Time-courses meeting October 2012

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)
• 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) File:02 Adipogenesis time course, RIKEN fall meeting 2012.pdf
• 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

10.45AM 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
• 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
• 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

12.55PM 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
• 2.30PM Time course analysis of erythroid differentiation: transcriptional regulation of erythropoiesis - (Louise Winteringham) File:02 Winteringham fantom5 Oct 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
• 3.10PM ARPE-19 retinal pigment epithelial cell line, epithelial to mesenchyme transition - (Soichi Ogishima) File:Ogishima FANTOM5 meeting slide.pdf
• 3.30PM Gene regulatory networks in T cell lineage specification - (Tomokatsu Ikawa) File:05 121031 IKAWA FANTOM5 meeting.ppt
• 3.50PM Immediate-early genes as regulators in cancer and vascular disease - (Levon Khachigian) File:Levon FANTOM5-1.pdf

4:10PM COFFEE BREAK

Session 4 - Satellite discussions (chair: Piero Carninci)

• 4.40PM Future FANTOM - (Yoshihide Hayashizaki)(CHANGED)
• 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
• 9.30AM De novo motif analyses for time course data sets - (Michael Rehli) File:02 FANTOM2 MR.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
• 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

10.30AM COFFEE BREAK

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

• 11.10AM Gene expression and promoter usage during neuronal differentiation - (Boris Lenhard)
• 11.30AM Promoter switching in the FANTOM time-courses - (Emmanuel Dimont) File:02 Day4 RIKEN - Promoter Switching - Emmanuel Dimont.ppt
• 11.50AM Definition and analysis of gene sets from time series data - (Finn Drablos and Morten Rye) File:Finn Drablos FANTOM 2012.pdf
• 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
• 12.30PM Time profiles clustering with multivariate statistics - (Kim-Anh Le Cao) File:05 F5 LeCao.pdf

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

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 File:Publication strategy-Fantom5-oct31-2012.pptx(Piero's notes)

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)

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