Time-courses meeting October 2012: Difference between revisions

From Wiki
Jump to navigationJump to search
Line 81: Line 81:
*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]]
*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)
*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]]
*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]]


Revision as of 09:32, 31 October 2012

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)

  • 11.15AM Interindividual variation and stimulus specificity in the inflammatory response - (Kenneth Baillie)
  • 11.35AM Identification of functional non-coding RNAs during bi-directional differentiation from mouse mesenchymal stem cells to adipocytes/osteoblasts - (Yutaka Nakachi)
  • 11.55AM The transcriptome of macrophage activation & mycobacterium infection - (Frank Brombacher) File:Brombacher 11h55 Wed 31.pdf
  • 12.15PM Human lymphatic endothelial cells response to vascular endothelial growth factor-C - (Michael Detmar) File:Detmar FANTOM5 Oct31.pdf
  • 12.35PM Global transcriptome derivation of human skeletal muscle cell differentiation and Duchenne muscular dystrophy progression - (Valerio Orlando)


12.55PM LUNCH

Session 3 - Satellite presentation (chair: Harukazu Suzuki)

  • 2.10PM Time course analysis of erythroid differentiation: transcriptional regulation of erythropoiesis - (Louise Winteringham)
  • 2.30PM Elucidating gene regulatory networks underlying early brain development in Down syndrome with iPSC - (Ernst Wolvetang)
  • 2.50PM ARPE-19 retinal pigment epithelial cell line, epithelial to mesenchyme transition - (Soichi Ogishima)
  • 3.10PM Gene regulatory networks in T cell lineage specification - (Tomokatsu Ikawa)
  • 3.30PM Immediate-early genes as regulators in cancer and vascular disease - (Levon Khachigian)


3:50PM COFFEE BREAK

Session 4 - Satellite discussions (chair: Piero Carninci)

  • 4.20PM Future FANTOM - (Yoshihide Hayashizaki)(CHANGED)
  • 4.50PM 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)
  • 9.30AM De novo motif analyses for time course data sets - (Michael Rehli)
  • 9.50AM CAGE-defined enhancer-TSS dynamics within time courses - a new resource within FANTOM5 - (Albin Sandelin and Robin Andersson)
  • 10.10AM Finding key TFs with regulatory roles linked to gene expression changes in time-course data - (Wyeth Wasserman and Anthony Mathelier)


10.30AM COFFEE BREAK

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

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


12.40PM 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


3.00PM COFFEE BREAK

  • 3.30PM OSC Award
  • 4.00PM Discussion about satellite papers/time-courses and consensus about Day 3


4.30PM COFFEE BREAK

  • 5.00PM Plan for integrated paper/satellite papers


6.30PM END OF MAIN MEETING DAY 2 --> BEER PARTY


8.00PM BEER PARTY END

Day 5 Friday November 2nd - Education and discussion session

Registration open from 8.30AM


Workshop - Implementation of the discussion of Day 3-4


  • 9.00AM Working on the satellite papers and main paper


10.30AM COFFEE BREAK

  • 10.45AM Working on the satellite papers and main paper


12.15PM LUNCH

  • 1.30PM Working on the satellite papers and main paper


3.30PM COFFEE BREAK

  • 3.45PM Working on the satellite papers and main paper


5.15PM COFFEE BREAK

  • 5.30PM Summarizing results


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
Retrieved from "http://fantom5-collaboration.gsc.riken.jp/wiki/index.php?title=Time-courses_meeting_October_2012&oldid=5701"