Personal tools

Coexpression cluster:C4702

From FANTOM5_SSTAR

Revision as of 07:54, 26 November 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C4702_bone_corpus_Endothelial_optic_diencephalon_thalamus_Wilms



Phase1 CAGE Peaks

  Short description
Hg19::chr7:86688940..86688951,- p4@KIAA1324L
Hg19::chr7:86688955..86688988,- p1@KIAA1324L
Hg19::chr7:86688990..86689026,- p2@KIAA1324L


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


No GOStat results

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data


Uber Anatomy
Ontology termp-valuen
adult organism3.17e-31114
neural tube5.50e-2756
neural rod5.50e-2756
future spinal cord5.50e-2756
neural keel5.50e-2756
regional part of nervous system3.04e-2553
regional part of brain3.04e-2553
central nervous system6.22e-2381
nervous system3.05e-2289
regional part of forebrain2.90e-2141
forebrain2.90e-2141
anterior neural tube2.90e-2141
future forebrain2.90e-2141
brain5.60e-2168
future brain5.60e-2168
neural plate1.24e-1982
presumptive neural plate1.24e-1982
neurectoderm5.27e-1986
telencephalon4.43e-1834
brain grey matter6.16e-1834
gray matter6.16e-1834
cerebral hemisphere6.56e-1732
regional part of telencephalon7.20e-1732
pre-chordal neural plate1.03e-1361
regional part of cerebral cortex1.89e-1322
ecto-epithelium6.79e-13104
cerebral cortex8.65e-1325
pallium8.65e-1325
neocortex1.99e-1220
structure with developmental contribution from neural crest7.71e-12132
tube5.22e-10192
anatomical conduit8.23e-10240
ectoderm-derived structure1.88e-07171
ectoderm1.88e-07171
presumptive ectoderm1.88e-07171
blood vessel endothelium5.07e-0718
endothelium5.07e-0718
cardiovascular system endothelium5.07e-0718
anatomical cluster5.08e-07373
posterior neural tube5.79e-0715
chordal neural plate5.79e-0715


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


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

TF#promotersEnrichmentp-valueq-value
CCNT2#90536.336201576962630.003930750035764890.0191145692128905
CTCF#1066435.360256373075030.0064925092527670.0281333986328825
CTCFL#140690319.74647435897440.0001298372005551160.00172344527056124
E2F1#186934.907389214879320.008460985347239390.0327753736389724
E2F6#187635.017155731697390.00791769806886330.032430640388031
EBF1#187938.9064668465690.00141523283560980.00919302787151713
EGR1#195834.988179094810140.008056488137383440.0322478753863326
FOXA1#3169311.08141974938550.000734755275698670.00584263029074869
HMGN3#932438.178547723350590.001827766942164210.0109211140038153
IRF1#365937.63716375356390.002244692747297240.0128738860974726
RAD21#5885310.35503389545630.0009004912073565420.00668655536474297
SIN3A#2594235.408884726815140.006318961977991520.0278282129462136
SMC3#9126315.04493284493280.0002935825420371870.00310810614372243
TAF7#6879311.43306940492390.0006690181981945830.00545743900658002
TCF12#6938310.63446490218640.0008313523990202070.006320105779682
ZBTB7A#5134137.35190930787590.002516255860282270.0140916534823325



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.