FANTOM5 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.

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 and guest password for the conference. Please find them below:

Conference id: 24711

Guest password: 3502

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".

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

• "Analysis update", Hideya Kawaji, RIKEN Omics Science Center. Presentation files: File:120112-telecon-kawaji.pdf

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

• "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

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

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

December 1st

Chair: Alistair Forrest

AGENDA

• "Status report on the ongoing analysis", Hideya kawaji, RIKEN OSC, Japan. File:111131-F5telecon-kawaji.pdf

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

November 24th

Chair: Piero Carninci

AGENDA

• "Status report on the ongoing analysis", RIKEN OSC, Japan. Presentation file will be uploaded before the call File:111124-f5-telecon-kawaji.pdf
• Sample QC page by Al
  

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

• "Brief Status report on the Promoterome paper", Alistair Forrest, RIKEN OSC, Japan. Promoterome update from Al Media:Promoterome_update_Nov17.doc

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

November 10th

Chair: Piero Carninci

AGENDA

• "Update on main paper analysis ", Promoterome update from Al File:Promoterome update Nov10.doc

• "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

• "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

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

September 29nd

Chair: Piero Carninci

AGENDA

• "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 29nd: File:110929 F5 Telecon.zip.

September 22nd

Chair: Carsten Daub

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

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

September 15th

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

September 8th

Chair: Piero Carninci

AGENDA

• "The mammalian promoterome - paper punchlines", Alistair Forrest, RIKEN OSC, Japan. File:FANTOM5 TC – September 8th.ppt

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

September 1st

Chair: Piero Carninci

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

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

• "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: File:110804 F5 Telecon.zip

July 28th

Chair: Piero Carninci

AGENDA

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

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