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{{Coexpression_clusters
 
{{Coexpression_clusters
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|full_id=C1931_cholangiocellular_NK_cord_gall_glioma_CD4_mycosis
 
|full_id=C1931_cholangiocellular_NK_cord_gall_glioma_CD4_mycosis
 
|id=C1931
 
|id=C1931

Revision as of 05:34, 12 September 2012


Full id: C1931_cholangiocellular_NK_cord_gall_glioma_CD4_mycosis



Phase1 CAGE Peaks

  Short description
Hg19::chr3:98275070..98275077,- p@chr3:98275070..98275077
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Hg19::chr3:98275078..98275089,- p@chr3:98275078..98275089
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Hg19::chr3:98275094..98275103,- p@chr3:98275094..98275103
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Hg19::chr3:98275107..98275141,- p@chr3:98275107..98275141
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Hg19::chr3:98275166..98275178,- p@chr3:98275166..98275178
-


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


No GOStat results

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 cell4.20e-25182
hematopoietic stem cell3.67e-24172
angioblastic mesenchymal cell3.67e-24172
hematopoietic oligopotent progenitor cell4.00e-24165
hematopoietic multipotent progenitor cell4.00e-24165
leukocyte5.12e-21140
nongranular leukocyte1.14e-20119
hematopoietic lineage restricted progenitor cell2.42e-20124
CD14-positive, CD16-negative classical monocyte3.01e-1442
myeloid cell1.85e-13112
common myeloid progenitor1.85e-13112
classical monocyte7.77e-1345
lymphoid lineage restricted progenitor cell5.29e-1152
lymphocyte1.15e-1053
common lymphoid progenitor1.15e-1053
macrophage dendritic cell progenitor4.52e-1065
monopoietic cell1.42e-0963
monocyte1.42e-0963
monoblast1.42e-0963
promonocyte1.42e-0963
myeloid lineage restricted progenitor cell1.76e-0970
granulocyte monocyte progenitor cell2.20e-0971
T cell8.04e-0925
pro-T cell8.04e-0925
CD4-positive, alpha-beta T cell2.94e-086
myeloid leukocyte3.95e-0876
mature alpha-beta T cell1.06e-0718
alpha-beta T cell1.06e-0718
immature T cell1.06e-0718
mature T cell1.06e-0718
immature alpha-beta T cell1.06e-0718
circulating cell7.53e-076
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.79e-12102
blood island2.79e-12102
hemolymphoid system5.11e-11112
bone marrow2.72e-0880
bone element6.99e-0886
connective tissue5.25e-07375
immune system5.79e-07115


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
BATF#10538524.35780179230361.16482472299935e-076.73978555375786e-06
BCL11A#53335528.36945510360715.43377642717329e-083.44146862509127e-06
BCL3#602534.54710280373832.02839878970325e-081.44702145626924e-06
BCLAF1#9774521.65264761012182.09874458450681e-071.12060728865699e-05
CHD2#1106510.34402283411698.43981772346334e-060.000230383200005433
EBF1#187958.9064668465691.78355672307702e-050.000406620564508712
EP300#203356.77394172622327.00901578206049e-050.00110944922592091
IRF4#3662521.91451268674411.97628413609567e-071.0722137085179e-05
JUND#372756.994663941871035.97069468343598e-050.000985108028504534
MEF2A#4205518.74323090964414.31877656850983e-072.07188197537252e-05
MEF2C#4208541.31135449262418.29287828997783e-096.38246069069266e-07
NFKB1#479055.488063424193840.0002008162847462320.00239309127825327
PAX5#507956.669565531177837.57493746384605e-050.00117098711336089
PBX3#5090521.91451268674411.97628413609567e-071.07277099215018e-05
POU2F2#545259.106124057742521.59639992500654e-050.000370091924012782
RXRA#6256520.07461713913333.06418769543848e-071.54152552371821e-05
SP1#666755.69838137814090.000166391843712550.00204468734739322
SRF#6722513.79717826216781.9987012616697e-067.32429337079024e-05
TAF1#687253.343046285745290.002394600090870310.0135505872827484
TBP#690853.706770687096390.001428755106721120.00920018216849666
TCF12#6938510.63446490218647.34844389925727e-060.000211364398896869
TCF7L2#6934510.77017656313736.89693748574565e-060.000200030339926073
YY1#752854.911170749853860.00034993140821360.00353003828285715



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.