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Coexpression cluster:C3547

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Full id: C3547_granulocyte_acute_Eosinophils_salivary_hepatoblastoma_cerebellum_tridermal



Phase1 CAGE Peaks

  Short description
Hg19::chr16:2802623..2802721,+ p1@SRRM2
Hg19::chr19:5622779..5622813,- p1@SAFB2
Hg19::chr19:5623083..5623158,+ p1@SAFB


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:0003723RNA binding0.00137547276961258



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
hematopoietic stem cell8.18e-33168
angioblastic mesenchymal cell8.18e-33168
hematopoietic cell5.89e-31177
hematopoietic oligopotent progenitor cell7.21e-31161
hematopoietic multipotent progenitor cell7.21e-31161
leukocyte1.15e-24136
myeloid cell3.62e-23108
common myeloid progenitor3.62e-23108
hematopoietic lineage restricted progenitor cell6.94e-19120
nongranular leukocyte1.99e-17115
classical monocyte2.51e-1542
CD14-positive, CD16-negative classical monocyte2.51e-1542
myeloid leukocyte1.47e-1472
granulocyte monocyte progenitor cell3.90e-1267
myeloid lineage restricted progenitor cell1.74e-1166
defensive cell4.43e-1148
phagocyte4.43e-1148
macrophage dendritic cell progenitor3.68e-1061
monopoietic cell1.40e-0959
monocyte1.40e-0959
monoblast1.40e-0959
promonocyte1.40e-0959
nucleate cell6.26e-0855
lymphocyte1.70e-0753
common lymphoid progenitor1.70e-0753
lymphoid lineage restricted progenitor cell1.96e-0752
Uber Anatomy
Ontology termp-valuen
adult organism2.97e-22114
neural tube1.73e-1456
neural rod1.73e-1456
future spinal cord1.73e-1456
neural keel1.73e-1456
regional part of nervous system8.53e-1453
regional part of brain8.53e-1453
hematopoietic system4.43e-1398
blood island4.43e-1398
nervous system6.58e-1289
regional part of forebrain1.47e-1141
forebrain1.47e-1141
anterior neural tube1.47e-1141
future forebrain1.47e-1141
central nervous system2.00e-1181
brain4.20e-1168
future brain4.20e-1168
hemolymphoid system6.01e-11108
neurectoderm1.31e-1086
neural plate4.73e-1082
presumptive neural plate4.73e-1082
bone element1.31e-0982
brain grey matter1.32e-0934
gray matter1.32e-0934
telencephalon1.38e-0934
bone marrow1.47e-0976
regional part of telencephalon5.11e-0932
cerebral hemisphere1.15e-0832
immune system1.21e-0893
pre-chordal neural plate5.69e-0861
regional part of cerebral cortex1.62e-0722
neocortex6.27e-0720
Disease
Ontology termp-valuen
leukemia1.46e-0739
myeloid leukemia3.43e-0731
hematologic cancer4.07e-0751
immune system cancer4.07e-0751


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
CCNT2#90536.336201576962630.003930750035764890.0189732219339672
E2F1#186934.907389214879320.008460985347239390.0324718645015373
E2F4#1874312.66806031528440.0004917987006298980.00436537179118528
E2F6#187635.017155731697390.00791769806886330.0321532183145662
ELF1#199734.258097958807540.01295179875054610.0461348195671311
MAX#414936.452555509007120.003721913834265510.0186281189886833
MYC#460935.22228187160940.007020843755740150.0294017362767451
NANOG#79923329.24477848101273.99627955670032e-050.000736877543471443
NFKB1#479035.488063424193840.006049381815655430.0269248407178878
NRF1#4899312.21027944771090.0005492172401020010.00470585768635761
POU2F2#545239.106124057742520.001324165192682130.00881137231975336
SIN3A#2594235.408884726815140.006318961977991520.0276151171654304
TAF7#6879311.43306940492390.0006690181981945830.00541892287895487
THAP1#55145220.91276306856750.002983447413736940.0158641751664005
YY1#752834.911170749853860.008441455341808260.032874082871322
ZNF143#7702313.50087655222790.0004062804962997170.00388567113123133



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.