Time-courses meeting October 2012: Difference between revisions
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Session 3 - Satellite presentation (chair: Harukazu Suzuki) |
Session 3 - Satellite presentation (chair: Harukazu Suzuki) |
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*2.10PM ''Global transcriptome derivation of human skeletal muscle cell differentiation and Duchenne muscular dystrophy progression'' - (Valerio Orlando)[[File:01-01_F5_meeting_Orlando.pdf]] |
*2.10PM ''Global transcriptome derivation of human skeletal muscle cell differentiation and Duchenne muscular dystrophy progression'' - (Valerio Orlando)[[File:01-01_F5_meeting_Orlando.pdf]], [https://fantom5-collaboration.gsc.riken.jp/webdav/home/video/Time-courses/Valerio_Orlando.mp4 Video link] |
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*2.30PM ''Time course analysis of erythroid differentiation: transcriptional regulation of erythropoiesis'' - (Louise Winteringham) [[File:02_Winteringham_fantom5_Oct_2012.pdf]] |
*2.30PM ''Time course analysis of erythroid differentiation: transcriptional regulation of erythropoiesis'' - (Louise Winteringham) [[File:02_Winteringham_fantom5_Oct_2012.pdf]], [https://fantom5-collaboration.gsc.riken.jp/webdav/home/video/Time-courses/Louise_Winteringham.mp4 Video link] |
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*2.50PM ''Elucidating gene regulatory networks underlying early brain development in Down syndrome with iPSC'' - (Ernst Wolvetang) [[File:03_Wolvetang_yokohama_fantom_2012.pdf]] |
*2.50PM ''Elucidating gene regulatory networks underlying early brain development in Down syndrome with iPSC'' - (Ernst Wolvetang) [[File:03_Wolvetang_yokohama_fantom_2012.pdf]], [https://fantom5-collaboration.gsc.riken.jp/webdav/home/video/Time-courses/Ernst_Wolvetang.mp4 Video link] |
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*3.10PM ''ARPE-19 retinal pigment epithelial cell line, epithelial to mesenchyme transition'' - (Soichi Ogishima) [[File:Ogishima_FANTOM5_meeting_slide.pdf]] |
*3.10PM ''ARPE-19 retinal pigment epithelial cell line, epithelial to mesenchyme transition'' - (Soichi Ogishima) [[File:Ogishima_FANTOM5_meeting_slide.pdf]], [https://fantom5-collaboration.gsc.riken.jp/webdav/home/video/Time-courses/Soichi_Ogishima.mp4 Video link] |
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*3.30PM ''Gene regulatory networks in T cell lineage specification'' - (Tomokatsu Ikawa) [[File:05_121031_IKAWA_FANTOM5_meeting.ppt]] |
*3.30PM ''Gene regulatory networks in T cell lineage specification'' - (Tomokatsu Ikawa) [[File:05_121031_IKAWA_FANTOM5_meeting.ppt]], [https://fantom5-collaboration.gsc.riken.jp/webdav/home/video/Time-courses/Tomokatsu_Ikawa.mp4 Video link] |
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*3.50PM ''Immediate-early genes as regulators in cancer and vascular disease'' - (Levon Khachigian) [[File:Levon_FANTOM5-1.pdf]] |
*3.50PM ''Immediate-early genes as regulators in cancer and vascular disease'' - (Levon Khachigian) [[File:Levon_FANTOM5-1.pdf]], [https://fantom5-collaboration.gsc.riken.jp/webdav/home/video/Time-courses/Levon_Khachigian.mp4 Video link] |
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<br> 4:10PM COFFEE BREAK |
<br> 4:10PM COFFEE BREAK |
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*9.00AM ''Summary from Main Day 1'' - (Erik Arner) |
*9.00AM ''Summary from Main Day 1'' - (Erik Arner) |
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*9.10AM ''From Integrated Motif Activity Response Analysis to causal regulatory links'' - (Erik van Nimwegen) [[File:Nimwegen_riken_oct2012.pdf]] |
*9.10AM ''From Integrated Motif Activity Response Analysis to causal regulatory links'' - (Erik van Nimwegen) [[File:Nimwegen_riken_oct2012.pdf]], [https://fantom5-collaboration.gsc.riken.jp/webdav/home/video/Time-courses/Erik_van_Nimwegen.mp4 Video link] |
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*9.30AM ''De novo motif analyses for time course data sets'' - (Michael Rehli) [[File:02_FANTOM2_MR.pdf]] |
*9.30AM ''De novo motif analyses for time course data sets'' - (Michael Rehli) [[File:02_FANTOM2_MR.pdf]], [https://fantom5-collaboration.gsc.riken.jp/webdav/home/video/Time-courses/Michael_Rehli.mp4 Video link] |
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*9.50AM ''CAGE-defined enhancer-TSS dynamics within time courses - a new resource within FANTOM5'' - (Albin Sandelin and Robin Andersson) [[File: 03_FANTOM_main_meeting_Andersson_Sandelin.pdf]] |
*9.50AM ''CAGE-defined enhancer-TSS dynamics within time courses - a new resource within FANTOM5'' - (Albin Sandelin and Robin Andersson) [[File: 03_FANTOM_main_meeting_Andersson_Sandelin.pdf]], [https://fantom5-collaboration.gsc.riken.jp/webdav/home/video/Time-courses/Albin_Sandelin_and_Robin_Andersson.mp4 Video link] |
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*10.10AM ''Finding key TFs with regulatory roles linked to gene expression changes in time-course data'' - (Wyeth Wasserman and Anthony Mathelier) [[File:WWW_AM_compact_F5TC.pdf]] |
*10.10AM ''Finding key TFs with regulatory roles linked to gene expression changes in time-course data'' - (Wyeth Wasserman and Anthony Mathelier) [[File:WWW_AM_compact_F5TC.pdf]], [https://fantom5-collaboration.gsc.riken.jp/webdav/home/video/Time-courses/Wyeth_Wasserman_and_Anthony_Mathelier.mp4 Video link] |
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<br> 10.30AM COFFEE BREAK |
<br> 10.30AM COFFEE BREAK |
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Session 2 - Integrated analysis - presentations (chair: Timo Lassmann) |
Session 2 - Integrated analysis - presentations (chair: Timo Lassmann) |
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*11.10AM ''Gene expression and promoter usage during neuronal differentiation'' - (Boris Lenhard) [[File:Haberle_Lenhard_FANTOM5_20121101.pdf]] |
*11.10AM ''Gene expression and promoter usage during neuronal differentiation'' - (Boris Lenhard) [[File:Haberle_Lenhard_FANTOM5_20121101.pdf]], [https://fantom5-collaboration.gsc.riken.jp/webdav/home/video/Time-courses/Boris_Lenhard.mp4 Video link] |
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*11.30AM ''Promoter switching in the FANTOM time-courses'' - (Emmanuel Dimont) [[File:02_Day4_RIKEN_-_Promoter_Switching_-_Emmanuel_Dimont.ppt]] |
*11.30AM ''Promoter switching in the FANTOM time-courses'' - (Emmanuel Dimont) [[File:02_Day4_RIKEN_-_Promoter_Switching_-_Emmanuel_Dimont.ppt]], [https://fantom5-collaboration.gsc.riken.jp/webdav/home/video/Time-courses/Emmanuel_Dimont.mp4 Video link] |
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*11.50AM ''Definition and analysis of gene sets from time series data'' - (Finn Drablos and Morten Rye) [[File:Finn_Drablos_FANTOM_2012.pdf]] |
*11.50AM ''Definition and analysis of gene sets from time series data'' - (Finn Drablos and Morten Rye) [[File:Finn_Drablos_FANTOM_2012.pdf]], [https://fantom5-collaboration.gsc.riken.jp/webdav/home/video/Time-courses/Finn_Drablos_and_Morten_Rye.mp4 Video link] |
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*12.10PM ''Decoupling linear and nonlinear associations in time course signals'' - (Carlo Cannistraci) [[File:04_Carlo_Vittorio_Cannistraci_-_Presentation_31_oct_2012_-_Fantom_5.pptx]] |
*12.10PM ''Decoupling linear and nonlinear associations in time course signals'' - (Carlo Cannistraci) [[File:04_Carlo_Vittorio_Cannistraci_-_Presentation_31_oct_2012_-_Fantom_5.pptx]], [https://fantom5-collaboration.gsc.riken.jp/webdav/home/video/Time-courses/Carlo_Cannistraci.mp4 Video link] |
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*12.30PM ''Time profiles clustering with multivariate statistics'' - (Kim-Anh Le Cao) [[File:05_F5_LeCao.pdf]] |
*12.30PM ''Time profiles clustering with multivariate statistics'' - (Kim-Anh Le Cao) [[File:05_F5_LeCao.pdf]], [https://fantom5-collaboration.gsc.riken.jp/webdav/home/video/Time-courses/Kim-Anh_Le_Cao.mp4 Video link] |
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<br> 12.50PM LUNCH |
<br> 12.50PM LUNCH |
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Session 3 - Integrated analysis - discussion (chair: Carsten Daub, Alistair Forrest, Piero Carninci) |
Session 3 - Integrated analysis - discussion (chair: Carsten Daub, Alistair Forrest, Piero Carninci) |
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*2.10PM ''Discussion about satellite papers/time-courses and consensus about Day 3'' |
*2.10PM ''Discussion about satellite papers/time-courses and consensus about Day 3'', [https://fantom5-collaboration.gsc.riken.jp/webdav/home/video/Time-courses/Discussion_about_satellite_papers.mp4 Video link] |
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<br> 3.00PM COFFEE BREAK |
<br> 3.00PM COFFEE BREAK |
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*3.30PM OSC Award [https://fantom5-collaboration.gsc.riken.jp/webdav/home/video/Time-courses/OSC_Award.mp4 Video link] |
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*3.30PM OSC Award |
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*4.00PM ''Discussion about satellite papers/time-courses and consensus about Day 3'' |
*4.00PM ''Discussion about satellite papers/time-courses and consensus about Day 3'', [https://fantom5-collaboration.gsc.riken.jp/webdav/home/video/Time-courses/Discussion_about_satellite_papers_02.mp4 Video link] |
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<br> 4.30PM COFFEE BREAK |
<br> 4.30PM COFFEE BREAK |
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*5.00PM Plan for integrated paper/satellite papers [[File:Publication_strategy-Fantom5-oct31-2012.pptx]](Piero's notes) |
*5.00PM Plan for integrated paper/satellite papers [[File:Publication_strategy-Fantom5-oct31-2012.pptx]](Piero's notes), [https://fantom5-collaboration.gsc.riken.jp/webdav/home/video/Time-courses/Plan_for_integrated_paper-satellite_papers.mp4 Video link 1] [https://fantom5-collaboration.gsc.riken.jp/webdav/home/video/Time-courses/Publication_strategy.mp4 Video link 2] |
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<br>6.30PM END OF MAIN MEETING DAY 2 --> BEER PARTY |
<br>6.30PM END OF MAIN MEETING DAY 2 --> BEER PARTY |
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*9.00AM ''Working on the satellite papers and main paper'' [[File:Publication_strategy-Fantom5-oct31-2012.pptx]] (Piero's notes) |
*9.00AM ''Working on the satellite papers and main paper'' [[File:Publication_strategy-Fantom5-oct31-2012.pptx]] (Piero's notes), [https://fantom5-collaboration.gsc.riken.jp/webdav/home/video/Time-courses/Working_on_the_satellite_papers_and_main_paper.mp4 Video link] |
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<br> 10.30AM COFFEE BREAK |
<br> 10.30AM COFFEE BREAK |
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*10.45AM ''Working on the satellite papers and main paper'' |
*10.45AM ''Working on the satellite papers and main paper'', [https://fantom5-collaboration.gsc.riken.jp/webdav/home/video/Time-courses/Working_on_the_satellite_papers_and_main_paper_02.mp4 Video link] |
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<br> 12.15PM LUNCH |
<br> 12.15PM LUNCH |
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*1.30PM ''Working on the satellite papers and main paper'' |
*1.30PM ''Working on the satellite papers and main paper'', [https://fantom5-collaboration.gsc.riken.jp/webdav/home/video/Time-courses/Working_on_the_satellite_papers_and_main_paper_03.mp4 Video link] |
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<br> 3.30PM COFFEE BREAK |
<br> 3.30PM COFFEE BREAK |
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*3.45PM ''Working on the satellite papers and main paper'' |
*3.45PM ''Working on the satellite papers and main paper'', [https://fantom5-collaboration.gsc.riken.jp/webdav/home/video/Time-courses/Working_on_the_satellite_papers_and_main_paper_04.mp4 Video link] |
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<br> 5.15PM COFFEE BREAK |
<br> 5.15PM COFFEE BREAK |
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Latest revision as of 11:53, 14 February 2013
Meeting Booklet
Here is a copy of the FANTOM5 Time-courses meeting booklet including abstracts for oral presentations and contact list of participants File:FANTOM5 Timecourses booklet.pdf. Please note that the booklet contains confidential information that should be treated in accordance with the confidentiality agreement.
Logo and Cover Art by Watanabe Kazufumi.
Video Streaming
Here you can find video recordings of the oral presentations from main meeting Day 3 (Oct-31) and Day 4 (Nov-1).
Video upload to WebDav completed! (01/29/13)
Video files can be found at fantom5 collaboration sharing site - webdav. https://fantom5-collaboration.gsc.riken.jp/webdav/home/video/Time-courses/
You can also find link to individual presentation videos next to presentation titles in the program below [in progress 01/30/13].
Due to technical problems, two presentations have parts of with no audio. We apologize for the inconvenience!
Agenda
Day 1 Monday October 29th - Education and discussion session
Registration open from 8.30AM
Workshop
- 9.00AM Welcome - (Yoshihide Hayashizaki)
- 9.10AM Quality control of time-course data - (Erik Arner) File:Timecourse meeting qc 20121029.pptx
- 10.10AM DPI clustering - (Hideya Kawaji) File:121028-DPI.pdf
10.30AM COFFEE BREAK
- 11.00AM TSS classifier - (Timo Lassman) File:TSSLassmann.pdf
- 11.20AM ZENBU - (Jessica Severin) File:Zenbu fantom5 meeting oct29 2012 v5.pptx
- 11.50AM FANTOM Resource Browser - (Hisashi Shimoji and Hideya Kawaji) File:FANTOM resource browser F5mtg 20121029.pdf
1.00PM LUNCH + free discussion (note 1)
- 3.00PM Workshop: Biology of immediate early repsonses (continued) - (session leader: Christine Wells) File:FANTOM time course CW.pdf
- Early responsive genes in MCF-7 breast cancer cells - (Mariko Okada) File:FANTOM Early gene 2012-short Okada.pdf
- "Neuronal type specification and Transcription factors in cerebellar development" - (Thomas Ha) File:TH TFs in cerebellum development 121029.pdf
- Early Time Point AnalysisSAOS2 calcification - (Kim Summers) File:Time points KMS.pdf
4.20PM COFFEE BREAK
- 4.40 ''Workshop: Biology of immediate early repsonses (continued) - (session leader: Christine Wells)
Examples of upstream antisense induction at IER genes - EGR1, FOS, NR4A1 from Al in Mariko's MCF7 series File:Upstream antisense MCF7 ALexamples.pdf
6.00PM END OF DAY 1
note 1 Long break is due to the fact that OSC members are required to attend a RIKEN internal briefing. You will be free to use the extra time to refresh or hold informal discussion groups.
Day 2 Tuesday October 30th - Education and discussion session
Registration open from 8.30AM
Workshop
- 9.00AM Summary from Day 1 - (Carsten Daub) File:Day 1 summary - Carsten.pptx
- 9.15AM Workshop: Motifs and composite elements for time-courses - (session leader:Peter Pemberton-Ross) File:301012 MotifSession F5TC.pdf
- 9.20AM Strategies for de novo motif finding in timecourse data - (Michael Rehli) File:FANTOM MR.pdf
- 9.50AM MotifLab - A workbench for analysing regulatory regions - (Kjetil Klepper) File:MotifLab presentation.zip
- 10.10AM MARA and the FANTOM5 Time-courses - (Peter Pemberton-Ross)
10.45AM COFFEE BREAK
- 11.15AM Workshop: Motifs and composite elements for time-courses (continued) - (session leader:Peter Pemberton-Ross)
- 11.15AM Sequence analysis of TSSs for mRNAs translationally regulated by mTOR cascade - (Ivan Kulakovskiy) File:MTOR Kulakovskiy 29102012 VIGG.pdf
- 11.30AM Motif analysis for the phase 1 main paper - (Ulf Schaefer & Yulia Medvedeva) File:KAUST Phase 1 – Ab-initio Motif analysis1.pdf
- 11.45AM Preferred pair distance templates for detection of TFBS composite elements in FANTOM5 Timecourse data (Vsevolod Makeev/Ivan Kulakovskiy) File:CompositeElements Makeev VIGG.pdf
12.45PM LUNCH
- 2.15PM Workshop: Gene expression, changes during time-courses. Expression clustering: immediate early response and other patterns, TSS Switch, Stimulus psecific promoters - (session leader: Owen Rackham)
- 2:15PM Erik: Early response analysis File:Timecourse meeting ier 20121030.pptx
- 2:45PM Owen: Gene Clustering using SOMs File:F5 TC.pdf
- 3:15PM Sarah: Sample Complexity File:F5TC Complexity SB.pdf
- 3:45PM Emmanuel: TSS/Promoter Switching File:Day2 RIKEN - Promoter Switching - Emmanuel Dimont.ppt
4.15PM COFFEE BREAK
- 4.45PM Enhancers: expression, usage in time-courses, etc. - (session leader: Albin Sandelin and group members) File:FANTOM5 enhancers 301012.pptx
- 5.45PM miRNA and other non-coding RNA (Pal Saetrom) File:30Oct2012-Fantom5-miRNAs3.pdf
6.45 END OF DAY 2
Day 3 Wednesday October 31st Main meeting Day 1 - Satellite papers
Program change
(Oct-30-12) File:FANTOM Program Oct31-change.pdf
Registration open from 8.30AM
Session 1 - Satellite presentation (chair: Carsten Daub)
- 9.00AM Welcome - (Yoshihide Hayashizaki) Video link
- 9.15AM Phase 1 and Promoterome paper - (Alistair Forrest) File:FANTOM5 timecourse meeting 9AM.pdf, Video link
- 9.45AM Analysis of adipogenesis in human primary adipose-derived stem cells - (Anna Ehrlund) File:02 Adipogenesis time course, RIKEN fall meeting 2012.pdf, Video link
- 10.05AM Analysis of FANTOM5 cerebellum development time course CAGE library - (Thomas Ha)File:TH cerebellum development 121031.pdf, Video link
- 10.25AM Early and late changes in gene expression during mineralization of SAOS-2, a human osteosarcoma cell line model for bone formation - (Kim Summers) File:04 FANTOM5 KS Oct31 2012.pdf, Video link
10.45AM COFFEE BREAK
Session 2 - Satellite presentation (chair: Alistair Forrest)
- 11.15AM Interindividual variation and stimulus specificity in the inflammatory response - (Kenneth Baillie) File:01 Baillie FANTOM5 TIMECOURSE 5 pruned.pptx, Video link
- 11.35AM Identification of functional non-coding RNAs during bi-directional differentiation from mouse mesenchymal stem cells to adipocytes/osteoblasts - (Yutaka Nakachi) File:02 FANTOM5 presentation nakachiy 121031.pdf, Video link
- 11.55AM The transcriptome of macrophage activation & mycobacterium infection - (Frank Brombacher) File:Brombacher 11h55 Wed 31.pdf, Video link
- 12.15PM Human lymphatic endothelial cells response to vascular endothelial growth factor-C - (Michael Detmar) File:Detmar FANTOM5 Oct31.pdf, Video link
12.55PM LUNCH
Session 3 - Satellite presentation (chair: Harukazu Suzuki)
- 2.10PM Global transcriptome derivation of human skeletal muscle cell differentiation and Duchenne muscular dystrophy progression - (Valerio Orlando)File:01-01 F5 meeting Orlando.pdf, Video link
- 2.30PM Time course analysis of erythroid differentiation: transcriptional regulation of erythropoiesis - (Louise Winteringham) File:02 Winteringham fantom5 Oct 2012.pdf, Video link
- 2.50PM Elucidating gene regulatory networks underlying early brain development in Down syndrome with iPSC - (Ernst Wolvetang) File:03 Wolvetang yokohama fantom 2012.pdf, Video link
- 3.10PM ARPE-19 retinal pigment epithelial cell line, epithelial to mesenchyme transition - (Soichi Ogishima) File:Ogishima FANTOM5 meeting slide.pdf, Video link
- 3.30PM Gene regulatory networks in T cell lineage specification - (Tomokatsu Ikawa) File:05 121031 IKAWA FANTOM5 meeting.ppt, Video link
- 3.50PM Immediate-early genes as regulators in cancer and vascular disease - (Levon Khachigian) File:Levon FANTOM5-1.pdf, Video link
4:10PM COFFEE BREAK
Session 4 - Satellite discussions (chair: Piero Carninci)
- 4.40PM Future FANTOM - (Yoshihide Hayashizaki)(CHANGED) File:121031FANTOM5 Time Course Meeting ver8 Wiki.pdf
- 5.10PM Publication strategy: individual vs. integrated analysis
6.20PM END OF DAY 1 --> WELCOME DINNER
8.00PM WELCOME DINNER END
Day 4 Thursday November 1st - Main meeting Day 2 - Integrated analysis
Registration open from 8.30AM
Session 1 - Integrated analysis - presentations (chair: Erik Arner)
- 9.00AM Summary from Main Day 1 - (Erik Arner)
- 9.10AM From Integrated Motif Activity Response Analysis to causal regulatory links - (Erik van Nimwegen) File:Nimwegen riken oct2012.pdf, Video link
- 9.30AM De novo motif analyses for time course data sets - (Michael Rehli) File:02 FANTOM2 MR.pdf, Video link
- 9.50AM CAGE-defined enhancer-TSS dynamics within time courses - a new resource within FANTOM5 - (Albin Sandelin and Robin Andersson) File:03 FANTOM main meeting Andersson Sandelin.pdf, Video link
- 10.10AM Finding key TFs with regulatory roles linked to gene expression changes in time-course data - (Wyeth Wasserman and Anthony Mathelier) File:WWW AM compact F5TC.pdf, Video link
10.30AM COFFEE BREAK
Session 2 - Integrated analysis - presentations (chair: Timo Lassmann)
- 11.10AM Gene expression and promoter usage during neuronal differentiation - (Boris Lenhard) File:Haberle Lenhard FANTOM5 20121101.pdf, Video link
- 11.30AM Promoter switching in the FANTOM time-courses - (Emmanuel Dimont) File:02 Day4 RIKEN - Promoter Switching - Emmanuel Dimont.ppt, Video link
- 11.50AM Definition and analysis of gene sets from time series data - (Finn Drablos and Morten Rye) File:Finn Drablos FANTOM 2012.pdf, Video link
- 12.10PM Decoupling linear and nonlinear associations in time course signals - (Carlo Cannistraci) File:04 Carlo Vittorio Cannistraci - Presentation 31 oct 2012 - Fantom 5.pptx, Video link
- 12.30PM Time profiles clustering with multivariate statistics - (Kim-Anh Le Cao) File:05 F5 LeCao.pdf, Video link
12.50PM LUNCH
Session 3 - Integrated analysis - discussion (chair: Carsten Daub, Alistair Forrest, Piero Carninci)
- 2.10PM Discussion about satellite papers/time-courses and consensus about Day 3, Video link
3.00PM COFFEE BREAK
- 3.30PM OSC Award Video link
- 4.00PM Discussion about satellite papers/time-courses and consensus about Day 3, Video link
4.30PM COFFEE BREAK
- 5.00PM Plan for integrated paper/satellite papers File:Publication strategy-Fantom5-oct31-2012.pptx(Piero's notes), Video link 1 Video link 2
6.30PM END OF MAIN MEETING DAY 2 --> BEER PARTY
8.00PM BEER PARTY END
Day 5 Friday November 2nd
Registration open from 8.30AM
Workshop - Implementation of the discussion of Day 3-4
- 9.00AM Working on the satellite papers and main paper File:Publication strategy-Fantom5-oct31-2012.pptx (Piero's notes), Video link
10.30AM COFFEE BREAK
- 10.45AM Working on the satellite papers and main paper, Video link
12.15PM LUNCH
- 1.30PM Working on the satellite papers and main paper, Video link
3.30PM COFFEE BREAK
- 3.45PM Working on the satellite papers and main paper, Video link
5.15PM COFFEE BREAK
- 5.30PM Summarizing results File:Publication strategy and Analysis Strategy Nov2-2012.pptx
6.30PM END OF DAY 5
