FANTOM5 analysis call

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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.

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 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)

September 20th

Chair: Piero Carninci


AGENDA

1. Progress report by OSC

2. Presentation by Lenhard group

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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