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Coexpression cluster:C1600

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Full id: C1600_blood_Whole_optic_spinal_locus_globus_thalamus



Phase1 CAGE Peaks

Hg19::chr10:92922581..92922624,+p5@PCGF5
Hg19::chr10:92922625..92922667,+p6@PCGF5
Hg19::chr12:861717..861770,+p1@WNK1
Hg19::chr5:61602025..61602053,+p2@KIF2A
Hg19::chr5:61602055..61602083,+p3@KIF2A


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:0005813centrosome0.00275378218751093
GO:0005815microtubule organizing center0.00275378218751093
GO:0015630microtubule cytoskeleton0.0226534454319709



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>


Cell Type
Ontology termp-valuen
lymphoid lineage restricted progenitor cell2.03e-0952
lymphocyte4.39e-0953
common lymphoid progenitor4.39e-0953
Uber Anatomy
Ontology termp-valuen
adult organism1.44e-50115
neural tube5.36e-2657
neural rod5.36e-2657
future spinal cord5.36e-2657
neural keel5.36e-2657
anterior neural tube3.60e-2242
regional part of forebrain1.07e-2141
forebrain1.07e-2141
future forebrain1.07e-2141
central nervous system9.47e-2182
regional part of brain3.98e-2059
regional part of nervous system1.02e-1994
nervous system1.02e-1994
brain1.68e-1969
future brain1.68e-1969
gray matter3.90e-1834
brain grey matter3.90e-1834
telencephalon6.18e-1834
regional part of telencephalon1.83e-1733
cerebral hemisphere1.01e-1632
neural plate1.48e-1486
presumptive neural plate1.48e-1486
regional part of cerebral cortex5.27e-1422
neurectoderm2.19e-1390
cerebral cortex7.00e-1325
pallium7.00e-1325
neocortex8.82e-1320
anterior region of body1.02e-11129
craniocervical region1.02e-11129
pre-chordal neural plate2.35e-1161
head3.36e-10123
ectoderm-derived structure1.17e-08169
blood2.90e-0815
haemolymphatic fluid2.90e-0815
organism substance2.90e-0815
ectoderm3.73e-08173
presumptive ectoderm3.73e-08173
nucleus of brain8.43e-079
neural nucleus8.43e-079


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
ATF3#467313.47790471560530.0008241088551409360.00627234402580267
BCLAF1#9774312.99158856607310.0009178032402542550.00667510115660962
CHD2#110636.206413700470110.007774550126275590.0319445369674284
E2F1#186954.907389214879320.0003512818099256460.00352121325912511
EGR1#195854.988179094810140.0003237398000590710.00330315171730845
ETS1#211335.83725655332140.009253279045631430.0349639366948879
HDAC8#558692310.6336134453781.6469764092501e-050.000380129434708667
NANOG#79923317.54686708860760.0003794200090681830.00375960591338443
NRF1#489937.326167668626540.004839689817117540.0226843355538075
POU2F2#545235.463674434645510.01115650094469780.040998374460355
SETDB1#9869216.12801047120420.00585057846659340.0262672411861641
SIN3A#2594255.408884726815140.0002159522671657270.00247762702741089
STAT2#6773226.10550847457630.002275903944310060.0129209138964883
TFAP2C#702248.647382887888180.0003390518878174050.00344792990377429



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.