First FANTOM5 meeting in February

The first FANTOM5 meeting (the Ume Blossom meeting) was held February 20-25th. 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 submitted abstracts File:FANTOM5 Ume Blossom Meeting Book.pdf, a list of the participants File:Updated participants list 110222.xls, and photos taken during the meeting https://fantom5-collaboration.gsc.riken.jp/webdav/home/_f5_photos/2011_Feb/.

Day 1 Sunday February 20th

Session 1

• 10 years of FANTOM, where we’ ve been and where we are going - (Yoshihide Hayashizaki) Media:110220_Hayashizaki_FANTOM5_Opening_Remarks_ver5_.ppt
• Overview of FANTOM5, phase1 and 2, sample collection strategy and production status - (Alistair Forrest) Media:Introduction_to_FANTOM5_1520_1550_SUNDAY_Forrest.ppt‎
• HeliscopeCAGE - (Masayoshi Itoh) Media:Masaca.pdf
• Mapping Helicos Reads - (Timo Lassmann) Media:MappingHelicosReads.pdf
• NanoCAGE and CAGE-scan - (Charles Plessy)Media:nanoCAGE.pdf

• Comparison of transcriptome profiling platform - (Hideya Kawaji)Media:110220-F5ume-platform-comparison-Kawaji.pdf
• F5 CAGE promoter annotation : strategy and application of CAGEscan - (Nicolas Bertin) Media:UmeMeetingNicolas.pdf‎
• ZENBU - a system for secured scientific collaborations, data integration and omics visualization - (Jessica Severin) Media:Jessica_zenbu_fantom5_meeting_feb20_2011_v2.ppt‎
• Fantom5 web resource - (Marina Lizio / Hideya Kawaji) Media:110220-The_FANTOM5_Web_Resource_M_Lizio_HK.pdf‎

Session 2

• Main Paper: The promoterome - introduction - (Piero Carninci) Media:Piero-Fantom-5_Promoters.pdf
• Main Paper: Conservation of a transcriptional network between tissues, individuals, and 5 species - (Alistair Forrest) Media:Paper4_overview_6PM_SUNDAY.ppt
• Main Paper: Specific and general transcriptome hallmarks of cell - (Carsten Daub) Media:Main_Paper_2.pdf
• Main Paper: noncoding RNA - (Piero Carninci) Media:Piero-Fantom-5-paper-3-ncRNAs.pdf‎
• Main Paper: cell conversion - (Harukazu Suzuki) Media:FANTOM5_Cell_conversion3.pdf‎
• Data Freeze, publication schedule, authorship, call to collaborate - (Alistair Forrest) Media:Closing_7PM_SUNDAY.ppt

Video files: https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/video/day1-intro-FANTOM5/

Day 2 Monday February 21st

Session 1: TSS clustering, characterization and usage (Chair: Piero Carninci)

• OSC CAGE Promoter clustering - (Michiel De Hoon) Media:Ume_promoters.pdf
• Clustering CAGE tags by density - (Martin Frith) Media:Paraclu.ppt
• Classification of CAGE signal - (Timo Lassmann) Media:CAGE_classification.pdf
• Distinguishing promoters from noise - (Ulf Shaefer) Media:Ulf_Schaefer_distingishing_promoters_from_noise.pdf
• A Novel Approach to Detect Transcription Start Site Dynamics in Pluripotent Lineages - (Emmanuel Dimont) Media:21_Feb_2010_0955am_FANTOM5_presentation_-_TSS_Bias_and_Switching_-_Emmanuel_Dimont.pdf‎
• Decomposition of FANTOM5 HeliScopeCAGE expression - (Hideya Kawaji) Media:110221-F5ume-expression-decomposition-Kawaji.pdf
• Characterization of tissue specific promoters across human tissues and cell types on different biological levels - (Albin Sandelin) Media:Fantom5_meeting_v2_sandelin.pdf‎
• Promoter activity profiles reveal novel insights into gene regulation - (Colin Semple) Media:fantom5_talk_feb2011.pdf

Session 2: Beyond the proximal promoter (chair: Atsutaka Kubosaki)

• Probing the spatial genomic basis of cellular identity with 5C, ChIA-PET and Hi-C - (Josee Dostie) Media:FANTOM5_talk_feb_20_dostie.pdf‎
• CAGE, promoter-enhancer interactions and developmental gene regulation - (Boris Lenhard) Media:Lenhard_FANTOM5_Meeting.pdf

Session 3: Gene Families and novel loci (chair: Alka Saxena)

• Role of the fibrillin gene superfamily in development and differentiation of connective tissues - (Kim Summers) Media:Fantom5_final_Summers.pdf‎
• Ectopic expression of Olfactory Receptors surveyed in Fantom5 libraries - (Giovanni Pascarella) Media:FANTOM5_Pascarella.pdf‎
• Investigating Rett Syndrome in the FANTOM5 project - (Alka Saxena) Media:Investigating_Rett_Syndrome.ppt‎
• Regions of high transcriptional activity - (Sebastian Schmeier) Media:Schmeier_20110221.pdf‎

Session 4: Repetitive elements and other signals (chair: Charles Plessy)

• Impact of exon/intron painting on digital gene expression level - (Anton Kratz) Media:F5_slides_Monday_AK.ppt‎
• Capping along long and short annotated transcripts - (Sarah Djebali) Media:CAGE_in_Gencode_long_small_exons_feb21st2011_Riken.pdf‎
• Repetitive elements transcription and mobilization contribute to human skeletal muscle differentiation and Duchenne muscular dystrophy progression - (Beatrice Bodega) Media:Fantom5-Bodega.pdf‎
• Long non-coding antisense RNA controls UCHL1 protein synthesis through the 5’ overlapping region and an embedded SINEB2 repeat - (Stefano Gustincich) Media:Stefano_FANTOM_february_2011.pdf‎

Session 5: Non human models (chair: Al Forrest)

• Expression/network conservation across 5 species - (Alistair Forrest) Media:AL_250PM_MONDAY.ppt
• The evolution of transcriptional regulation - (Martin Taylor) Media:MartinTaylor20110220.pdf‎
• Eliminating common to focus on specifics - (Vladmir Bajic) Media:Vlad_Bajic_Eliminating_common_to_focus_on_specifics_Feb19_2011.pdf
• Transcriptional Regulation in Macrophages - (David Hume) Media:HUME_RIKEN_Talk_Final.ppt‎

Video files: https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/video/day2-oral_presentations/

Day 3 Tuesday February 22nd

Session 1: Network analysis, vizualisation and lineage classification (chair: Carsten Daub)

• BioLayout Express3D: A Powerful Resource for Analysis and Integration of Fantom5 Data - (Tom Freeman)
• Elucidating Core Modules Underlying the Steady State Cellular Transcriptional Landscape - (Jessica Mar)
• A machine learning pipeline for identification of core promoters predictive of embryonic layers in FANTOM5 - (Cesare Furlanello) Media:FBK-MLpipeline-Riken_UmeBlossom_v.1.6.pdf
• Nonlinear dimension reduction and clustering by Minimum Curvilinearity for the exploration of the CAGE/Helicos expression data - (Timothy Ravasi)
• Motif activity calculations in FANTOM 5 - (Michiel de Hoon)
• Follow ups on the FANTOM4 TSS clustering scheme and transcriptional network reconstruction: Human and mouse promoteromes and Motif Activity Response Analysis - (Piotr Balwierz) Media:PiotrBalwierz-promoteromeMara.pdf‎
• Cell specific transcription regulation - (Vlad Bajic)

• Pathway fingerprintingtechnologies - (Gabriel Altshuler) Media:G_Altschuler_FANTOM5_presentation.pdf‎
• Inference of Gene Regulatory Networks from deep-CAGE data based on Stepwise-Addition Bayesian Network Method - (Hideo Matsuda)
• Condition-specific activated network discovery / Global gene network comparison between different species - (Jun Sese) Media:Sese_20110222fantom.pdf
• Systems biology of the human lncRNAome: computational-experimental integration assigns long non-coding RNA molecules to specific regulatory networks - (Leonard Lipovich) Media:Fantom5-LL.ppt

Session 2: Stem cells, disease and regeneration (chair: Yuki Hasegawa)

• Common regulatory events marked by specific TSS in normal and aberrant development - (Winston Hide) Media:Hide_RIKEN.TSS.SWITCH.pdf‎
• Polycomb complexes co-associate with non-productive RNA polymerase II genome-wide, and repress both silent developmental and active metabolic genes in ES cells - (Ana Pombo) Media:Pombo_2011-02Fantom5-forPDF.pdf
• Functional and molecular profile of stromal precursor cells in high-grade serous ovarian cancer - (Claudio Schneider)
• Engineering an Artificial Salivary Gland - (Swati Prahdhan)
• Whole tissue samples for FANTOM5 - (Juha Kere) Media:Kere-fantom.ppt‎
• Cell conversion - (Jay Shin) Media:SHIN_JAY_FANTOM5_UME_meeting_110222.pdf‎

Session 3: Timecourse analysis (chair: Harukazu Suzuki )

• Signaling and transcription network of the growth hormone-induced differentiation of MCF-7 breast cancer cells - (Mariko Okada)
• In vitro models of erythropoiesis - (Louise Winteringham)
• Time-course change of mouse hematopoietic stem cells - (Daisuke Sugiyama)
• In vitro model of T-cell differentiation - (Tomokatsu Ikawa)
• Towards A Network Based Inference of Genes Required for Cell Reprogramming - (Owen Rackhama) Media:Owenrackham_presentation_plum.pdf‎

Video files: https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/video/day3-oral_presentations/2_22%20mov%23E0B7/

Day 4 Wednesday February 23rd

Video files: https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/video/day4-presentations_discussions/

Working Groups

• Working Group 1 - Tag clustering
• Working Group 2 - Expression visualization and clustering
• Working Group 3 - Motifs and conservation
• Working Group 4 - Sample annotation+ additional samples
• Working Group 5 - Validation and extra datasets
• Working Group 6 - Public data dissemination strategies
• Working Group 7 - Network Basins
• Working Group 8 - Non-coding RNAs + cluster annotation

Day 5 Thursday February 24th

Working Groups

• Working Group 1: Long range regulation, methylation, promoter shape, TFs regulating epigenetic marks, other signals in CAGE
• Working Group 2: Blood
• Working Group 3: Comprehensive regulatory networks, pathogen-host interactions
• Working Group 4: Brain, conservation, evolution
• Working Group 5: Alternative promoters and olfactory receptors
• Working Group 6: Cell specific regulation; Human specific promoters and networks
• Working Group 7: Stem Cells and Satellite Paper proposal

Day 6 Friday February 25th

• Media:Fantom-5_Promoters-Day6.pdf‎ (Piero Carninci)

Video files conclusion: https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/video/day6-morning_meeting/

At the end of the meeting we made a call for Satellite paper proposals. The video of this session and a current listing of proposed satellite is provided below.

Video files Satellites: https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/video/day6-satellites_conclusions/

• Satellite Papers proposals

https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/Satellite_papers