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Coexpression cluster:C4449

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Full id: C4449_brain_temporal_occipital_cerebellum_duodenum_Neurons_parietal



Phase1 CAGE Peaks

  Short description
Hg19::chr5:111092930..111092941,- p7@C5orf13
Hg19::chr5:111093123..111093136,- p6@C5orf13
Hg19::chr5:111093169..111093178,- p8@C5orf13


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


Cell Type
Ontology termp-valuen
non-terminally differentiated cell2.14e-08180
Uber Anatomy
Ontology termp-valuen
regional part of nervous system1.83e-2594
nervous system1.83e-2594
central nervous system7.21e-2582
brain1.55e-2069
future brain1.55e-2069
neural tube1.21e-1757
neural rod1.21e-1757
future spinal cord1.21e-1757
neural keel1.21e-1757
regional part of brain1.79e-1759
ectoderm1.06e-16173
presumptive ectoderm1.06e-16173
ectoderm-derived structure2.02e-16169
neurectoderm5.51e-1690
neural plate7.46e-1686
presumptive neural plate7.46e-1686
cerebral hemisphere9.29e-1432
regional part of forebrain9.65e-1441
forebrain9.65e-1441
future forebrain9.65e-1441
cerebral cortex1.10e-1325
pallium1.10e-1325
telencephalon1.69e-1334
regional part of cerebral cortex4.81e-1322
head4.83e-13123
regional part of telencephalon6.70e-1333
gray matter6.75e-1334
brain grey matter6.75e-1334
anterior neural tube9.10e-1342
anterior region of body1.01e-12129
craniocervical region1.01e-12129
neocortex2.41e-1220
pre-chordal neural plate1.16e-1161
tube1.35e-11194
organism subdivision1.47e-10365
multi-cellular organism1.61e-10659
cell layer3.38e-10312
epithelium4.74e-10309
anatomical conduit1.11e-07241
anatomical cluster1.51e-07286
embryo7.48e-07612


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
CEBPB#105137.971147625824820.001974187055288560.0115618304192946
CTBP2#1488362.71700033932814.049570681927e-060.000130213396690201
CTCF#1066435.360256373075030.0064925092527670.0280798067686655
CTCFL#140690319.74647435897440.0001298372005551160.00172191331920963
E2F1#186934.907389214879320.008460985347239390.0327013858589421
EP300#203336.77394172622320.003216880500103790.0168118385983957
GTF2F1#2962312.73966087675770.0004835525047438590.00435359827956413
JUND#372736.994663941871030.002921845042734990.0157401647711456
MAFF#23764356.31535648994525.59409009993116e-060.00016919813957333
MAFK#7975327.10073313782995.02195559325033e-050.000858830882926922
RAD21#5885310.35503389545630.0009004912073565420.0066713769741867
SMC3#9126315.04493284493280.0002935825420371870.00310338735909127
STAT1#6772320.70658749719920.0001125992441046670.00155244256832308
STAT3#6774310.51946499715420.0008589184530415310.00644753714635265
YY1#752834.911170749853860.008441455341808260.033073872840753
ZNF263#1012738.221841637010680.001799043925565870.0109870971605271
ZZZ3#260093239.4132124352337.25894005043406e-084.38217595333689e-06



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.