Personal tools

Coexpression cluster:C1916

From FANTOM5_SSTAR

Revision as of 11:50, 19 October 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C1916_Fibroblast_amniotic_Adipocyte_Smooth_immature_CD14_normal



Phase1 CAGE Peaks

Hg19::chr3:105085383..105085403,+p7@ALCAM
Hg19::chr3:105085428..105085442,+p6@ALCAM
Hg19::chr3:105085548..105085584,+p2@ALCAM
Hg19::chr3:105085587..105085610,+p3@ALCAM
Hg19::chr3:105085734..105085760,+p1@ALCAM


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data


No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>


Cell Type
Ontology termp-valuen
fibroblast1.29e-0976
Uber Anatomy
Ontology termp-valuen
multi-cellular organism3.68e-11656
embryonic structure2.08e-10564
anatomical system2.16e-10624
developing anatomical structure2.68e-10581
anatomical group4.08e-10625
germ layer4.17e-10560
germ layer / neural crest4.17e-10560
embryonic tissue4.17e-10560
presumptive structure4.17e-10560
germ layer / neural crest derived structure4.17e-10560
epiblast (generic)4.17e-10560
embryo2.08e-08592
musculoskeletal system2.12e-08167
neural tube2.47e-0856
neural rod2.47e-0856
future spinal cord2.47e-0856
neural keel2.47e-0856
neural plate2.57e-0882
presumptive neural plate2.57e-0882
structure with developmental contribution from neural crest4.44e-08132
organ1.29e-07503
regional part of nervous system1.30e-0753
regional part of brain1.30e-0753
ectoderm-derived structure1.33e-07171
ectoderm1.33e-07171
presumptive ectoderm1.33e-07171
neurectoderm1.47e-0786
brain2.36e-0768
future brain2.36e-0768
skeletal system5.80e-07100
pre-chordal neural plate6.59e-0761
regional part of forebrain8.10e-0741
forebrain8.10e-0741
anterior neural tube8.10e-0741
future forebrain8.10e-0741


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CTCF#1066455.360256373075030.0002259278299937090.00250060159354736
E2F1#186954.907389214879320.0003512818099256460.00353308175527971
E2F4#1874512.66806031528443.06319883889696e-060.00010356666349484
E2F6#187655.017155731697390.0003144978599297790.00323095042231027
ELF1#199754.258097958807540.0007142416939776840.00573584684946831
FOS#235358.99795530889441.69470025615156e-050.000389594541167098
GATA2#2624512.7449317335542.9719152914525e-060.000101234136048274
JUND#372745.595731153496820.001849593301755460.0109376408381201
MAX#414956.452555509007128.93743970843928e-050.00130749021671059
MYC#460955.22228187160940.0002573944848850610.00276706357250755
NFKB1#479055.488063424193840.0002008162847462320.00239254528434995
NR3C1#2908411.97841866493849.4122920812787e-050.00136643087667037
PAX5#507945.335652424942260.002223389586187790.0127811858758183
RAD21#5885510.35503389545638.39503550283973e-060.000229701103715242
SMC3#9126515.04493284493281.29633924985553e-065.16355358183302e-05
SP1#666755.69838137814090.000166391843712550.00204444679594059
TAF1#687253.343046285745290.002394600090870310.0135483850095024
TCF12#693836.380678941311850.007185168653258840.0298350758976503
USF1#739156.361499277207969.59569864925045e-050.00137020121852484
YY1#752854.911170749853860.00034993140821360.00352901567617035
ZNF143#7702410.80070124178230.0001415223430863190.00184455909017747



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data


This analysis result is provided for C0 - C305 clusters.