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Coexpression cluster:C779

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Full id: C779_testis_medial_occipital_brain_temporal_postcentral_insula



Phase1 CAGE Peaks

Hg19::chr10:134145640..134145724,+p1@LRRC27
Hg19::chr11:72504681..72504716,-p6@STARD10
Hg19::chr11:73882263..73882276,+p5@PPME1
Hg19::chr11:73882283..73882309,+p3@PPME1
Hg19::chr12:121341939..121341985,-p3@SPPL3
Hg19::chr12:50101500..50101550,+p23@TMBIM6
Hg19::chr13:37006398..37006417,+p5@CCNA1
Hg19::chr14:105767100..105767153,+p3@PACS2
Hg19::chr15:33486929..33486977,-p5@FMN1
Hg19::chr9:34665983..34666063,-p1@ENST00000416454
p1@ENST00000421828
p1@ENST00000544078
p1@ENST00000556719


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:0051722protein C-terminal methylesterase activity0.00735856827869091
GO:0051723protein methylesterase activity0.00735856827869091
GO:0006482protein amino acid demethylation0.00735856827869091
GO:0008214protein amino acid dealkylation0.00735856827869091
GO:0007141male meiosis I0.00882976206266084
GO:0051721protein phosphatase 2A binding0.00981026913500083
GO:0007140male meiosis0.0147128048027599
GO:0019903protein phosphatase binding0.0312463083769772
GO:0019902phosphatase binding0.0359328864606653
GO:0004864protein phosphatase inhibitor activity0.0428416640546203
GO:0019212phosphatase inhibitor activity0.0428416640546203
GO:0008601protein phosphatase type 2A regulator activity0.0428416640546203



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
non-terminally differentiated cell3.30e-08180
neurectodermal cell4.25e-0859
migratory neural crest cell9.89e-0741
Uber Anatomy
Ontology termp-valuen
regional part of nervous system2.82e-3794
nervous system2.82e-3794
central nervous system2.61e-3482
neural tube3.22e-3257
neural rod3.22e-3257
future spinal cord3.22e-3257
neural keel3.22e-3257
neurectoderm4.31e-3190
brain2.50e-2969
future brain2.50e-2969
neural plate2.62e-2986
presumptive neural plate2.62e-2986
regional part of brain1.44e-2859
ectoderm9.90e-28173
presumptive ectoderm9.90e-28173
ectoderm-derived structure4.30e-26169
adult organism2.60e-25115
regional part of forebrain1.27e-2441
forebrain1.27e-2441
future forebrain1.27e-2441
anterior neural tube8.90e-2442
telencephalon1.09e-2034
gray matter1.35e-2034
brain grey matter1.35e-2034
organism subdivision2.09e-20365
pre-chordal neural plate2.64e-2061
regional part of telencephalon4.91e-2033
head1.28e-19123
cerebral hemisphere1.41e-1932
anterior region of body4.12e-19129
craniocervical region4.12e-19129
cerebral cortex2.02e-1525
pallium2.02e-1525
regional part of cerebral cortex1.75e-1422
tube2.82e-14194
multi-cellular organism4.41e-14659
multi-tissue structure7.42e-14347
epithelium1.27e-13309
neocortex2.76e-1320
cell layer2.83e-13312
anatomical conduit1.25e-12241
anatomical cluster2.51e-12286
organ part3.82e-11219
embryo6.88e-11612
anatomical system1.27e-09625
anatomical group1.68e-09626
posterior neural tube1.69e-0915
chordal neural plate1.69e-0915
embryonic structure1.85e-09605
developing anatomical structure1.85e-09605
germ layer3.01e-09604
embryonic tissue3.01e-09604
presumptive structure3.01e-09604
epiblast (generic)3.01e-09604
organ7.30e-09511
segmental subdivision of nervous system2.34e-0813
segmental subdivision of hindbrain6.59e-0812
hindbrain6.59e-0812
presumptive hindbrain6.59e-0812
basal ganglion9.85e-079
nuclear complex of neuraxis9.85e-079
aggregate regional part of brain9.85e-079
collection of basal ganglia9.85e-079
cerebral subcortex9.85e-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#46748.98526981040350.0006636746018777640.00542613995189539
BRCA1#67236.055269192967130.01121625560138660.0411860811037627
CHD2#110666.206413700470110.0001213341309247110.001643794953904
CTCFL#14069035.923942307692310.01190857855768930.0433336830070909
E2F1#186973.435172450415530.0009731854789143080.00699604338052942
E2F4#187456.334030157642220.0005501567218568720.00469848866415978
E2F6#187694.515440158527654.07099158370721e-060.000129546096895429
EGR1#195862.992907456886080.006446587185075730.0280087827199486
ELF1#199772.980668571165280.002378202870469130.0134709366302704
GATA3#262538.17095490716180.004888573999674950.0228754773937924
IRF1#365975.346014627494735.49768438584683e-050.000930587778887289
MAX#414963.871533305404270.001649602786473820.0103163392464994
MXI1#460143.984628651503720.01296562982531040.0460114649448043
MYC#460973.655597310126580.000654500840128410.00535994771757006
NANOG#7992338.77343354430380.004002360774245590.0191876317145483
NRF1#489956.105139723855450.0006527262974630640.00534583451856532
PAX5#507964.00173931870670.001379489661762990.00898599892626862
PRDM1#639226.36619115549220.002484962521039670.0139553154129624
RAD21#588544.142013558182530.01132276475674040.0415275399785508
RDBP#7936230.7276807980050.001839920449249570.0108878379397799
RFX5#599356.023955413597550.0006945114068748440.00559676518692916
SIN3A#2594263.245330836089080.004223840630485730.0201008699356283
SMC3#912646.017973137973140.002957963916685310.0157688118776324
SP1#666773.988866964698630.0003734365591501510.00371123235332407
STAT1#677236.211976249159760.01045841177951960.0387465792068552
TAF1#687272.34013240002170.01040839844348330.0386298054384843
THAP1#5514539.41074338085540.003283183553142890.0170009622245372
USF1#739163.816899566324770.001780928663791640.010926942117127
USF2#739245.196878954027840.005046003840154460.023504731950488
YY1#752862.946702449912310.006987247873951880.0295358068849986



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.