User:Kawaji/120209 resource browser memo

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To-do

  1. [general] reasonable scheme to refresh properties
  2. [general] add search box to search "genes, samples, or motifs" from their names (=> Al's point 3 at 2nd March); in progress
  3. [general] make search "case-insensitive".
  4. [general] keyword search box should find synonyms too.
  5. [Expression graph] add "short description" in the graph visible (ex. EntrezGene: 2597)
  6. [TF expression enrichment] CAGE peak ID => short description
  7. [Sample page] add link to its parent ontology
  8. [TF list] add "transcription factor" property to gene based on https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/File:FANTOM5_Transcriptional_regulator_list_March2012AL.xls . So that we can make a query to list all transcription factors
  9. Browse_gene page should have a search box for genes only. (and other pages too)
  10. [GOstat] Motif => GO enrichment (from Erik)
  11. [FF enrichment] https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/120322-FFontology/v6_ontology_term_enrichment/


To-do (in future)

  • [general] import the other "facet" from FONSE - not yet. FONSE is not updated.
  • re order samples in a meaningful manner
  • group replicates and generate average with SD
  • consider Anthony's request - see [fantom5:01500]

Wishlist for javascript

  • network with cytoscepeWeb / canvasxpress
  • dynamic filtering of sample names
  • heatmap with canvasexpress
  • sortable barchart



Access point

[done]


FF ontologies

[done]

  • Load FF ids by using template

[to be done]

  • Load other ontologies (such as UBERON) by using template
  • Update FF ontology when Chris updated

Swissregulon motifs

[done] 

 {TopMotifsInMaraPhase1
|top_motifs=ALX1.p1;2.17630682572,ALX4.p1;1.87630682572,
}
  • motif activities
    • assign activities to each Swissregulon motif
    • activities are comma separated
 {MotifActivitiesInMaraPhase1
|motif_activities= 0.139020440771,-0.287767627519
}
  • add sequence logo for swissregulon motif

EntrezGene

[done]

page name

  • EntrezGene:${NUMBER}

Individual column's property (from README file)

  • tax_id:
  • GeneID:
  • Symbol:
  • LocusTag:
  • Synonyms:
  • dbXrefs:
  • chromosome:
  • map location:
  • description:
  • type of gene:
  • Symbol from nomenclature authority:
  • Full name from nomenclature authority:
  • Nomenclature status:
  • Other designations:
  • Modification date:

Transcription factors

[to be done]

CAGE peaks

[done]

data

page name

  • FFCP_PHASE1_hg19::chr1:123..456,+
  • FFCP_PHASE1_mm9::chr1:123..456,+

feature

  • id (ex. FFCP_PHASE1_hg19::chr1:123..456,+ )
  • short_description
  • description
  • association_with_transcript
  • EntrezGene
  • HGNC (only for human)
  • UniProt
  • phase1_expression (comma separated, in the same order to column)


ab-initio motifs


Individual pages

Motif Activity Page

[to be done]

  • link to the swissregulon motifs
  • link to heat map
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