Task assignments

Task1: Sample acquisition/provision:
Committed names: Al Forrest, Peter Klinken, Peter Heutink, Claudio Schneider, Kim Summers, Terry Meehan
Output requirements/formats: Sample list - text
Milestones:
      1. List of missing cellular states on wiki – March 10
      2. Potential sources for missing states – March 10
      3. Acceptance of last snapshots for phase 1 – March 31

Task2: Sample Annotation:
Committed names: Terry Meehan, Win Hide, Tom Freeman, Al Forrest + sample providers
Output requirements/formats: Cell ontology mapping, Tissue ontology mapping
  Tom’s suggested Sample Annotation
     1. UniqueID: Riken tracking number
     2. Unique_sample_name: Adult_liver.r1 , Tcell_HPC-induced_10h (preferably short, informed by Cell_Ontology)
     3. Species: Hs., Mm., etc.
     4. Sample_Class: Adult_tissue (AT.), Foetal_tissue (FT.), Primary_cell (PC.), Cell_culture (CC.), Time_course (TC-PC.), (TC-CC) etc.
     5. Developmental stage: Adult, Foetal
     6. Pathology: Normal, disease
     7. Tissue: Liver, brain, heart etc
     8. Cell_Ontology (maybe more than one level, to be used in primary sample ordering): Mesenchymal etc, etc
     9. Cell_type: CO approved name e.g. Monocyte, Smooth_muscle, Intestinal_epithelium etc.
    10. Pertubation: LPS, HPC
    11. Time: 0, 1h, 2h, 3h etc
    12. Replicate: r1, r2, r3
    13. Collection_method: FACS_sorting etc. with short description
    14. Collection_method_reference: Pubmed_ID, web_address, protocol
    15. Source: Roslin_Institute
    16. Primary_contact: Joe_Bloggs
    17. Email: joe.bloggs@roslin.ed.ac.uk
    18. Tel: 0044 131 123 4567
    19. Unique Donor ID

Milestones:
     1. Annotation of Data freeze 1 samples (cell, tissue – minimum to compare replicates)
     2. Cell ontology – completion by March 15?
     3. Tissue ontology – March 15

Task3: Mapping:
Committed names: Timo Lassmann, Geoff Faulkner
Output requirements/formats:
     BAM
     CTSS
Milestones:
     1. Rescuing assessment (March 5)
     2. Decision (March 7)
     3. Genome version agreement – comment on pseudoautosomal regions
     4. Mapping of Data freeze 1 (GENAS??)

Task4: Tag clustering:
Committed names: Piero Carninci, Cesare, Piotr Balwierz, Martin Taylor, Martin Frith, Kawaji-san, Boris Lenhard, Albin Sandelin - clustering. David Hume, Ben Brown, Al Forrest - assessment
Output requirements/formats:
     1. Clusters defined as regions on a genome with strand, start, stop, peak and build(Bed?)
     2. Intersect of the defined regions as an expression matrix/table across all samples (ie. intersect of clusters with expression in all libraries)
     3. Possibly.. intersected CTSS file of same regions to allow study of independent peak regulation
     4. Peak rec
 Tom’s suggestion
     Data Matrix Annotation
     To be provided by Riken as raw counts (.raw) and tags per million (.tpm) but ultimately data may be normalised by other methods (.xxx)
     1. UniqueID: Gene Level (MGD, HGNC ID), Transcript or promoter level (ABC1.1, ABC1.2 etc), ncRNA (Leonard’s ID)
     2. Class: Gene_promoter, ncRNA_promoter, other
     3. Chromosomal_location: e.g. alignment range, promoter peak
     4. Chromosome: Chr1
     5. Associated_seqs: refseq, ensembl_gene/transcript, ncRNA_ref
     6. Other_associations: KEGG, GO etc

Milestones:
    1. Agreement on format (March 5)
    2. Competitive tracks available – March 25
    3. Assessment – April 5
    4. Run over paper 1 data freeze – mid April

Task5: State enriched motif predictions (ab-initio and known):
Committed names:Vlad Bajic, Michiel de Hoon, Boris Lenhard, Kenneth Baiulie, Timo Lassmann, Piotr Balwierz, Yulia Medvedeva
Output requirements/formats:
Milestones:
     1. Ranked list of motifs enriched in each state for release 010
     2. Bed file(or similar) with actual predictions for release 010
     3. As above on FREEZE 1

Task5: Tag Cluster Annotation:
Committed names: Piero Carninci, Laurens Wilming, Timo Lassmann, Richard Baldarelli, Juha Kere, Leonard Lipovich(ncRNA), Boris Lenhard(enhancers), Alison Meynert
Output requirements/formats:
Milestones:
     1. Agreement on annotations to use (now?)
     2. Annotation of release 009 clusters using agreed strategy – available ASAP
     3. Annotation of data freeze 1 (ASAP after the clusters are provided)

Cross species promoter mapping:
Committed names: Martin Taylor, Colin Semple, Vlad Bajic, Peter Heutink, Max, Soichi Ogishima
Output requirements/formats:
species1_tag_cluster_ID
species1_genome_assembly_ID
species1_chrom
species1_refPos
species1_strand
species2_tag_cluster_ID
species2_genome_assembly_ID
species2_chrom
species2_refPos
species2_strand
projection_method (a list of rule sets whose criteria were met*)
projection_distance (a measure of confidence in the projection)
projection_result (e.g. species1_rescue, species2_rescue....)

*e.g. identical projected modal tag position, quantile overlap of
projected tag cluster distributions, cluster coordinate overlap.

Milestones:
1. Prediction/mapping of human promoters using mouse data (April 15)
2. Validation on the matched 10-30 human-mouse pairs (ie predict with mouse and check with actual human data). Assessment of strategy.
3. Prediction of human counterpart promoters for the rare mouse cells that we have collected (eg. intestinal stem cells, inner ear hair cells etc.).

Expression visualization (gene level AND TSScluster level):
Committed names: Tom Freeman,Kenneth Baillie, Carsten Daub, Win Hide, Boris, Albin,
Output requirements/formats: potential figures for displaying relationship of samples based on expression clustering
Milestones:
1. Gene level information humanx3 -> Biolayout webstart
2. Distance matrix, genes and pathways that separate each state - win

Promoter level expression analysis (differentially expressed genes/markers/transcription factors/ncRNAs):
Committed names: Piero, Al, Albin, Vlad, Yulia, Kawaji, Ben, Tom, Haru, Colin,David, Cesare, Kenney and Jess M, Ravasi
Output requirements/formats:
Milestones:
1. Agreement on metric for specificity/enrichment – entropy Ravasi March 5
2. Ranked list of most specific TFs for each state
3. Ranked list of ncRNAs specific for each state
4. Ranked list of all genes specific for each state

Expression data mining:
Committed names: Carlo, Tim
Output requirements/formats:
Milestones:

Motif activity and TF expression integration:
Committed names: Vlad, Michiel, Piotr, Yulia, Matthias, Al
Output requirements/formats:
Milestones:
1. Expanding Motifs
2. Core predicted set
3. Attempt at integrating list of sample enriched TFs and sample enriched motifs.
4. Prioritized orphan associations for validation

Boosting, SVMs

Sanity check:
Committed names: Al Forrest, Piero
Output requirements/formats:
Milestones:
1. Assessment of strategy above
2. OK or repeat from step XYZ

Data dissemination and nomenclature:
Committed names: Win Hide, David Hume, Piero Carninci, Richard, Vlad, Tom, YH, JQ, Laurens, Terry, Kawaji, Timo, Albin
Output requirements/formats:
‘Promoter’ – dissemination
‘expression’ – dissemination
‘cell/sample’ – dissemination?
Milestones:
1. Agreement on strategy
2. Agreement on formats
3. Agreement on third party data repositories
4. Core promoters with accessions and link to our data nomenclature

ChipSeq Validation:
Committed names: RIKEN OSC, Tim, Al, Matthias, WP9
Output requirements/formats:
Milestones:
1. Target selection – considering cell type, predictions, chip grade antibody, impact
2. Assessment of targets
3. Motif finding
4. Public chip-seq data,

Literature validation:
Vlad, David, Yulia, Louise, Thomas, Terry, Matthias
5. mouse KO-JAX
6. Public chip-seq
7. Known edges lit mining vlad

KDCAGE Validation:
Committed names: RIKEN OSC, WP9 (intersection of chip-seq known and )
Output requirements/formats:
Milestones:
1. Target selection – considering cell type, predictions, impact
2. Assessment of targets
3. Motif finding

In-situ validation:
Committed names: Juha? Peter H? Silivia,
Output requirements/formats:
Milestones:
1. Literature
2. Allen brain
3. Eurexpress
4. Emage
5. Human protein atlas
6. Target selection
7. In-situ on a small set of human samples
8. Likely very late in the project

Cross species network conservation:
Committed names: Al Forrest, Martin Taylor, Peter Heutink, Michiel de Hoon, Mamoon, Colin, Vlad, Max, Soichi Ogishima
Output requirements/formats:
Milestones:
1. Gene level ortholog pairs (CDS matching)
2. TSS cluster level ortholog pairs (genome matching)
3. Ortholog expression correlations (use expression data from above group, and ortholog mappings from 1 and 2)
4. State specific motif enrichment (conservation independent)
5. Tf state specific expression
6. siRNA KD of SMC specific TFs in multiple species
7. Potential chip-seq
8. Availability of Macaque samples? Aortic SMC, hepatocytes, Bone marrow MSCs
9. Macrophages across all species? Peripheral blood (PBMCs)