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Coexpression cluster:C3962

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Full id: C3962_occipital_brain_duodenum_merkel_Neurons_retinoblastoma_parietal



Phase1 CAGE Peaks

  Short description
Hg19::chr1:26232902..26232918,- p1@STMN1
Hg19::chr1:26232930..26232945,- p1@MIR3917
Hg19::chr1:26232951..26232959,- p2@STMN1


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


GO IDGO nameFDR corrected p-value
GO:0007052mitotic spindle organization and biogenesis0.0115094783939715
GO:0007051spindle organization and biogenesis0.0115094783939715
GO:0007019microtubule depolymerization0.0115094783939715
GO:0031109microtubule polymerization or depolymerization0.0120098904980572
GO:0051261protein depolymerization0.0138113740727658
GO:0015631tubulin binding0.0167638054868715
GO:0000226microtubule cytoskeleton organization and biogenesis0.0218751576928899
GO:0005874microtubule0.0489403037795832
GO:0007017microtubule-based process0.0489403037795832
GO:0000278mitotic cell cycle0.0489403037795832



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
disease_data


Cell Type
Ontology termp-valuen
neural cell2.23e-0825
neurectodermal cell2.19e-0759
Uber Anatomy
Ontology termp-valuen
regional part of nervous system1.88e-1394
nervous system1.88e-1394
central nervous system3.62e-1282
ectoderm1.27e-10173
presumptive ectoderm1.27e-10173
ectoderm-derived structure1.07e-09169
pre-chordal neural plate1.87e-0961
brain3.37e-0969
future brain3.37e-0969
neurectoderm4.83e-0990
cerebral hemisphere6.93e-0932
cerebral cortex9.23e-0925
pallium9.23e-0925
telencephalon1.49e-0834
anterior region of body3.56e-08129
craniocervical region3.56e-08129
regional part of forebrain3.91e-0841
forebrain3.91e-0841
future forebrain3.91e-0841
regional part of telencephalon3.96e-0833
neural plate4.89e-0886
presumptive neural plate4.89e-0886
gray matter5.45e-0834
brain grey matter5.45e-0834
neocortex7.46e-0820
head8.31e-08123
anterior neural tube1.50e-0742
regional part of cerebral cortex1.81e-0722
neural tube6.21e-0757
neural rod6.21e-0757
future spinal cord6.21e-0757
neural keel6.21e-0757
Disease
Ontology termp-valuen
cancer1.34e-21235
disease of cellular proliferation4.33e-21239
hematologic cancer5.75e-2051
immune system cancer5.75e-2051
leukemia2.87e-1839
organ system cancer5.06e-17137
myeloid leukemia4.70e-1431


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
ATF3#467322.46317452600878.81932387510763e-050.00129674977642174
BHLHE40#8553344.87181354697741.10603738662898e-050.000284726247528085
CCNT2#90536.336201576962630.003930750035764890.0190206923497776
CHD2#1106310.34402283411690.0009033701102746880.00660786321242318
E2F1#186934.907389214879320.008460985347239390.0325640053316751
E2F4#1874312.66806031528440.0004917987006298980.00437541225786574
E2F6#187635.017155731697390.00791769806886330.0322548062805326
EGR1#195834.988179094810140.008056488137383440.0320916726259655
ELF1#199734.258097958807540.01295179875054610.0462705380621291
ETS1#211339.728760922202340.001085840092584840.00762944385289745
FOS#235338.99795530889440.001372499272417130.00898135661102585
GTF2F1#2962312.73966087675770.0004835525047438590.00434348843579117
HMGN3#932438.178547723350590.001827766942164210.0108794113571577
IRF1#365937.63716375356390.002244692747297240.0128182768787236
JUND#372736.994663941871030.002921845042734990.0156899878872024
MAX#414936.452555509007120.003721913834265510.0186719645949109
MYC#460935.22228187160940.007020843755740150.0294773829550049
NFE2#4778377.2042606516292.17039522930409e-067.83254690232516e-05
NFKB1#479035.488063424193840.006049381815655430.0269800310648349
NFYA#4800318.42558069983050.0001598135507814160.0019981763953143
NFYB#4801316.75979325353650.0002123649923296180.00246025373642962
PAX5#507936.669565531177830.003370290999677260.0173053009692868
POU2F2#545239.106124057742520.001324165192682130.00882937422961942
RDBP#79363153.6384039900252.75057764221434e-071.39925756636738e-05
REST#597839.650028716128020.001112636247114590.00768230973240782
SIN3A#2594235.408884726815140.006318961977991520.0277067076711641
SIRT6#515483153.6384039900252.75057764221434e-071.3999394657662e-05
SIX5#147912317.0867153554590.0002004060546325010.00239887770083252
SMARCB1#6598318.25271578115740.000164397760679890.00203261959602782
SP1#666735.69838137814090.005403962701712170.0246757808938491
TAF7#6879311.43306940492390.0006690181981945830.0054353630183776
TAL1#6886329.86861667744023.75103522793067e-050.000720269108604249
TCF12#6938310.63446490218640.0008313523990202070.00629718691625119
TCF7L2#6934310.77017656313730.0008003181298398380.00614230049693878
USF1#739136.361499277207960.00388404057290560.0190443809105018
USF2#7392312.99219738506960.0004558979393427810.00421881312130256
YY1#752834.911170749853860.008441455341808260.032972442009242
ZBTB7A#5134137.35190930787590.002516255860282270.0140337095905169
ZNF143#7702313.50087655222790.0004062804962997170.00389351520949221



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.