Berlin Proteomics Forum 2013 CHPP

07:30-09:00 Principal Investigator Council (PIC) Meeting

Chair: Young-Ki Paik & William S. Hancock

  • Matters related to the Leadership & Membership of the Consortium
  • Team organization (policy on the replacement of the consortium members)
  • Annual Report and Evaluation System
  • Designation of Global Resources Centers
  • Data sharing between teams (format, credits, deposit),
  • Channeling with ENCODE: guidelines, cell lines, and other resources,
  • RNAseq services through the major providers (e.g., BGI etc.)
  • C-HPP scientific workshop plans during the Yokohama HUPO meeting (9/14-18)
  • New directions for the Genome-wide multidisciplinary platform for the C-HPP
  • Coordination with B/D-HPP teams to make synergistic outputs and more.
  • JPR Special Issue in Jan 2014 (Deadline: August 1, 2013)

9:30-11:00 Plenary Session I (10 minutes each)

Chair: William S. Hancock

  • Mike Snyder (Stanford Univ., Stanford, CA, USA): Transcriptome and Proteome: RNA-seq and proteomic evidence for ENCODE project (non-coding RNA and ASVs-amino acid polymorphisms)
  • Ian Wilson (Imperial College of London, London, UK): Large Scale Metabolic Phenotyping in a Systems Medicine World
  • Emma Lundberg (KTH Royal Institute of Technology, Stockholm, Sweden): Update on the Human Protein Atlas
  • Ruedi Aebersold (Institute of Molecular Systems Biology, ETH Zurich, Switzerland): Networking Proteomics

Plenary Session II (10 minutes each)

Chair: György Marko-Varga

  • Juan Antonio Vizcaino (EBI, Honxton, UK) ProteomeXchange: globally co-ordinated proteomics data submission and dissemination
  • Siqi Liu (Beijing, China): BGI and support of C-HPP transcriptomic works
  • William S. Hancock (Boston, USA): An approach to define the missing parts list for a chromosome and PTM characterization in an alternative spliced variant (sEGFR)

11:00-11:20 Discussion

11:35-12:30 Part 1: Working Group Session 1: C-HPP Bioinformatics

Chair: William S. Hancock

  • C-HPP Web Browsers Update.
  • Peter Horvatovich: C-HPP Wiki. Presentation can be download here.
  • Ping Xu: Caper, Chr 1,
  • Ed Nice (on behalf of Rob Goode): The Proteome Browser, TPB, Chr 7 Seul-Ki Jeong: GenomewidePDB, Chr 13
  • Andrey Lisitsa: Chromosome-Centric KB

13:30-15:00 Part 2: General Data Management

  • Implementation of the standard metrics for the HPP and C-HPP
  • Integrated DB for all teams; Data submission;
  • Informatics tools and resources for the C-HPP
  • Integration of PeptideAtlas and GPM protein identifications
  • Uploading individual lab data sets and compare with what is known
  • Integration of RNAseq data
  • Collaboration between ENCODE and C-HPP: How ENCODE datasets can be integrated into our C-HPP work to produce more insightful meaning of biological readouts?
  • SRM peptides

15:50-16:30 Working Group Session 2: Brief Progress Updates (7 min each)

Chair: Young-Ki Paik

  • Chr 5: Rainer Bischoff (The Netherlands)
  • Chr 6: Leonard Foster (on behalf of Paul Keown) (Canada)
  • Chr 9: Je-Yoel Cho (Korea)
  • Chr14: Jerome Garin (France)
  • Chr15: Gilberto B Domont (Brazil)
  • Chr18: Alexander Archakov (Russia)
  • Chr 19: Transcriptomic study. Carol Nilson (USA)
  • Mitochondria: Andrea Urbani (Italy)

16:30-17:20 Working Group Session 3: Resources & Bio-banks (10 minutes each)

Chair: György Marko-Varga

  • Bio-banks and its utilization, Cell Lines: Gyorgy Marko-Varga
  • Rare tissues (nasal epithelia): William S. Hancock
  • Antibody: Ed Nice, Emma Lundburg and Tadashi Yamamoto (Antibody Ranker)

17:20-17:30 Wrapping Up and Announcement

Young-Ki Paik, William S. Hancock and György Marko-Varga

Other presentations

  • Power Point presentation of William Hancock can be download here.