Data source

Data sources used in the database(s)

old info on the top page

• CAGE peaks (only the robust set), their association with genes, and their expression based on RLE TPM.
  • [1]
  • [2]
• Swissregulon motifs, and Motif Activity Response Analysis (MARA)
  • [3]
  • [4]
• FF Ontology
  • [5]
• facet classification based on FF ontology
  • [6] FONSE (Fantomy ONtology Sample Explorer)

FANTOM5 Resource Browser

CAGE peaks

• CAGE peak location (with the robust threshold) , annotation, and expression
  • [7]
  • [8]
• Ontology-based sample term enrichment analysis
  • [9]

Co expression cluster

• CP member list
  • [10]
• Sample ontology enrichment analysis
  • [11]
• GOstat analysis
  • [12]
• KEGG enrichment
  • [13]

Gene

• EntrezGene
  • [14]
  • [15]
• Transcription factors
  • [16]
  • [17]
  • [18]
  • [19]

Motifs

• SwissRegulon (known)
  • https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/Motif/Swissregulon

Sample information

• sample name and attributes
  • [20]
• GOstat analysis based on ranked expression for human libraries in phase 1 freeze samples
  • [21]
• TF expression and enrichment table on FF sample page
  • [22]
  • [23]
  • [24]
  • [25]

Ontology

• Sample ontology(FF), Cell ontology(CL), Human disease ontology(DOID) and Uber anatomy ontology (UBERON)
  • [26]
• Ontology mapping: FF sample <--> CL, DOID, UBERON, FF term
  • [27]

Network

• MARA netwrok
  • [28]

FANTOM5 BioMart

CAGE peak annotation

• CAGE peak location (with the permissive threshold) and its association with genes
  • hg19: [29]
  • mm9: [30]

• CAGE peak location (with the robust threshold) and its association with genes
  • hg19: [31]
  • mm9: [32]

• CAGE peak descriptions
  • hg19: [33]
  • mm9: [34]

• CpG island and TATA-box annotation
  • hg19: [35]
  • mm9: [36]

• Machine learning classification as TSS-like or not (KAUST)
  • hg19: [37]
  • mm9: [38]

• T. Lassmann tss-like classifier (score):
  • hg19: [39]
  • mm9: [40]

CAGE peak expression (for the ones with the robust threshold)

• Counts
  • hg19: [41]
  • mm9: [42]

• TPM (RLE normalization-based)
  • hg19: [43]
  • mm9: [44]

• Relative expression
  • hg19: [45]
  • mm9: [46]