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Coexpression cluster:C1558

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Full id: C1558_CD19_CD8_CD4_Mesenchymal_MCF7_CD14CD16_CD14



Phase1 CAGE Peaks

  Short description
Hg19::chr10:104614236..104614277,- p@chr10:104614236..104614277
-
Hg19::chr16:2827358..2827403,+ p1@AK056451
Hg19::chr1:245027971..245027998,+ p@chr1:245027971..245027998
+
Hg19::chr5:43484033..43484098,+ p1@ENST00000504469
Hg19::chr8:135725363..135725407,+ p@chr8:135725363..135725407
+


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
leukocyte1.37e-38136
hematopoietic stem cell3.19e-34168
angioblastic mesenchymal cell3.19e-34168
hematopoietic cell5.88e-34177
hematopoietic lineage restricted progenitor cell2.49e-32120
hematopoietic oligopotent progenitor cell3.97e-31161
hematopoietic multipotent progenitor cell3.97e-31161
nongranular leukocyte4.11e-30115
myeloid leukocyte2.47e-1872
nucleate cell2.90e-1655
classical monocyte3.28e-1642
CD14-positive, CD16-negative classical monocyte3.28e-1642
lymphoid lineage restricted progenitor cell7.40e-1652
lymphocyte1.13e-1553
common lymphoid progenitor1.13e-1553
myeloid lineage restricted progenitor cell1.44e-1566
myeloid cell1.86e-15108
common myeloid progenitor1.86e-15108
granulocyte monocyte progenitor cell3.24e-1567
defensive cell2.29e-1448
phagocyte2.29e-1448
macrophage dendritic cell progenitor4.36e-1461
monopoietic cell2.17e-1359
monocyte2.17e-1359
monoblast2.17e-1359
promonocyte2.17e-1359
mature alpha-beta T cell3.76e-1118
alpha-beta T cell3.76e-1118
immature T cell3.76e-1118
mature T cell3.76e-1118
immature alpha-beta T cell3.76e-1118
T cell2.97e-0825
pro-T cell2.97e-0825
CD8-positive, alpha-beta T cell3.24e-0811
B cell1.28e-0714
lymphocyte of B lineage2.32e-0724
pro-B cell2.32e-0724
mesenchymal cell4.19e-07354
motile cell6.69e-07386
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.36e-2098
blood island1.36e-2098
hemolymphoid system1.28e-18108
bone marrow2.79e-1576
immune system2.18e-1493
bone element1.74e-1282
skeletal element2.95e-0990
regional part of nervous system1.63e-0853
regional part of brain1.63e-0853
neural tube3.14e-0856
neural rod3.14e-0856
future spinal cord3.14e-0856
neural keel3.14e-0856
lateral plate mesoderm3.78e-08203
skeletal system2.63e-07100


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#90545.068961261570110.002709998091280770.0148876698046011
E2F6#187644.013724585357910.006632118233933880.0282830459874978
ELF1#199743.406478367046030.01235066105299550.0447179992967167
ETS1#211347.783008737761870.0005121035947688870.00443847197793094
GTF2B#2959425.55506394745944.67711684449311e-060.000145206125482169
GTF2F1#296237.643796526054590.00428415496412050.0203424805773031
HEY1#2346254.040111043105710.0009288852205177990.00673412769302085
IRF1#365946.109731002851120.001315525264767990.00880493098738173
MYC#460955.22228187160940.0002573944848850610.00276194622489581
NFKB1#479044.390450739355070.004707732692524960.022192322034512
NRF1#489937.326167668626540.004839689817117540.0226833175429672
REST#597835.790017229676810.009468788694433940.0356827171270111
SIX5#147912310.25202921327540.001832291068677690.0108469927968274
TAF1#687253.343046285745290.002394600090870310.0135081364853843
TAF7#687936.859841642954350.005843286407019040.0262378859393208
TBP#690853.706770687096390.001428755106721120.00917529081908918
TCF12#693836.380678941311850.007185168653258840.0298232187019196
YY1#752854.911170749853860.00034993140821360.00352357176459893
ZNF143#770238.100525931336740.003624870512090980.0183259682162973



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.