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Coexpression cluster:C3484

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Full id: C3484_CD4_cerebellum_CD8_pineal_thalamus_substantia_optic



Phase1 CAGE Peaks

Hg19::chr15:40987282..40987311,-p1@LOC100505648
Hg19::chr21:34144448..34144480,+p1@C21orf49
Hg19::chr7:149535455..149535555,+p1@ZNF862


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>


Uber Anatomy
Ontology termp-valuen
adult organism6.61e-37115
neural tube1.06e-2357
neural rod1.06e-2357
future spinal cord1.06e-2357
neural keel1.06e-2357
regional part of brain1.40e-2059
brain5.11e-2069
future brain5.11e-2069
central nervous system3.44e-1982
regional part of nervous system8.75e-1994
nervous system8.75e-1994
regional part of forebrain1.59e-1841
forebrain1.59e-1841
future forebrain1.59e-1841
anterior neural tube5.64e-1842
neurectoderm8.32e-1790
neural plate5.02e-1686
presumptive neural plate5.02e-1686
telencephalon7.48e-1534
gray matter8.01e-1534
brain grey matter8.01e-1534
regional part of telencephalon2.01e-1433
cerebral hemisphere1.35e-1332
anterior region of body2.71e-13129
craniocervical region2.71e-13129
pre-chordal neural plate2.20e-1261
head1.87e-11123
regional part of cerebral cortex1.04e-1022
cerebral cortex2.08e-1025
pallium2.08e-1025
neocortex3.88e-1020
ectoderm7.06e-10173
presumptive ectoderm7.06e-10173
ectoderm-derived structure2.98e-09169
posterior neural tube6.11e-0715
chordal neural plate6.11e-0715


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
BRCA1#672213.45615376214920.007119807716084560.0296178442627322
CHD2#1106310.34402283411690.0009033701102746880.00659539118818442
E2F1#186934.907389214879320.008460985347239390.0324492086031263
E2F4#1874312.66806031528440.0004917987006298980.00436351750021969
E2F6#187635.017155731697390.00791769806886330.0321369736354597
ELF1#199734.258097958807540.01295179875054610.0461175176335032
ETS1#211339.728760922202340.001085840092584840.00760947818757752
IRF1#365937.63716375356390.002244692747297240.012784025838967
MXI1#460139.96157162875930.001011470541259020.00719303907521115
MYC#460935.22228187160940.007020843755740150.0293911295897766
NRF1#4899312.21027944771090.0005492172401020010.00470392810718492
POLR3A#111281113.0440366972480.00882009881003120.0334980290054493
SIN3A#2594235.408884726815140.006318961977991520.0276001033005502
SP1#666735.69838137814090.005403962701712170.0245994185853688
TFAP2A#7020211.01242291536330.01054990655215560.0390039183829722
USF1#739136.361499277207960.00388404057290560.0189944424702045
XRCC4#751811432.767441860460.0006977913838891460.00561237076180196
ZZZ3#26009179.80440414507770.0124784379082580.0451571578898321



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.