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Coexpression cluster:C2448

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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 organism8.41e-68115
neural tube3.53e-2757
neural rod3.53e-2757
future spinal cord3.53e-2757
neural keel3.53e-2757
anatomical conduit1.87e-25241
neurectoderm2.24e-2490
neural plate9.80e-2486
presumptive neural plate9.80e-2486
tube2.27e-23194
anatomical cluster2.20e-22286
anterior neural tube4.16e-2242
regional part of brain8.03e-2259
regional part of forebrain3.88e-2141
forebrain3.88e-2141
future forebrain3.88e-2141
central nervous system2.24e-2082
brain1.12e-1869
future brain1.12e-1869
regional part of nervous system1.35e-1894
nervous system1.35e-1894
endothelium8.42e-1818
blood vessel endothelium8.42e-1818
cardiovascular system endothelium8.42e-1818
gray matter1.98e-1734
brain grey matter1.98e-1734
telencephalon3.22e-1734
regional part of telencephalon1.17e-1633
pre-chordal neural plate1.87e-1661
cerebral hemisphere3.38e-1632
epithelium7.60e-15309
anterior region of body9.16e-15129
craniocervical region9.16e-15129
regional part of cerebral cortex1.36e-1422
simple squamous epithelium1.55e-1422
cell layer2.26e-14312
neocortex2.12e-1320
multi-cellular organism3.03e-13659
head6.38e-13123
ectoderm7.11e-13173
presumptive ectoderm7.11e-13173
ectoderm-derived structure2.98e-12169
cerebral cortex4.57e-1225
pallium4.57e-1225
squamous epithelium6.09e-1225
anatomical system1.09e-10625
anatomical group1.38e-10626
embryo3.98e-10612
endothelial tube4.16e-109
arterial system endothelium4.16e-109
endothelium of artery4.16e-109
organ part8.92e-10219
vessel2.96e-0869
embryonic structure4.02e-08605
developing anatomical structure4.02e-08605
multi-tissue structure6.98e-08347
germ layer8.49e-08604
embryonic tissue8.49e-08604
presumptive structure8.49e-08604
epiblast (generic)8.49e-08604
male reproductive organ2.56e-0711
brainstem4.45e-078
splanchnic layer of lateral plate mesoderm4.80e-0784
organ4.88e-07511
nucleus of brain5.66e-079
neural nucleus5.66e-079
basal ganglion7.24e-079
nuclear complex of neuraxis7.24e-079
aggregate regional part of brain7.24e-079
collection of basal ganglia7.24e-079
cerebral subcortex7.24e-079
vasculature7.36e-0779
vascular system7.36e-0779
compound organ8.75e-0769


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.