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Difference between revisions of "Coexpression cluster:C3547"

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{{Coexpression_clusters
 
{{Coexpression_clusters
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|full_id=C3547_granulocyte_acute_Eosinophils_salivary_hepatoblastoma_cerebellum_tridermal
 
|full_id=C3547_granulocyte_acute_Eosinophils_salivary_hepatoblastoma_cerebellum_tridermal
 
|gostat_on_coexpression_clusters=GO:0003723!RNA binding!0.00137547276961258!23524;6294;9667
 
|gostat_on_coexpression_clusters=GO:0003723!RNA binding!0.00137547276961258!23524;6294;9667

Revision as of 07:29, 12 September 2012


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


Cell Type
Ontology termp-valuen
hematopoietic stem cell1.32e-31172
angioblastic mesenchymal cell1.32e-31172
hematopoietic oligopotent progenitor cell7.91e-30165
hematopoietic multipotent progenitor cell7.91e-30165
hematopoietic cell2.02e-29182
leukocyte6.21e-25140
myeloid cell1.06e-21112
common myeloid progenitor1.06e-21112
hematopoietic lineage restricted progenitor cell6.37e-19124
nongranular leukocyte2.04e-17119
CD14-positive, CD16-negative classical monocyte1.21e-1542
classical monocyte1.31e-1445
myeloid leukocyte1.97e-1476
granulocyte monocyte progenitor cell6.05e-1271
myeloid lineage restricted progenitor cell3.66e-1170
macrophage dendritic cell progenitor6.12e-1065
monopoietic cell2.30e-0963
monocyte2.30e-0963
monoblast2.30e-0963
promonocyte2.30e-0963
lymphocyte9.56e-0853
common lymphoid progenitor9.56e-0853
lymphoid lineage restricted progenitor cell1.06e-0752
Uber Anatomy
Ontology termp-valuen
adult organism1.62e-23115
neural tube3.03e-1557
neural rod3.03e-1557
future spinal cord3.03e-1557
neural keel3.03e-1557
hematopoietic system2.27e-13102
blood island2.27e-13102
regional part of forebrain2.20e-1241
forebrain2.20e-1241
future forebrain2.20e-1241
anterior neural tube3.66e-1242
brain6.09e-1269
future brain6.09e-1269
central nervous system7.25e-1282
regional part of nervous system1.06e-1194
nervous system1.06e-1194
regional part of brain1.06e-1159
neurectoderm1.58e-1190
hemolymphoid system3.19e-11112
neural plate6.51e-1186
presumptive neural plate6.51e-1186
gray matter7.66e-1034
brain grey matter7.66e-1034
telencephalon9.58e-1034
bone element1.08e-0986
bone marrow1.35e-0980
regional part of telencephalon1.54e-0933
cerebral hemisphere6.34e-0932
pre-chordal neural plate5.28e-0861
regional part of cerebral cortex1.06e-0722
immune system3.36e-07115
neocortex5.53e-0720


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.