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Coexpression cluster:C3687: Difference between revisions

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|tf_chipseq_enrich=EBF1#1879;3:8.906466846569:0.0014152328356098:0.00914581412773048!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0320366876553529!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00897067723336708!FOSL1#8061;3:39.713579716373:1.59554825631833e-05:0.000370964969594012!FOSL2#2355;3:16.9302006045617:0.000206016205317162:0.00242900501999538!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00391045284238798!HNF4A#3172;3:23.1322903629537:8.07584663437677e-05:0.0012277050169544!HNF4G#3174;3:28.7534225264468:4.20470658818262e-05:0.000756477780126106!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0127958880975371!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00443932208967464!JUNB#3726;3:30.6106326598211:3.4847716247536e-05:0.000680145886222466!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156618032446212!NR2C2#7182;3:32.6146109052409:2.88098172333076e-05:0.000604797688850134!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.027641720210239!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.014006035590898
|tf_chipseq_enrich=EBF1#1879;3:8.906466846569:0.0014152328356098:0.00914581412773048!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0320366876553529!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00897067723336708!FOSL1#8061;3:39.713579716373:1.59554825631833e-05:0.000370964969594012!FOSL2#2355;3:16.9302006045617:0.000206016205317162:0.00242900501999538!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00391045284238798!HNF4A#3172;3:23.1322903629537:8.07584663437677e-05:0.0012277050169544!HNF4G#3174;3:28.7534225264468:4.20470658818262e-05:0.000756477780126106!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0127958880975371!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00443932208967464!JUNB#3726;3:30.6106326598211:3.4847716247536e-05:0.000680145886222466!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156618032446212!NR2C2#7182;3:32.6146109052409:2.88098172333076e-05:0.000604797688850134!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.027641720210239!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.014006035590898
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}}
}}

Revision as of 16:17, 26 November 2012


Full id: C3687_Pericytes_Burkitt_NK_hereditary_hepatocellular_B_hairy



Phase1 CAGE Peaks

Hg19::chr17:75446607..75446628,+p27@SEPT9
Hg19::chr17:75446629..75446671,+p10@SEPT9
Hg19::chr17:75446672..75446686,+p18@SEPT9


Enriched pathways on this co-expression cluster<b>Summary:</b><br>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.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> 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. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>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. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
nongranular leukocyte2.21e-30115
leukocyte3.06e-28136
hematopoietic lineage restricted progenitor cell7.56e-26120
hematopoietic cell3.87e-23177
hematopoietic stem cell3.65e-20168
angioblastic mesenchymal cell3.65e-20168
lymphocyte4.42e-2053
common lymphoid progenitor4.42e-2053
lymphoid lineage restricted progenitor cell1.63e-1952
nucleate cell1.62e-1855
hematopoietic oligopotent progenitor cell2.21e-18161
hematopoietic multipotent progenitor cell2.21e-18161
classical monocyte1.19e-1142
CD14-positive, CD16-negative classical monocyte1.19e-1142
defensive cell2.12e-1148
phagocyte2.12e-1148
lymphocyte of B lineage2.23e-1124
pro-B cell2.23e-1124
monopoietic cell4.33e-1059
monocyte4.33e-1059
monoblast4.33e-1059
promonocyte4.33e-1059
T cell1.69e-0925
pro-T cell1.69e-0925
myeloid lineage restricted progenitor cell2.83e-0966
macrophage dendritic cell progenitor3.12e-0961
myeloid leukocyte4.01e-0972
granulocyte monocyte progenitor cell6.85e-0967
mature alpha-beta T cell1.82e-0818
alpha-beta T cell1.82e-0818
immature T cell1.82e-0818
mature T cell1.82e-0818
immature alpha-beta T cell1.82e-0818
melanocyte1.92e-0710
melanoblast1.92e-0710
intermediate monocyte3.74e-079
CD14-positive, CD16-positive monocyte3.74e-079
stuff accumulating cell5.72e-0787
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.72e-1498
blood island2.72e-1498
hemolymphoid system1.63e-13108
immune system1.85e-0993
bone marrow2.46e-0776


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>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. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> 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. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
EBF1#187938.9064668465690.00141523283560980.00914581412773048
EGR1#195834.988179094810140.008056488137383440.0320366876553529
FOS#235338.99795530889440.001372499272417130.00897067723336708
FOSL1#8061339.7135797163731.59554825631833e-050.000370964969594012
FOSL2#2355316.93020060456170.0002060162053171620.00242900501999538
HDAC2#3066313.41562023662630.0004140761399857210.00391045284238798
HNF4A#3172323.13229036295378.07584663437677e-050.0012277050169544
HNF4G#3174328.75342252644684.20470658818262e-050.000756477780126106
IRF1#365937.63716375356390.002244692747297240.0127958880975371
JUN#3725312.51282919233630.0005103313992726250.00443932208967464
JUNB#3726330.61063265982113.4847716247536e-050.000680145886222466
JUND#372736.994663941871030.002921845042734990.0156618032446212
NR2C2#7182332.61461090524092.88098172333076e-050.000604797688850134
SIN3A#2594235.408884726815140.006318961977991520.027641720210239
ZBTB7A#5134137.35190930787590.002516255860282270.014006035590898



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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