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Coexpression cluster:C2448: Difference between revisions

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|tf_chipseq_enrich=GATA2#2624;3:9.5586988001655:0.00181815161835744:0.0108979532179541
|tf_chipseq_enrich=GATA2#2624;3:9.5586988001655:0.00181815161835744:0.0108979532179541
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}}
}}

Revision as of 15:30, 26 November 2012


Full id: C2448_lung_heart_adipose_uterus_spleen_penis_diaphragm



Phase1 CAGE Peaks

Hg19::chr17:8213590..8213603,+p4@ARHGEF15
Hg19::chr19:34756467..34756506,+p2@KIAA0355
Hg19::chr9:130524452..130524471,-p12@SH2D3C
Hg19::chr9:130524481..130524502,-p7@SH2D3C


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

GO IDGO nameFDR corrected p-value
GO:0005085guanyl-nucleotide exchange factor activity0.00288634203040242
GO:0030695GTPase regulator activity0.00741965680807329
GO:0007264small GTPase mediated signal transduction0.00771334966124877
GO:0005070SH3/SH2 adaptor activity0.0174971520527603
GO:0007242intracellular signaling cascade0.0174971520527603
GO:0060090molecular adaptor activity0.0174971520527603
GO:0007254JNK cascade0.0174971520527603
GO:0031098stress-activated protein kinase signaling pathway0.0174971520527603
GO:0030674protein binding, bridging0.0208065528489527
GO:0000165MAPKKK cascade0.0260896311395252
GO:0005089Rho guanyl-nucleotide exchange factor activity0.0260896311395252
GO:0035023regulation of Rho protein signal transduction0.0260896311395252
GO:0005088Ras guanyl-nucleotide exchange factor activity0.0260896311395252
GO:0007266Rho protein signal transduction0.0275936887220312
GO:0005096GTPase activator activity0.042169007212996
GO:0046578regulation of Ras protein signal transduction0.042169007212996
GO:0007243protein kinase cascade0.042169007212996
GO:0007165signal transduction0.042169007212996
GO:0007265Ras protein signal transduction0.042169007212996
GO:0008047enzyme activator activity0.042169007212996
GO:0007154cell communication0.042169007212996
GO:0005083small GTPase regulator activity0.042169007212996
GO:0051056regulation of small GTPase mediated signal transduction0.042169007212996



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>

Uber Anatomy
Ontology termp-valuen
adult organism1.71e-83114
anatomical conduit2.99e-26240
anatomical cluster1.11e-25373
neural tube1.25e-2556
neural rod1.25e-2556
future spinal cord1.25e-2556
neural keel1.25e-2556
regional part of nervous system1.64e-2353
regional part of brain1.64e-2353
blood vessel endothelium1.01e-2218
endothelium1.01e-2218
cardiovascular system endothelium1.01e-2218
tube1.71e-22192
regional part of forebrain6.57e-2041
forebrain6.57e-2041
anterior neural tube6.57e-2041
future forebrain6.57e-2041
neural plate1.51e-1982
presumptive neural plate1.51e-1982
central nervous system2.45e-1881
neurectoderm5.38e-1886
simple squamous epithelium1.89e-1722
brain2.15e-1768
future brain2.15e-1768
brain grey matter1.98e-1634
gray matter1.98e-1634
telencephalon2.11e-1634
nervous system3.96e-1689
structure with developmental contribution from neural crest3.93e-15132
cerebral hemisphere5.23e-1532
regional part of telencephalon6.97e-1532
squamous epithelium1.26e-1425
ecto-epithelium2.11e-13104
organ system subdivision3.99e-13223
pre-chordal neural plate1.44e-1261
endothelial tube1.78e-129
arterial system endothelium1.78e-129
endothelium of artery1.78e-129
epithelium3.30e-12306
multi-cellular organism7.00e-12656
cell layer7.42e-12309
regional part of cerebral cortex8.12e-1222
vessel1.52e-1168
neocortex2.67e-1020
anatomical system4.86e-10624
multi-tissue structure5.08e-10342
anatomical group5.80e-10625
cerebral cortex6.73e-1025
pallium6.73e-1025
embryo4.21e-09592
splanchnic layer of lateral plate mesoderm6.41e-0983
vasculature6.88e-0978
vascular system6.88e-0978
neural nucleus1.02e-089
nucleus of brain1.02e-089
epithelial tube open at both ends1.09e-0859
blood vessel1.09e-0859
blood vasculature1.09e-0859
vascular cord1.09e-0859
basal ganglion1.34e-089
nuclear complex of neuraxis1.34e-089
aggregate regional part of brain1.34e-089
collection of basal ganglia1.34e-089
cerebral subcortex1.34e-089
developing anatomical structure3.19e-08581
embryonic structure3.50e-08564
organ part4.27e-08218
germ layer4.35e-08560
germ layer / neural crest4.35e-08560
embryonic tissue4.35e-08560
presumptive structure4.35e-08560
germ layer / neural crest derived structure4.35e-08560
epiblast (generic)4.35e-08560
ectoderm-derived structure4.37e-08171
ectoderm4.37e-08171
presumptive ectoderm4.37e-08171
circulatory system1.04e-07112
vein2.16e-079
venous blood vessel2.16e-079
venous system2.16e-079
compound organ3.13e-0768
telencephalic nucleus4.63e-077
posterior neural tube6.00e-0715
chordal neural plate6.00e-0715
brainstem7.20e-076
lymphoid system7.61e-0710


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
GATA2#262439.55869880016550.001818151618357440.0108979532179541



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.

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