pdf]]
'''Audio File'''
*"Using MARA for analyzing time-courses" Piotr Balwierz , Universität Basel, Biozentrum, Switzerland.[[Image:Mara-timecourses-balwierz.pdf]]
Audio file from the call on October 27th: [[File:111027_F5_Telecon.zip]]


'''Audio File''' Audio file from the call on September 29nd:[[Image:111007 F5 Telecon.zip]]


= October 13th =
= September 29nd =


Chair: Piero Carninci
The Analysis Call on October 13th has been cancelled. We are looking forward to meeting many of you here for the Koyo meeting!


'''AGENDA'''
=October 7th=


*"Motif activity calculations on Update 11", Michiel de Hoon, RIKEN OSC, Japan. [[Image:MARA Michiel 20110929.pdf]]
Chair: Piero Carninci
*"Motif analysis of Fantom5 data: First insights" Vladimir Bajic, KAUST CBRC, Saubia Arabia. [[Image:Teleconference Sep 29 2011 Vlad.pdf]]


'''Audio File''' Audio file from the call on September 29nd: [[Image:110929 F5 Telecon.zip]].
'''AGENDA'''
* "Homo sapiens complex motif collection (HoCoMoCo) and homotypic clusters of transcription factor binding sites", Ivan Kulakovskiy, Russian Academy of Sciences, Vavilov Institute of General Genetics, Russia. [[File:HOCOMOCO_and_homotypic_clusters_Kulakovskiy_et_al.pdf]]
* "Using MARA for analyzing time-courses" Piotr Balwierz , Universität Basel, Biozentrum, Switzerland.[[File:Mara-timecourses-balwierz.pdf]]


= September 22nd =
'''Audio File'''
Audio file from the call on September 29nd:[[File:111007_F5_Telecon.zip]]


Chair: Carsten Daub
=September 29nd=


'''AGENDA'''
Chair: Piero Carninci


*"TSS Classification", Timo Lassmann, RIKEN OSC, Japan and Sebastian Schmeier, KAUST CBRC, Saubia Arabia. Presentation file will be uploaded before the meeting [[Image:TSSprediction Sep22.pdf]] [[Image:20110922 schmeier.pdf]]
'''AGENDA'''
*"De novo motif analysis of FANTOM5 CAGE-data" Michael Rehli, University Hospital Regensburg, Germany. Presentation: [[Image:Rehli Motifs2.pdf]]
* "Motif activity calculations on Update 11", Michiel de Hoon, RIKEN OSC, Japan. [[File:MARA_Michiel_20110929.pdf]]
* "Motif analysis of Fantom5 data: First insights" Vladimir Bajic, KAUST CBRC, Saubia Arabia. [[File:Teleconference_Sep_29_2011_Vlad.pdf]]


'''Audio File''' Audio file from the call on September 22nd: [[Image:110922 F5 Telecon.zip]]
'''Audio File'''
Audio file from the call on September 29nd: [[File:110929_F5_Telecon.zip]].


=September 22nd=
= September 15th =


Chair: Carsten Daub
Chair: Piero Carninci


'''AGENDA'''
'''AGENDA'''
* "TSS Classification", Timo Lassmann, RIKEN OSC, Japan and Sebastian Schmeier, KAUST CBRC, Saubia Arabia. Presentation file will be uploaded before the meeting [[file:TSSprediction_Sep22.pdf]] [[file:20110922_schmeier.pdf]]
* "De novo motif analysis of FANTOM5 CAGE-data" Michael Rehli, University Hospital Regensburg, Germany. Presentation: [[file:Rehli_Motifs2.pdf]]


*"Time-course sample kick-off: data availability, strategy, next steps", Carsten O. Daub, RIKEN OSC, Japan. Presentation [[Image:FANTOM5 TC - Time course kick-off.pdf]]
'''Audio File'''
*"NcRNAs in F5 time-courses: examples, resource, proposal" (5 minutes), Leonard Lipovich, Wayne State Univ., USA. [[Image:F5 Lipovich 15sep2011AnalysisCall mini.ppt]] [[Image:F5 Lipovich 15sep2011AnalysisCall mini.pdf]]
Audio file from the call on September 22nd: [[File:110922_F5_Telecon.zip]]


'''Audio File''' Audio file from the call on September 15th: [[Image:110915 F5 Telecon.zip]]
=September 15th=


= September 8th =
Chair: Piero Carninci


Chair: Piero Carninci
'''AGENDA'''
* "Time-course sample kick-off: data availability, strategy, next steps", Carsten O. Daub, RIKEN OSC, Japan. Presentation [[file:FANTOM5_TC_-_Time_course_kick-off.pdf]]
* "NcRNAs in F5 time-courses: examples, resource, proposal" (5 minutes), Leonard Lipovich, Wayne State Univ., USA. [[file:F5_Lipovich_15sep2011AnalysisCall_mini.ppt]] [[file:F5_Lipovich_15sep2011AnalysisCall_mini.pdf]]


'''Audio File'''
'''AGENDA'''
Audio file from the call on September 15th: [[File:110915_F5_Telecon.zip]]


*"The mammalian promoterome - paper punchlines", Alistair Forrest, RIKEN OSC, Japan. [[Image:FANTOM5 TC – September 8th.ppt]]
=September 8th=


'''Audio File''' Audio file from the call on September 8th: [[Image:110908 F5 Telecon.zip]]
Chair: Piero Carninci


= September 1st =
'''AGENDA'''
* "The mammalian promoterome - paper punchlines", Alistair Forrest, RIKEN OSC, Japan. [[file:FANTOM5_TC_–_September_8th.ppt‎]]


Chair: Piero Carninci
'''Audio File'''
Audio file from the call on September 8th: [[File:110908_F5_Telecon.zip]]


'''AGENDA'''
=September 1st=


*"Status Update ", Hideya Kawaji, RIKEN OSC, Japan. [[Image:110901-telecon-kawaji.pdf]]
Chair: Piero Carninci
*"Proposal for CAGE cluster annotation", Hideya Kawaji, RIKEN OSC, Japan. [[Image:110901-cluster-annotation.pdf]]


'''Audio File''' Audio file from the call on September 1st: [[Image:110901 F5 Telecon.zip]]
'''AGENDA'''
* "Status Update ", Hideya Kawaji, RIKEN OSC, Japan. [[file:110901-telecon-kawaji.pdf‎]]
* "Proposal for CAGE cluster annotation", Hideya Kawaji, RIKEN OSC, Japan. [[file:110901-cluster-annotation.pdf]]


= August 18th =
'''Audio File'''
Audio file from the call on September 1st: [[File:110901_F5_Telecon.zip]]


Chair: Piero Carninci
=August 18th=


'''AGENDA'''
Chair: Piero Carninci


*"Exploring promoter type switching in developmental time courses", Boris Lenhard, University of Bergen, Norway. Presentation in PDF format: [[Image:Lenhard Analysis Call 20110818.pdf]] . Please let me know (boris.lenhard@bio.uib.no) if you need the original Keynote file.
'''AGENDA'''


'''Audio File''' Audio file from the call on August 18th 2011: [[Image:110818 F5 Telecon.zip]].
* "Exploring promoter type switching in developmental time courses", Boris Lenhard, University of Bergen, Norway. Presentation in PDF format: [[file:Lenhard_Analysis_Call_20110818.pdf]] . Please let me know (boris.lenhard@bio.uib.no) if you need the original Keynote file.


= August 11th =
'''Audio File'''
Audio file from the call on August 18th 2011: [[File:110818_F5_Telecon.zip]].


Chair: Piero Carninci
=August 11th=


'''AGENDA'''
Chair: Piero Carninci


*"Status Update", Alistair Forrest, RIKEN OSC
'''AGENDA'''
*"F5 lncRNAome integration with hCAGE: inferring function and networks", Leonard Lipovich, Wayne State University, Detroit, USA


___(PPT: [[Media:F5_Lipovich_11aug2011AnalysisCall.ppt]], PDF: [[Media:F5_Lipovich_11aug2011AnalysisCall.pdf]])
* "Status Update", Alistair Forrest, RIKEN OSC
* "F5 lncRNAome integration with hCAGE: inferring function and networks", Leonard Lipovich, Wayne State University, Detroit, USA
___(PPT: [[Media:F5_Lipovich_11aug2011AnalysisCall.ppt]], PDF: [[Media:F5_Lipovich_11aug2011AnalysisCall.pdf]])


'''Audio File''' Audio file from the call on August 11th 2011: [[Image:110811 F5 Telecon.zip]]‎
'''Audio File'''
Audio file from the call on August 11th 2011: [[File:110811_F5_Telecon.zip]]‎


=August 4th=
= August 4th =


Chair: Piero Carninci
Chair: Piero Carninci


'''AGENDA'''
'''AGENDA'''


* "Promoterome paper - plan, observations, requests for analysis ", Alistair Forrest, RIKEN OSC (presentation file - https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/File:AL_TC_AUG04.ppt)
*"Promoterome paper - plan, observations, requests for analysis ", Alistair Forrest, RIKEN OSC (presentation file - https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/File:AL_TC_AUG04.ppt)


'''Audio File''' Audio file from the call on August 4th 2011: [[Image:110804 F5 Telecon.zip]]
'''Audio File'''
Audio file from the call on August 4th 2011: [[File:110804_F5_Telecon.zip]]


=July 28th=
= July 28th =


Chair: Piero Carninci
Chair: Piero Carninci


'''AGENDA'''
'''AGENDA'''


* "CAGE clusters for the main paper", Hideya Kawaji, RIKEN OSC (presentation file - [[File:110728-F5-telecon-kawaji.pdf]])
*"CAGE clusters for the main paper", Hideya Kawaji, RIKEN OSC (presentation file - [[Image:110728-F5-telecon-kawaji.pdf]])


'''Audio File''' Audio file from the call on July 28th 2011: [[Image:110728 F5 Telecon.zip]]
'''Audio File'''
Audio file from the call on July 28th 2011: [[File:110728_F5_Telecon.zip]]

Latest revision as of 10:53, 3 July 2015

FANTOM5 Analysis Call has been reincarnated as RNA analysis call.

For the time-being the call will be held intermittently at the Thursday teleconference time-slot. Notifications will be sent through FANTOM 5 mailing list as usual.

The agenda is decided by the FANTOM5 Management group at RIKEN. Suggestions can be sent to Michiel de Hoon. Agenda will be announced to the FANTOM5 mailing list every Wednesday. Presentation materials will be available on this page before each meeting.

The meetings will be recorded and saved here for later reference.


Phone numbers:

From outside of Japan: +81-3-4333-4000

From anywhere in Japan: 050-3786-6666 (in Japanese) or 0570-03-4444 (in English)

From the Tokyo Area: 03-4333-4444 (in Japanese) or 03-4333-4000 (in English)

From the Osaka Area: 06-7637-2222


You will be asked to enter conference ID followed by # and guest password followed by # to join the conference. Please find them below:

Conference id: 24711

Guest password: 3502

You will also be asked to state your name and press the # key.


TIPS ON USAGE:

We recommend putting your line in "listen-only" mode during presentation sessions of the call to avoid noise and other interferences.

To enable "listen-only" mode press 97.

To disable "listen-only" mode press 96.


Call In Instructions for guest users (English)

Call In Instructions for guest users (Japanese)

July 2nd -- FANTOM5 lncRNA Analysis Call

Topic: FANTOM5 lncRNA Analysis

  • Presentation file:

Audio File: The audio file from the call (uploaded after the call): File:150702 002.MP3.zip

June 10th -- FANTOM5 lncRNA Analysis Call

Topic: FANTOM5 lncRNA Analysis

  • Presentation file:

Audio File: The audio file from the call (uploaded after the call): [recording missed]

May 28th -- FANTOM5 lncRNA Analysis Call

Topic: FANTOM5 lncRNA Analysis

  • Presentation file:


Audio File: The audio file from the call: [recording missed]

May 7th -- FANTOM5 lncRNA Analysis Call

Topic: FANTOM5 lncRNA Analysis (Chung Chau HON)

Audio File: The audio file from the call (uploaded after the call): [[]]

April 9nd -- FANTOM5 lncRNA Analysis Call

Topic: FANTOM5 lncRNA Analysis (Chung Chau HON)

Audio File: The audio file from the call (uploaded after the call): File:150409 001.mp3.zip

April 2nd -- FANTOM5 short RNA Analysis Call

Topic: FANTOM5 short RNA Analysis (Michiel de Hoon)

Audio File: The audio file from the call (uploaded after the call): File:150402 F5 Telecon.MP3.zip

March 26th -- FANTOM5 lncRNA Analysis Call

Topic: FANTOM5 lncRNA Analysis (Chung)

Audio File: The audio file from the call (uploaded after the call): File:150326 F5 Telecon.MP3.zip

March 19th -- FANTOM5 short RNA Analysis Call

Topic: FANTOM5 short RNA Analysis (Tanvir Alam)

Audio File: The audio file from the call (uploaded after the call): File:150319 F5 Telecon.MP3.zip

March 12th -- FANTOM5 RNA Analysis Call

Topic: FANTOM5 lncRNA Analysis: FANTOM CAT: p_lncRNA vs e_lncRNA

Audio File : The audio file from the call (uploaded after the call): File:150312 F5 Telecon.MP3.zip

March 5th -- FANTOM5 short RNA Analysis Call

Topic: FANTOM5 short RNA Analysis (Michiel de Hoon)

Audio File : The audio file from the call (uploaded after the call): File:150305 F5 Telecon.MP3.zip

February 26th -- FANTOM5 lncRNA Analysis Call

Topic: FANTOM5 lncRNA Analysis (Chung Chau HON)

February 19th -- FANTOM5 short RNA Analysis Call

Topic: FANTOM5 short RNA Analysis (Michiel de Hoon)

Audio File : The audio file from the call (uploaded after the call): File:150219 F5 Telecon.zip

February 12th -- FANTOM5 lncRNA Analysis Call

Topic: FANTOM5 lncRNA Analysis (Chung Chau Hon)

Audio File : The audio file from the call (uploaded after the call): File:150212 F5 Telecon.zip

February 5th -- FANTOM5 short RNA Analysis Call

Topic: FANTOM5 short RNA Analysis (Michiel de Hoon)

Audio File : The audio file from the call (uploaded after the call): File:150205 001.MP3.zip

January 22nd -- FANTOM5 short RNA Analysis Call

Topic: FANTOM5 short RNA Analysis (Michiel de Hoon)

Audio File : The audio file from the call (uploaded after the call): File:150122 F5 Telecon.zip

October 23rd -- FANTOM5 short RNA Analysis Call

Topic: Update on the FANTOM5 short RNA main paper (Michiel de Hoon)

Audio File : The audio file from the call (uploaded after the call): No recording

October 2nd -- FANTOM5 lncRNA Analysis Call

Topic: FANTOM5 RNA-seq lncRNA catalog and some on-going analyses on lncRNA properties; plan on analysing lncRNA expression patterns, sub-classifying lncRNAs and intersecting lncRNA catalog with ENCODE data by Hon Chung Chau (RIKEN DGT)

Audio File : The audio file from the call (uploaded after the call): File:141002 F5 Telecon.zip

April 10th -- FANTOM5 short RNA Analysis Call

Topic: Update on the FANTOM5 short RNA main paper (Michiel de Hoon)

Audio File : The audio file from the call (uploaded after the call): File:140410 F5 Telecon.zip

September 5th -- FANTOM5 short RNA & lncRNA Analysis Call

Topic: Identifying promoters of primary microRNA transcripts by Michiel de Hoon

Audio File : The audio file from the call (uploaded after the call): File:130905 F5 Telecon.zip

May 30th -- FANTOM5 short RNA & lncRNA Analysis Call

Topic: Presentation on lncRNA Freeze2 Overview & Data availability (Nicolas Bertin)

Audio File : The audio file from the call (uploaded after the call): File:130530 F5 Telecon.zip

May 9th -- FANTOM5 short RNA & lncRNA Analysis Call

Topic : FANTOM5 short RNA analysis [Michiel de Hoon]

Topic : Update of the lncRNA analysis [Nicolas Bertin]

Audio File : The audio file from the call (uploaded after the call): File:130509 F5 Telecon.zip

April 18th -- FANTOM5 lncRNAome Analysis Call

Topic : Overview of the lncRNAome build 1 and call for help on specific topics / figures

Audio File The audio file from the call (uploaded after the call): File:130418 F5 lcnRNAome telecon.zip

FANTOM5 Promoterome Analysis Call has been discontinued (posted Jan-10-13)

December 13th

CANCELLED


December 7th

CANCELLED

This week's telecon will not be held.


November 8th

CANCELLED

This week's telecon will not be held.


November 1st

CANCELLED

This week's telecon will not be held due to the FANTOM5 Time-courses meeting being held at RIKEN OSC.


October 25th

Chair: Piero Carninci


CANCELLED

October 18th

Chair: Piero Carninci


AGENDA

1. Progress report by OSC

Some analysis on Motifs and first results of a F3/4/5 comparison. File:TalkOct18lassmann.pdf

2. Other topics, if any


Analysis Call Tip:

If concerned about the noise, we recommend putting your line in "listen-only" mode during presentation sessions of the call.

To enable "listen-only" mode press 97.

To disable "listen-only" mode press 96.


Audio File The audio file from the call on October 18th (uploaded after the call): File:121018 F5 Telecon.zip


October 11th

Chair: Piero Carninci


AGENDA

1. Macroape results summary - VIGG (questions from Al File:Motifs check 2 seva.pdf), presentation files: 1. File:Cluster structure.zip, 2. File:BH distance distributions Kn Dn^Lx.xls, 3. File:BestHits between databases IK.ppt, 4. File:Annotation vs SelfAnnotation.xls

2. TomTom results summary - Michiel (Ohmiya) File:Fantom5 20121011 michiel.pptx

3. PWM scanning Michiel

4. Any other updates from collaborators


Analysis Call Tip:

If concerned about the noise, we recommend putting your line in "listen-only" mode during presentation sessions of the call.

To enable "listen-only" mode press 97.

To disable "listen-only" mode press 96.


Audio File The audio file from the call on October 11th (uploaded after the call): File:121011 F5 Telecon.zip

October 4th

Chair: Piero Carninci


AGENDA

1. Progress report by OSC

2. Other topics


Analysis Call Tip:

If concerned about the noise, we recommend putting your line in "listen-only" mode during presentation sessions of the call.

To enable "listen-only" mode press 97.

To disable "listen-only" mode press 96.


Audio File The audio file from the call on October 4th (uploaded after the call): File:121004 F5 Telecon.zip

September 27th

Chair: Piero Carninci


AGENDA

1. Progress report by OSC

2. Presentation by VIGG File:VIGG Clustering 27 09 from dropbox.ppt (an old file - File:VIGG Clustering 27 09.ppt )

3. Other topics


Analysis Call Tip:

If concerned about the noise, we recommend putting your line in "listen-only" mode during presentation sessions of the call.

To enable "listen-only" mode press 97.

To disable "listen-only" mode press 96.


Audio File The audio file from the call on September 27th (uploaded after the call): File:120927 F5 Telecon.zip

September 20th

Chair: Piero Carninci


AGENDA

1. Progress report by OSC

2. Presentation by Lenhard group - temporary link: Sequence_and_chromatin_landscape_sharp_vs_broad_promoters.pdf

3. Other topics


Analysis Call Tip:

If concerned about the noise, we recommend putting your line in "listen-only" mode during presentation sessions of the call.

To enable "listen-only" mode press 97.

To disable "listen-only" mode press 96.


Audio File The audio file from the call on September 20th (uploaded after the call): File:120920 F5 Telecon.zip

September 13th

Chair: Piero Carninci


AGENDA

1. Main paper updates (Al)

2. ENCODE- implications for FANTOM5 Project

3. Other topics


Analysis Call Tip:

If concerned about the noise, we recommend putting your line in "listen-only" mode during presentation sessions of the call.

To enable "listen-only" mode press 97.

To disable "listen-only" mode press 96.


Audio File The audio file from the call on September 13th (uploaded after the call): File:120913 F5 Telecon.zip


September 6th

Chair: Piero Carninci


AGENDA

1. Progress report by OSC

2.


Analysis Call Tip:

If concerned about the noise, we recommend putting your line in "listen-only" mode during presentation sessions of the call.

To enable "listen-only" mode press 97.

To disable "listen-only" mode press 96.


Audio File The audio file from the call on September 6th (uploaded after the call): File:120906 F5 Telecon.zip

August 30th

Chair: Piero Carninci


AGENDA

1. Progress report by OSC

2.


Analysis Call Tip:

If concerned about the noise, we recommend putting your line in "listen-only" mode during presentation sessions of the call.

To enable "listen-only" mode press 97.

To disable "listen-only" mode press 96.


Audio File The audio file from the call on August 30th (uploaded after the call): File:120830 F5 Telecon.zip

August 23th

CANCELLED

The Analysis Call will not be held due to OSC summer break.

August 16th

CANCELLED

AGENDA

1. Progress report by OSC

2.


Analysis Call Tip:

If concerned about the noise, we recommend putting your line in "listen-only" mode during presentation sessions of the call.

To enable "listen-only" mode press 97.

To disable "listen-only" mode press 96.


Audio File The audio file from the call on August 16th (uploaded after the call): File:120816 F5 Telecon.zip

August 9th

Chair: Piero Carninci


AGENDA

1. Progress report by OSC

2.


Analysis Call Tip:

If concerned about the noise, we recommend putting your line in "listen-only" mode during presentation sessions of the call.

To enable "listen-only" mode press 97.

To disable "listen-only" mode press 96.


Audio File The audio file from the call on August 9th (uploaded after the call): File:120809 F5 Telecon.zip

August 2nd

Chair: Piero Carninci


AGENDA

1.

2.


Analysis Call Tip:

If concerned about the noise, we recommend putting your line in "listen-only" mode during presentation sessions of the call.

To enable "listen-only" mode press 97.

To disable "listen-only" mode press 96.


Audio File The audio file from the call on August 2nd (uploaded after the call): File:120802 F5 Telecon.zip

July 26th

Chair: Piero Carninci


AGENDA

1. Reports by the Promoterome main paper section leaders

2. Update on the motif evaluations (Michiel) File:Teleconference-20120726.pptx p-value heatmap


Analysis Call Tip:

If concerned about the noise, we recommend putting your line in "listen-only" mode during presentation sessions of the call.

To enable "listen-only" mode press 97.

To disable "listen-only" mode press 96.


Audio File The audio file from the call on July 26th (uploaded after the call): File:120726 F5 Telecon.zip

July 19th

Chair: Piero Carninci


AGENDA

1. Reports by the Promoterome main paper section leaders

2. Update on motif activity calculations (Michiel) Heatmap Ranks

3. recent updates and the discussions on the resource browser

  • pathway enrichment analysis of co-expression module - example:C3
  • synchronize with FF sample ontology v019_01
  • link to the genome browsers - example:p1@CNNM1 and link back
  • under discussion/improvement
    • table export as CSV
    • sorting function of the expression graph (line chart)
    • revision of sample order in the expression graph (line chart)
    • default order of tables
    • revision of sample enrichment analysis
    • revision of side bar content
    • interaction with other tools (biomart, bioLayout, Albin's promoter/enhancer selector, bioGPS, FONSE)
    • genomic view
    • nanopublication


Analysis Call Tip:

If concerned about the noise, we recommend putting your line in "listen-only" mode during presentation sessions of the call.

To enable "listen-only" mode press 97.

To disable "listen-only" mode press 96.


Audio File The audio file from the call on July 19th (uploaded after the call): File:120719 F5 Telecon.zip

July 12th

Chair: Piero Carninci

AGENDA

1. Reports by the Promoterome main paper section leaders


Analysis Call Tip:

If concerned about the noise, we recommend putting your line in "listen-only" mode during presentation sessions of the call.

To enable "listen-only" mode press 97.

To disable "listen-only" mode press 96.


Audio File The audio file from the call on July 12th (uploaded after the call): File:120712 F5 Telecon.zip

July 5th

Chair: Piero Carninci

AGENDA

1. Reports by the Promoterome main paper section leaders


Analysis Call Tip:

If concerned about the noise, we recommend putting your line in "listen-only" mode during presentation sessions of the call.

To enable "listen-only" mode press 97.

To disable "listen-only" mode press 96.


Audio File The audio file from the call on July 5th (uploaded after the call): File:120705 F5 Telecon.zip


June 28th

Analysis call CANCELLED.

The next analysis call will be held on July 5th.


June 21th

Chair: Piero Carninci


AGENDA

1. Progress report by RIKEN OSC

File:Promoterome draft figs June20.pdf

File:Promoterome draft supp figs June20.pdf


Analysis Call Tip:

If concerned about the noise, we recommend putting your line in "listen-only" mode during presentation sessions of the call.

To enable "listen-only" mode press 97.

To disable "listen-only" mode press 96.


Audio File The audio file from the call on June 21th (uploaded after the call): File:120621 F5 Telecon.zip

June 14th

Chair: Piero Carninci


AGENDA

1. Draft figures and section progress File:Promoterome draft figs June14.pdf


Analysis Call Tip:

If concerned about the noise, we recommend putting your line in "listen-only" mode during presentation sessions of the call.

To enable "listen-only" mode press 97.

To disable "listen-only" mode press 96.


Audio File The audio file from the call on June 14th (uploaded after the call): File:120614 F5 Telecon.zip

June 7th

Chair: Piero Carninci


AGENDA

1. Progress report by RIKEN OSC

2. Mini TSS prediction update (Timo, OSC) File:TSSprediction June7.pdf


Analysis Call Tip:

If concerned about the noise, we recommend putting your line in "listen-only" mode during presentation sessions of the call.

To enable "listen-only" mode press 97.

To disable "listen-only" mode press 96.


Audio File The audio file from the call on June 7th (uploaded after the call): File:120607 F5 Telecon.zip

May 31st

Chair: Piero Carninci


AGENDA

1. Brief progress report by the paper section leaders



Analysis Call Tip:

If concerned about the noise, we recommend putting your line in "listen-only" mode during presentation sessions of the call.

To enable "listen-only" mode press 97.

To disable "listen-only" mode press 96.


Audio File The audio file from the call on May 31st (uploaded after the call): File:120531 F5 Telecon.zip

May 24th

Chair: Piero Carninci


AGENDA

1. Flash report by paper section leaders



Analysis Call Tip:

If concerned about the noise, we recommend putting your line in "listen-only" mode during presentation sessions of the call.

To enable "listen-only" mode press 97.

To disable "listen-only" mode press 96.


Audio File The audio file from the call on May 24th (uploaded after the call): File:120524 F5 Telecon.zip

May 17th

Chair: Piero Carninci


AGENDA

1. First draft of the promoterome paper from Al

File:Promoterome May17 2012.doc CONFIDENTIAL - NOT FOR DISTRIBUTION OUTSIDE OF F5 File:Promoterome draft figsMay17.pdf CONFIDENTIAL - NOT FOR DISTRIBUTION OUTSIDE OF F5


Audio File The audio file from the call on May 17th (uploaded after the call): File:120517 F5 Telecon.zip

May 10th

Chair: Alistair Forrest


AGENDA

1. Progress report for this week by RIKEN OSC (Al Forrest)

2. MARA update (Michiel De Hoon, OSC) File:Teleconference-20120510.pptx

3. Short RNAs update (Max Burroughs, OSC) File:F5 small RNA update.pptx


Audio File The audio file from the call on May 10th (uploaded after the call): File:120510 F5 Telecon.zip

May 3rd

CANCELLED

Due to a national holiday in Japan, FANTOM5 Analysis Call will not be held.


April 26th

Chair: Piero Carninci


AGENDA

1. Progress report for this week by RIKEN OSC (Alistair FORREST) File:F5 Teleconference april26.ppt


Audio File The audio file from the call on April 26th (uploaded after the call): File:120426 F5 Telecon.zip

April 19th

Chair: Piero Carninci


AGENDA

1. Progress report for this week by RIKEN OSC

2. Presentation by Tom Freeman, Roslin Institute Presentation materials

3. A brief presentation by Kenneth Baillie, Roslin Institute Presentation materials (user name and password are the same as for the FANTOM5 Wiki page)



Audio File The audio file from the call on April 19th (uploaded after the call): File:120419 F5 Telecon.zip


April 12th

Chair: Piero Carninci


AGENDA

1. Progress report for this week by RIKEN OSC


Audio File The audio file from the call on April 12th (uploaded after the call): File:120412 F5 Telecon.zip

April 5th

Chair: Piero Carninci


AGENDA

1. Progress report for this week by RIKEN OSC(Hideya KAWAJI and Alistair FORREST) File:120405-f5-telecon-kawaji.pdf

2. F5 core promoters(Albin SANDELIN, University of Copenhagen) File:F5 core promoters sandelin.pdf


Audio File The audio file from the call on April 5th (uploaded after the call): File:120405 F5 Telecon.zip

March 29th

CANCELLED

Chair: Piero Carninci


AGENDA

1. Progress reports for this week by RIKEN OSC

2.


Audio File The audio file from the call on March 29th (uploaded after the call): File:120329 F5 Telecon.zip


March 22nd

Chair: Piero Carninci


AGENDA

1. Progress reports for this week by RIKEN OSC

2. Presentation by Boris Lenhard and Vanja Haberle (Imperial College London/University of Bergen): "Distribution and enrichment of TF motifs and ChIPseq binding sites in cell-type specific promoters from ENCODE cell lines". Media:Distribution_of_TF_binding_sites_ENCODE_cell_lines.pdf

3. Presentation by Ryota Mori from Asai-Lab: "Analyzing the secondary structures of human lncRNAome". Media:LncRNA_2ndarystructure_080322.pdf

Audio File The audio file from the call on March 22nd (uploaded after the call): File:120322 F5 Telecon.zip

March 15th

Chair: Piero Carninci


AGENDA

1. Progress reports for this week by RIKEN OSC

2. Presentation by group of Albin Sandelin, University of Copenhagen

Audio File The audio file from the call on March 15th (uploaded after the call): File:120315 F5 Telecon.zip

March 8th

Chair: Piero Carninci


AGENDA

1. Progress reports for this week by RIKEN OSC(Timo Lassmann)

2. gencode10 lncRNA set by Andrea Tanzer (CRG) lncRNA classification in gen10

Audio File The audio file from the call on March 1st (uploaded after the call): File:120308 F5 Telecon.zip

3. Motif discussion points - Continued analysis from Michael and Christian's effect of background and length (minor interpretation from Al). Media:Length_and_background_effects.pdf

March 1st

Chair: Piero Carninci


AGENDA

1. Progress reports for this week Deadlines and milestones for the promoterome and lncRNAome papers Media:Deadlines_UPDATE_March1_2012.xls

2. Brief Presentation on RNA analysis by Cedric Notredame Media:RNAmapping_01032012.ppt

3. Motif discussion points - Link to Michael's comparative analysis - effect of background and length. 

https://fantom5-collaboration.gsc.riken.jp/webdav/home/rehli/ab%20initio%20motifs.pptx

- Motif finding vs Motif scoring - target vs background discussion

- CpG island promoters - tissue specificity in the CpG or the flanking sequences?


Audio File The audio file from the call on March 1st (uploaded after the call): File:120301 F5 Telecon.zip

February 23rd

Chair: Piero Carninci


AGENDA

1. Progress reports for this week Deadlines and milestones for the promoterome and lncRNAome papers Media:Deadlines_UPDATE_Feb23_2012.xls

Audio File The audio file from the call on February 23rd (uploaded after the call): File:120223 F5 Telecon.zip


February 16th

Chair: Piero Carninci


AGENDA

1. Progress reports for this week

2. Discussion on motifs

3. Discussion on publication timeline ,


Deadlines and milestones for the promoterome and lncRNAome papers Media:Deadlines_UPDATE_Feb16_2012.xls Publication timeline Media:Deadlines_Feb15_2012_for_distribution.xls


Audio File The audio file from the call on February 16th (uploaded after the call): File:120216 F5 Telecon.zip

February 9th

Chair: Piero Carninci


AGENDA

  • "Updates", RIKEN OSC, Japan

Deadlines and milestones for the promoterome and lncRNAome papers Media:Deadlines_Feb09_2012.xls

Audio File The audio file from the call on February 9th (uploaded after the call): File:120209 F5 Telecon.zip


February 2nd

Chair: Piero Carninci


AGENDA

  • "Using SUPERFAMILY to track evolutionary milestones in the FANTOM data.", Owen Rackham, University of Bristol, UK. Presentation files: File:F5evol.pdf
  • "Updates", RIKEN OSC, Japan

Audio File The audio file from the call on February 2nd (uploaded after the call): File:120202 F5 Telecon.zip



January 26th

Chair: Piero Carninci


AGENDA

  • "Analysis update", RIKEN Omics Science Center. Presentation files will be uploaded here before the call

Deadlines and milestones for the promoterome and lncRNAome papers Media:Deadlines_Jan26_2012.xls

Audio File The audio file from the call on January 12th (uploaded after the call): File:120126 F5 Telecon.zip


January 19th

Chair: Piero Carninci


AGENDA

  • "Analysis update", RIKEN Omics Science Center. Presentation files will be uploaded here before the call

Audio File The audio file from the call on January 12th (uploaded after the call): File:120119 F5 Telecon.zip


January 12th

Chair: Alistair Forrest

AGENDA

Audio File The audio file from the call on January 12th (uploaded after the call): File:120112 F5 Telecon.zip

January 5th

Analysis call CANCELED!

Next call will be held on January 12th


December 22nd

Chair: Piero Carninci

AGENDA


Audio File The audio file from the call on December 22nd (uploaded after the call): File:111222 F5 Telecon.zip


December 15th

Chair: Piero Carninci

AGENDA

  • "Time course quality control", Erik Arner, RIKEN Omics Science Center, Japan. Presentation file will be uploaded here before the call

File:Timecourse qc 20111215.pptx File:Timecourse qc 20111215.pdf

  • "Analysis update", RIKEN Omics Science Center


Audio File The audio file from the call on December 15th (uploaded after the call): File:111215 F5 Telecon.zip

December 8th

Chair: Piero Carninci

AGENDA

Audio File The audio file from the call on December 8th (uploaded after the call): File:111208 F5 Telecon.zip

December 1st

Chair: Alistair Forrest

AGENDA


Audio File The audio file from the call on December 1st: File:111201 F5 Telecon.zip

November 24th

Chair: Piero Carninci

AGENDA


Audio File Audio file from the call on November 24th (will be uploaded after the call): File:111124 F5 Telecon.zip

November 17th

Chair: Alistair Forrest

AGENDA


Audio File Audio file from the call on November 17th: File:111117 F5 Telecon.zip

November 10th

Chair: Piero Carninci

AGENDA

  • "Data analysis using the Fantom Sample Ontology", Chris Mungall, Lawrence Berkeley National Laboratory, USA. Presentation file: File:Fantom5-ontology.pptx


Audio File Audio file from the call on November 10th will be uploaded here after the call File:111110 F5 Telecon.zip

November 3rd

On Thursday November 3rd, no FANTOM5 Analysis Call will be held since this day is a Japanese Holiday.


October 27th

Chair: Piero Carninci

AGENDA

  • "Update on main paper analysis ", Hideya Kawaji, RIKEN OSC, Japan. Presentation file will be uploaded here before the call File:111027-telecon-kawaji.pdf

Audio File Audio file from the call on October 27th: File:111027 F5 Telecon.zip


October 13th

The Analysis Call on October 13th has been cancelled. We are looking forward to meeting many of you here for the Koyo meeting!

October 7th

Chair: Piero Carninci

AGENDA

Audio File Audio file from the call on September 29nd:File:111007 F5 Telecon.zip

September 29nd

Chair: Piero Carninci

AGENDA

Audio File Audio file from the call on September 29nd: File:110929 F5 Telecon.zip.

September 22nd

Chair: Carsten Daub

AGENDA

Audio File Audio file from the call on September 22nd: File:110922 F5 Telecon.zip

September 15th

Chair: Piero Carninci

AGENDA

Audio File Audio file from the call on September 15th: File:110915 F5 Telecon.zip

September 8th

Chair: Piero Carninci

AGENDA

Audio File Audio file from the call on September 8th: File:110908 F5 Telecon.zip

September 1st

Chair: Piero Carninci

AGENDA

Audio File Audio file from the call on September 1st: File:110901 F5 Telecon.zip

August 18th

Chair: Piero Carninci

AGENDA

  • "Exploring promoter type switching in developmental time courses", Boris Lenhard, University of Bergen, Norway. Presentation in PDF format: File:Lenhard Analysis Call 20110818.pdf . Please let me know (boris.lenhard@bio.uib.no) if you need the original Keynote file.

Audio File Audio file from the call on August 18th 2011: File:110818 F5 Telecon.zip.

August 11th

Chair: Piero Carninci

AGENDA

  • "Status Update", Alistair Forrest, RIKEN OSC
  • "F5 lncRNAome integration with hCAGE: inferring function and networks", Leonard Lipovich, Wayne State University, Detroit, USA

___(PPT: Media:F5_Lipovich_11aug2011AnalysisCall.ppt, PDF: Media:F5_Lipovich_11aug2011AnalysisCall.pdf)

Audio File Audio file from the call on August 11th 2011: File:110811 F5 Telecon.zip‎

August 4th

Chair: Piero Carninci

AGENDA

Audio File Audio file from the call on August 4th 2011: File:110804 F5 Telecon.zip

July 28th

Chair: Piero Carninci

AGENDA

Audio File Audio file from the call on July 28th 2011: File:110728 F5 Telecon.zip

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