Time-courses meeting October 2012: Difference between revisions

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[[File:Fantom5_timecourses_logo.png]]

== Meeting Booklet ==

Here is a copy of the FANTOM5 Time-courses meeting booklet including abstracts for oral presentations and contact list of participants [[Image: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/ 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 ==
== Agenda ==
== Day 1 Monday October 29th - Education and discussion session ==
== Day 1 Monday October 29th - Education and discussion session ==
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Session 1 - Satellite presentation (chair: Carsten Daub)
Session 1 - Satellite presentation (chair: Carsten Daub)


*9.00AM ''Welcome'' - (Yoshihide Hayashizaki)
*9.00AM ''Welcome'' - (Yoshihide Hayashizaki) [https://fantom5-collaboration.gsc.riken.jp/webdav/home/video/Time-courses/2012-10-31_Hayashizaki.m4v Video link]
*9.15AM ''Phase 1 and Promoterome paper'' - (Alistair Forrest) [[File:FANTOM5_timecourse_meeting_9AM.pdf]]
*9.15AM ''Phase 1 and Promoterome paper'' - (Alistair Forrest) [[File:FANTOM5_timecourse_meeting_9AM.pdf]], [https://fantom5-collaboration.gsc.riken.jp/webdav/home/video/Time-courses/2012-10-31-Al.mov Video link]
*9.45AM ''Analysis of adipogenesis in human primary adipose-derived stem cells'' - (Anna Ehrlund)
*9.45AM ''Analysis of adipogenesis in human primary adipose-derived stem cells'' - (Anna Ehrlund) [[File:02_Adipogenesis_time_course,_RIKEN_fall_meeting_2012.pdf‎]], [https://fantom5-collaboration.gsc.riken.jp/webdav/home/video/Time-courses/Anna_Ehrlund.mov Video link]
*10.05AM ''Analysis of FANTOM5 cerebellum development time course CAGE library'' - (Thomas Ha)
*10.05AM ''Analysis of FANTOM5 cerebellum development time course CAGE library'' - (Thomas Ha)[[File:TH_cerebellum_development_121031.pdf]], [https://fantom5-collaboration.gsc.riken.jp/webdav/home/video/Time-courses/Thomas_Ha.mov 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]]
*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]], [https://fantom5-collaboration.gsc.riken.jp/webdav/home/video/Time-courses/Kim_Summers.mov Video link]


<br> 10.45AM COFFEE BREAK
<br> 10.45AM COFFEE BREAK
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Session 2 - Satellite presentation (chair: Alistair Forrest)
Session 2 - Satellite presentation (chair: Alistair Forrest)


*11.15AM ''Interindividual variation and stimulus specificity in the inflammatory response'' - (Kenneth Baillie)
*11.15AM ''Interindividual variation and stimulus specificity in the inflammatory response'' - (Kenneth Baillie) [[File:01_Baillie_FANTOM5_TIMECOURSE_5_pruned.pptx‎]], [https://fantom5-collaboration.gsc.riken.jp/webdav/home/video/Time-courses/Kenneth_Baillie.mp4 Video link]
*11.35AM ''Identification of functional non-coding RNAs during bi-directional differentiation from mouse mesenchymal stem cells to adipocytes/osteoblasts'' - (Yutaka Nakachi)
*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]], [https://fantom5-collaboration.gsc.riken.jp/webdav/home/video/Time-courses/Yutaka_Nakachi.mp4 Video link]
*11.55AM ''The transcriptome of macrophage activation & mycobacterium infection'' - (Frank Brombacher) [[File:Brombacher_11h55_Wed_31.pdf]]
*11.55AM ''The transcriptome of macrophage activation & mycobacterium infection'' - (Frank Brombacher) [[File:Brombacher_11h55_Wed_31.pdf]], [https://fantom5-collaboration.gsc.riken.jp/webdav/home/video/Time-courses/Frank_Brombacher.mp4 Video link]
*12.15PM ''Human lymphatic endothelial cells response to vascular endothelial growth factor-C'' - (Michael Detmar) [[File:Detmar_FANTOM5_Oct31.pdf‎]]
*12.15PM ''Human lymphatic endothelial cells response to vascular endothelial growth factor-C'' - (Michael Detmar) [[File:Detmar_FANTOM5_Oct31.pdf‎]], [https://fantom5-collaboration.gsc.riken.jp/webdav/home/video/Time-courses/Michael_Detmar.mp4 Video link]
⚫
*12.35PM ''Global transcriptome derivation of human skeletal muscle cell differentiation and Duchenne muscular dystrophy progression'' - (Valerio Orlando)


<br> 12.55PM LUNCH
<br> 12.55PM LUNCH
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Session 3 - Satellite presentation (chair: Harukazu Suzuki)
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]], [https://fantom5-collaboration.gsc.riken.jp/webdav/home/video/Time-courses/Valerio_Orlando.mp4 Video link]
*2.10PM ''Time course analysis of erythroid differentiation: transcriptional regulation of erythropoiesis'' - (Louise Winteringham)
*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]
*2.30PM ''Elucidating gene regulatory networks underlying early brain development in Down syndrome with iPSC'' - (Ernst Wolvetang)
*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]
*2.50PM ''ARPE-19 retinal pigment epithelial cell line, epithelial to mesenchyme transition'' - (Soichi Ogishima)
*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]
*3.10PM ''Gene regulatory networks in T cell lineage specification'' - (Tomokatsu Ikawa)
*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]
*3.30PM ''Immediate-early genes as regulators in cancer and vascular disease'' - (Levon Khachigian)
*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]


<br> 3:50PM COFFEE BREAK
<br> 4:10PM COFFEE BREAK


Session 4 - Satellite discussions (chair: Piero Carninci)
Session 4 - Satellite discussions (chair: Piero Carninci)


*'''4.20PM ''Future FANTOM'' - (Yoshihide Hayashizaki)(CHANGED)'''
*'''4.40PM ''Future FANTOM'' - (Yoshihide Hayashizaki)(CHANGED)''' [[File:121031FANTOM5_Time_Course_Meeting_ver8_Wiki.pdf]]
*4.50PM ''Publication strategy: individual vs. integrated analysis''
*5.10PM ''Publication strategy: individual vs. integrated analysis''


<br>6.20PM END OF DAY 1 --> WELCOME DINNER
<br>6.20PM END OF DAY 1 --> WELCOME DINNER
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*9.00AM ''Summary from Main Day 1'' - (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)
*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]
*9.30AM ''De novo motif analyses for time course data sets'' - (Michael Rehli)
*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]
*9.50AM ''CAGE-defined enhancer-TSS dynamics within time courses - a new resource within FANTOM5'' - (Albin Sandelin and Robin Andersson)
*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]
*10.10AM ''Finding key TFs with regulatory roles linked to gene expression changes in time-course data'' - (Wyeth Wasserman and Anthony Mathelier)
*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]


<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)


*11.00AM ''Gene expression and promoter usage during neuronal differentiation'' - (Boris Lenhard)
*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]
*11.20AM ''Promoter switching in the FANTOM time-courses'' - (Emmanuel Dimont)
*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]
*11.40AM ''Definition and analysis of gene sets from time series data'' - (Finn Drablos)
*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]
*12.00PM ''Decoupling linear and nonlinear associations in time course signals'' - (Timothy Ravasi)
*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]
*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]
*12.20PM ''Data integration of highly dimensional biological data sets with multivariate analysis'' - (Kim-Anh Le Cao)


<br> 12.40PM LUNCH
<br> 12.50PM LUNCH


Session 3 - Integrated analysis - discussion (chair: Carsten Daub, Alistair Forrest, Piero Carninci)
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''
*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]


<br> 3.00PM COFFEE BREAK
<br> 3.00PM COFFEE BREAK


*3.30PM OSC Award [https://fantom5-collaboration.gsc.riken.jp/webdav/home/video/Time-courses/OSC_Award.mp4 Video link]
*3.30PM OSC Award


*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]


<br> 4.30PM COFFEE BREAK
<br> 4.30PM COFFEE BREAK


*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]
*5.00PM Plan for integrated paper/satellite papers


<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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<br>8.00PM BEER PARTY END
<br>8.00PM BEER PARTY END


== Day 5 Friday November 2nd - Education and discussion session ==
== Day 5 Friday November 2nd ==


Registration open from 8.30AM
Registration open from 8.30AM
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*9.00AM ''Working on the satellite papers and main paper''
*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]


<br> 10.30AM COFFEE BREAK
<br> 10.30AM COFFEE BREAK


*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]


<br> 12.15PM LUNCH
<br> 12.15PM LUNCH


*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]


<br> 3.30PM COFFEE BREAK
<br> 3.30PM COFFEE BREAK


*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]


<br> 5.15PM COFFEE BREAK
<br> 5.15PM COFFEE BREAK


*5.30PM ''Summarizing results''
*5.30PM ''Summarizing results'' [[File:Publication_strategy_and_Analysis_Strategy_Nov2-2012.pptx]]


<br>6.30PM END OF DAY 5
<br>6.30PM END OF DAY 5

== Hands-on analysis sessions ==

=== Background ===
* Summary of Phase I
* Impact/utilization of ENCODE data

=== Biology of the time-courses ===
* Classify the time-courses to define similarity
** early: from iPS to ...
** late
** immediate early response (IER)
** germ-layer
** other meaningful criteria
* Cell-fate tree
** Based on the phase 1 promoterome clustering?

=== Computational aspects ===
* details of Erik's QC [Erik]
* DPI clustering [Kawaji]
* TSS classifier [Timo]?
* ZENBU [Jessica]
* FANTOM Resource Browser [Shimoji, Kawaji]
* Expression clustering: immediate early response and other patterns [Martin Taylor, Sarah Baker, Owen]
* Differential expression: changes during time-courses [who?]
* Motif Activity Response Analysis (MARA) including miRNAs [Erik vN, Peter]
* TSS usage in the time-course
** TSS Switch [Emmanuel]
** Stimulus specific promoters [Boris, Vanja]
* Regulatory elements
** De-novo motif signatures [Michael Rehli]
** Regulatory composite elements [Seva]
* Repeat elements [who?]
* Enhancers: expression, usage in time-couses, etc. [Robin, Albin, Ilka]
* miRNA and other non-coding RNA [Pål Sætrom]
* other topics???

=== Format of the sessions ===
* Flexible style
* Presentations incl. technical details and demonstration
* Detailed questions and follow-up discussions
* OSC researchers can join (needs to be planned ahead of the meeting!)

=== Technical aspects ===
* Internet access
* Shared data storage
* Projector for presentations
* Rooms for break-out sessions can be prepared

=== What should the participating collaborators bring? ===
* Bring your own laptop

Latest revision as of 11:53, 14 February 2013

Fantom5 timecourses logo.png

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


10.30AM COFFEE BREAK


1.00PM LUNCH + free discussion (note 1)


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

    • 9.20AM 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)


12.45PM LUNCH


4.15PM COFFEE BREAK


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)


10.45AM COFFEE BREAK

Session 2 - Satellite presentation (chair: Alistair Forrest)


12.55PM LUNCH

Session 3 - Satellite presentation (chair: Harukazu Suzuki)


4:10PM COFFEE BREAK

Session 4 - Satellite discussions (chair: Piero Carninci)


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)


10.30AM COFFEE BREAK

Session 2 - Integrated analysis - presentations (chair: Timo Lassmann)


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

  • 4.00PM Discussion about satellite papers/time-courses and consensus about Day 3, Video link


4.30PM COFFEE BREAK


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



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


6.30PM END OF DAY 5

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