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Coexpression cluster:C3902: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279559337806528!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167531556073771!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.0066426332253927!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0276962426565157!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.0030918087231846!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.0064281321617488!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00614139788114202!ZNF143#7702;3:13.5008765522279:0.000406280496299717:0.00389244369810532
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279559337806528!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167531556073771!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.0066426332253927!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0276962426565157!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.0030918087231846!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.0064281321617488!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00614139788114202!ZNF143#7702;3:13.5008765522279:0.000406280496299717:0.00389244369810532
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}}
}}

Revision as of 16:25, 26 November 2012


Full id: C3902_Hepatocyte_liver_hepatoma_Neutrophils_medulla_placenta_CD4



Phase1 CAGE Peaks

Hg19::chr1:169555677..169555678,-p4@F5
Hg19::chr1:169555684..169555705,-p2@F5
Hg19::chr1:169555709..169555730,-p1@F5


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
classical monocyte3.66e-2742
CD14-positive, CD16-negative classical monocyte3.66e-2742
myeloid leukocyte7.84e-2672
leukocyte3.28e-22136
defensive cell1.13e-2148
phagocyte1.13e-2148
myeloid lineage restricted progenitor cell1.17e-1966
granulocyte monocyte progenitor cell2.55e-1867
monopoietic cell3.92e-1859
monocyte3.92e-1859
monoblast3.92e-1859
promonocyte3.92e-1859
nongranular leukocyte5.91e-18115
hematopoietic lineage restricted progenitor cell1.03e-17120
macrophage dendritic cell progenitor5.19e-1761
hematopoietic stem cell4.48e-15168
angioblastic mesenchymal cell4.48e-15168
hematopoietic cell5.71e-15177
hematopoietic oligopotent progenitor cell2.53e-14161
hematopoietic multipotent progenitor cell2.53e-14161
myeloid cell4.03e-13108
common myeloid progenitor4.03e-13108
stuff accumulating cell1.11e-0887
granulocyte5.25e-088
Uber Anatomy
Ontology termp-valuen
adult organism4.27e-37114
hematopoietic system3.10e-2598
blood island3.10e-2598
hemolymphoid system1.99e-22108
immune system3.81e-1493
bone marrow3.87e-1476
blood6.08e-1215
haemolymphatic fluid6.08e-1215
organism substance6.08e-1215
bone element6.23e-1282
skeletal element1.56e-0990
neural tube8.27e-0956
neural rod8.27e-0956
future spinal cord8.27e-0956
neural keel8.27e-0956
regional part of nervous system2.73e-0853
regional part of brain2.73e-0853
skeletal system1.22e-07100


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
CTCF#1066435.360256373075030.0064925092527670.0279559337806528
EP300#203336.77394172622320.003216880500103790.0167531556073771
RAD21#5885310.35503389545630.0009004912073565420.0066426332253927
SIN3A#2594235.408884726815140.006318961977991520.0276962426565157
SMC3#9126315.04493284493280.0002935825420371870.0030918087231846
STAT3#6774310.51946499715420.0008589184530415310.0064281321617488
TCF7L2#6934310.77017656313730.0008003181298398380.00614139788114202
ZNF143#7702313.50087655222790.0004062804962997170.00389244369810532



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.