October meeting
The second FANTOM5 meeting (the Kōyō meeting) will be held October 17-20th. Copies of the presentation files and videos are provided below. Also included is the breakdown of working groups for each of the tasks and satellite areas.
Meeting Book
Here is a copy of the Koyo meeting book including abstracts for oral presentations, a list of poster titles and contact list of participants File:KoyoMeetingBookletALL.pdf and photos taken during the meeting https://fantom5-collaboration.gsc.riken.jp/webdav/home/_f5_photos/2011_Oct/.
Video Streaming
All sessions of the FANTOM5 Koyo Meeting is going to be streamed over the internet. This way you can see the sessions live if you do not have the opportunity to be at the meeting.
The url for the streaming is:
http://www.ustream.tv/channel/shika-koyo
The password is: momiji
Please be aware of the confidentiality of this meeting when you watch the streaming.
Day 1 Monday October 17th - Insights from Phase 1
Registration open from 8.30AM
Session 1: Promoterome (Chair: Piero Carninci)
- 9.15AM Welcome - (Yoshihide Hayashizaki)
- 9.25AM Data Production update - (Jun Kawai)
- 9.35AM Introduction and goals of the meeting - (Al Forrest) Media:Al_Forrest1.pdf
October_tasks_and_questions
- 10.00AM Building promoter(TSS)ome - (Kawaji Hideya) Media:111017-kawaji-Promotome.pdf
- 10.15AM Extracting "articulated transcription starting sites (ATSS)" with Factor Analysis on CAGE tag data. - (Kei Iida) Media:FANTOM5_BASE_Iida_ver20111015.pdf
- 10.35AM Genome-wide hCAGE-tag clusters annotation based on the best CpG islands model - (Yulia Medvedeva) Media:File5.pdf
10.50AM COFFEE BREAK
Session 2: Cluster annotation (chair: Kawaji Hideya)
- 11.20AM Using epigenetic marks to improve detection of tissue specific hCAGE-tag clusters - (Mamoon Rashid) Media:Mamoon_Rashid.pdf
- 11.30AM Pathway activity map for promotors and cells defines cellular lineage and timecourse functional relationships - (Winston Hide) Media:2_Hide_RIKEN.F5.Oct.2011.pdf
- 11.50AM SwitchEngine: A Novel Approach to Detect Transcription Start Site Switching in Developmental Lineages and Time Series Experiments - (Emmanuel Dimont) Media:Emmanuel_Dimont.ppt
- 12.10PM Computational analysis of regulatory regions using CAGE tags and histone modification data - (Finn Drabløs) Media:Finn_Drablos.pdf
- 12.20PM Nanopublications for FANTOM5 - (Erik Schultes) Media:Schultes.pdf
12.30PM LUNCH
Session 3: Motifs (chair: Timo Lassmann)
- 1.30PM Analysis of occurrence of transcription factor binding sites and homotypic clusters of TFBS in the vicinity of CAGE tag clusters. - (Vsevolod J. Makeev) Media:Makeev_FANTOM5_2011.ppt
- 1.55PM An atlas of de novo derived sequence motifs associated with gene promoters - (Michael Rehli) Media:FANTOM5_Rehli.pdf
- 2.15PM Genome hCAGE-tag cluster annotation using optimized models of TFBSs - (Vladimir B Bajic) Media:RIKEN_OCT2011_BAJIC.pdf
- 2.30PM Influence of DNA methylation on transcription factor binding sites and transcription regulation - (Yulia Medvedeva) Media:File13.pdf
- 2.45PM Motifs disussion - (Discussion leader: Carsten Daub) Media:Carsten_Daub_TFBSdiscussion.pdf
3.10PM COFFEE BREAK
Session 4: Biological insights (chair: Winston Hide)
- 3.40PM Leveraging the promoterome: new methods to detect genomic loci associated with disease - (Kenneth Baillie) Media:F5_JKB_GWAS6_online_small.pdf
- 4.00PM Infection of monocytes with a panel of pathogens and inflammatory ligands - (Christine Wells) Media:2_Wells_FANTOM_monocyte_2011.pdf
- 4.20PM CAGE on a mouse model of Rett - (Alka Saxena) Media:3_F5_Koyo_meeting_alka_1.pdf
- 4.35PM Extensive Regional Differences in Gene Expression and Promoter Usage in Aged Human Brain - (Margherita Francescatto) Media:Margherita_Francescatto.pdf
- 4.55PM Comparison of human preimplantation transcriptomes with FANTOM5 data - (Juha Kere) Media:5_Kere-FANTOM5-Oct.ppt
5.15PM SHORT BREAK
Session5: The promoterome paper
- 5.25PM Paper1 - where we are at - (Discussion leader: Piero Carninci) Media:File20.pdf
Video files: https://fantom5-collaboration.gsc.riken.jp/webdav/home/video/koyo/day1-oral_presentations/
7.00PM Welcome Dinner at RIKEN
9.00PM Go to hotel
Day 2 Tuesday October 18th - Timecourses
Session 1: Timecourses 1 (chair: Carsten Daub)
- 9.00AM FANTOM5 Timecourses - (Carsten Daub) Media:Time_courses_overview.pptx
- Please also see the Timecourses page.
- And the time-course and network analysis plan discussed on the last day. Media:Time-courses_analysis_plan.docx
- 9.25AM Quantitative transcriptional response underlies differentiation of MCF-7 breast cancer cells. - (Mariko Okada-Hatakeyama) Media:2_FANTOM5_Koyo_Oct18-MOkada.pdf
- 9.40AM Trophoblast differentiation - (Haruhiko Koseki) Media:File23.pdf
- 10.00AM Transcriptional analysis of red blood cell production - (Louise Winteringham) Media:File24.pdf
- 10.15AM Identification of VEGF-C-induced transcription factors in lymphangiogenesis - (Sarah Krampitz) Media:SarahKrampitz_20111018_VEGFCLymphatic.pdf
10.30AM COFFEE BREAK
Session 2: Timecourses 2 (chair: Tom Freeman)
- 11.00AM Early and late changes in gene expression during mineralisation of SAOS-2, a human osteosarcoma cell line model for bone formation. - (Kim M Summers) Media:Summers.pptx
- 11.25AM Expression analysis during macrophage activation and Mycobacterium tuberculosis infection - (Frank Brombacher) Media:MphTB_Brombacher.ppt
- 11.50AM Identification of transcriptional regulators for inner ear hair cell differentiation - (Judith S. Kempfle) Media:Kempfle_FANTOM5-Koyo_meeting_JSK_final.pptx
- 12.15PM Systematic search for natural antisense transcripts that are functioning during adipocyte or osteoblast differentiation in mice - (Yutaka Nakachi) Media:FANTOM5 presentation nakachi.pdf
12.35PM LUNCH
Session 3: Timecourses 3 (chair: Peter Heutink)
- Cerebellar development timecourse - (Thomas Ha) Media:File30.pdf
- Studies of adipogenesis - (Niklas Mejhert/Erik Arner) Media:Arner_f5_adipogenesis_111018.pptx
- Polycomb complexes co-associate with non-productive RNA polymerase II in ES cells, and repress both silent developmental and active metabolic genes. - (Inês de Santiago) Media:2011Oct-Fantom5-InesSantiago.pptx
- Promoter (re)interpretation in developmental time courses and terminal differentiation - (Vanja Haberle) Media:File33.pdf
3.05PM COFFEE BREAK
Session 4: Timecourse analysis gōkon (合コン)
- 3.35PM Timecourse analysis - Analyst and experimentalist pairing - (Discussion leader: Carsten Daub)
- Please see the Analyst_experimentalist_pairing page.
Video files: https://fantom5-collaboration.gsc.riken.jp/webdav/home/video/koyo/day2-oral_presentations/
5.05PM Poster Session
7.50PM Go to Tsurumi for dinner
Day 3 Wednesday October 19th - Networks
Session 1: Cellular networks 1 (chair: Al Forrest)
- 9.00AM Towards cell specific networks - (Al Forrest) Media:Al_forrest2.ppt
- 9.15AM Mogrify: Prediction of reprogramming factors for cell conversion - (Owen Rackham) Media:Talk_owenrackham.pdf
- 9.35AM Transcription factor usage in primary cell samples: differential expression and motif finding - (Sebastian Schmeier/Morana Vitezic) Media:Schmeier_Vitezic_Koyo_meeting.pdf
- 10.00AM Investigating TSS Plasticity in Donors and Consequences for Gene Regulatory Networks - (Jessica Mar) Media:4_F5_Oct_Jess.pptx
10.20AM COFFEE BREAK
Session 2: Cellular networks 2 (chair: Tim Ravasi)
- 10.50AM Discovering common patterns in the FANTOM5 primary cell line panel - (Carlo Vittorio Cannistraci) Media:1-carlo_vittorio_cannistraci_-_19oct2011.pptx
- 11.15AM Analysis of gene regulatory networks in the hematopoietic system - (Christian Schmidl) Media:2_Schmidl_Christian_FANTOM5.pptx
- 11.35AM Identifying Promoter-Based Network Modules Distinctive of Cell Stemness - (Cesare Furlanello) Media:Furlanello-Network-KoyoMeeting_v.2.1.pdf
- 11.50AM Quantifying regulatory complexity in gene expression - (Sarah Baker) Media:4_sbakerF5Kouyou.pdf
- 12.15PM A systems-biology approach for finding TSS-specific transcriptional regulation in the same gene - (Yishai Shimoni) Media:Yishai_shimoni.ppt
- 12.30PM Identifying cell specific genes - (Timo Lassmann) Media:koyotimolassmann.pdf
12.45PM LUNCH
Session 3: Technology (chair: Harukazu Suzuki)
- 1.45PM Validation technologies available at OSC - (Harukazu Suzuki) Media:FANTOM5_Koyo_ver4.pdf
- 2.00PM 3D genome organization in differentiating leukemia cells - (James Fraser) Media:J_Fraser_Riken_Talk.pdf
Session 4:
- 2.25PM Networks discussion - (Discussion Leader: Al Forrest) Media:File47.pdf
3.25PM COFFEE BREAK
Video files: https://fantom5-collaboration.gsc.riken.jp/webdav/home/video/koyo/day3-oral_presentations/
Working/discussion Groups
- Group 1: Promoterome Freeze
Minutes from the discussion (by Christine Wells): File:Minutes promoteome.docx
- Group 2: Motifs
Minutes from the discussion (by Carsten Daub): Media:Discussion_minutes_motifs_2011-10-19.pdf
Audio file: [[1]]
- Group 3: Comparison of Genlists/Key factors
Audio files from group discussions: https://fantom5-collaboration.gsc.riken.jp/webdav/home/Audio
Day 4 Thursday October 20th - Non-coding RNAs
Session 1: Non-coding RNAs 1 (chair: Leonard Lipovich)
- 9.00AM Non-coding RNAs in FANTOM5 - (Al Forrest) Media:Al_forrest3a.ppt
- 9.05AM F5 lncRNAome integration with hCAGE clusters: inferring function and networks from our unified nonredundant human lncRNA resource. - (Leonard Lipovich) Media:F5_Lipovich_KoyoMtg20oct2011.ppt
- 9.30AM Differences in transcription regulation program of non-coding and coding transcripts - (Boris Jankovic) Media:3_RIKEN_OCTOBER_2011_Differences_in_coding_non-coding_regulaiton_B_Jankovic.pdf
- 9.45AM CAGE tags associated with non-coding loci: lncRNAs and pseudogenes - (Laurens Wilming) Media:Laurens_Wilming_Fantom_5_Koyo.pdf
- 10.00AM Retrotransposon capture sequencing reveals somatic variation in the human brain - (Geoff Faulkner) Media:Faulkner_20min.ppt
- 10.15AM Tracing muscle-specific L1 retrotransposition activity during a deep time course of healthy and DMD myoblast cell differentiation. - (Geoff Faulkner - sub for Valerio Orlando) (see above)
10.20AM COFFEE BREAK
Session 2: Non-coding RNAs 2 (chair: Christine Wells)
- 10.50AM F5 hCAGE co-expressed sense-antisense mRNA-lncRNA pairs contain key transcriptional regulators: implications for cis- and trans-regulatory networks - (Emily J. Wood) Media:WoodTalk.pdf
- 11.15AM MicroRNA promoters1: Regression approaches to associate microRNA expression with CAGE expression - (Eivind Valen) Media:Eivind_FANTOM5_Koyo.ppt
- 11.25AM MicroRNA promoters2: KD approaches to identify putative microRNA promoters - (Kawaji Hideya) Media:111020-kawaji-miRNApromoter.pdf
- 11.40AM Cell-type specificity of transcribed enhancers and association with regulated promoters - (Robin Andersson) Media:Andersson_FANTOM5_Koyo.ppt
- 12.00PM Mass spectrometric analysis demonstrates that few human lncRNAs are translated - (Hui Jia) Media:5_F5-ENCODE_HJ.ppt
- 12.25PM RNA Editing in CAP-associated transcriptional regions - (Georges St Laurent) Media:File59.pdf
12.45PM LUNCH
Session 3
- 1.45PM Non-coding RNAs in FANTOM5 - (Discussion Leader: Piero Carninci) Media:File60.pdf
Working Groups
- The time-course and network analysis plan (Carsten Daub). Media:Time-courses_analysis_plan.docx
- Working Group 2: ..
- Working Group 3: ..
- Working Group 4: ..
- Working Group 5: ..
- Working Group 6: ..
- Working Group 7: ..
3.30PM COFFEE BREAK
Session 4
- 5.30PM Conclusion/consolidation
7.00PM FAREWELL DINNER
9.00PM Go to hotel
Video files conclusion: https://fantom5-collaboration.gsc.riken.jp/webdav/home/video/day4-morning_meeting/
Satellites
Satellite paper proposals made during the meeting will be compiled. The video of the Ume meeting session and a current listing of proposed satellite is provided below.
Video files Satellites: https://fantom5-collaboration.gsc.riken.jp/webdav/home/video/day4-satellites_conclusions/
- Satellite Papers proposals
https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/Satellite_papers
