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Coexpression cluster:C4278: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!1.25e-35!102;UBERON:0003061!1.25e-35!102;UBERON:0002193!7.26e-31!112;UBERON:0001474!2.56e-27!86;UBERON:0002371!3.33e-27!80;UBERON:0002405!2.91e-26!115;UBERON:0004765!6.04e-22!101;UBERON:0001434!6.04e-22!101;UBERON:0000178!2.96e-10!15;UBERON:0000179!2.96e-10!15;UBERON:0000463!2.96e-10!15
|ontology_enrichment_uberon=UBERON:0002390!1.25e-35!102;UBERON:0003061!1.25e-35!102;UBERON:0002193!7.26e-31!112;UBERON:0001474!2.56e-27!86;UBERON:0002371!3.33e-27!80;UBERON:0002405!2.91e-26!115;UBERON:0004765!6.04e-22!101;UBERON:0001434!6.04e-22!101;UBERON:0000178!2.96e-10!15;UBERON:0000179!2.96e-10!15;UBERON:0000463!2.96e-10!15
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280391669292368!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326518437970785!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154525898690717!HNF4A#3172;3:23.1322903629537:8.07584663437677e-05:0.00123110983308667!HNF4G#3174;3:28.7534225264468:4.20470658818262e-05:0.0007586996395356!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247211765485816
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}}
}}

Revision as of 12:32, 5 September 2012


Full id: C4278_liver_Monocytederived_hepatocellular_Macrophage_Hepatocyte_CD14_small



Phase1 CAGE Peaks

Hg19::chr3:126242976..126243008,+p1@CHST13
Hg19::chr3:126243130..126243153,+p2@CHST13
Hg19::chr3:126243162..126243176,+p3@CHST13


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
myeloid leukocyte1.72e-3676
myeloid lineage restricted progenitor cell1.13e-3270
granulocyte monocyte progenitor cell1.17e-3271
monopoietic cell9.37e-3163
monocyte9.37e-3163
monoblast9.37e-3163
promonocyte9.37e-3163
macrophage dendritic cell progenitor3.11e-3065
myeloid cell5.85e-28112
common myeloid progenitor5.85e-28112
CD14-positive, CD16-negative classical monocyte7.03e-2342
classical monocyte6.64e-2245
hematopoietic cell4.04e-14182
leukocyte5.09e-14140
hematopoietic stem cell5.71e-14172
angioblastic mesenchymal cell5.71e-14172
hematopoietic oligopotent progenitor cell1.06e-12165
hematopoietic multipotent progenitor cell1.06e-12165
hematopoietic lineage restricted progenitor cell5.68e-12124
nongranular leukocyte4.25e-11119
intermediate monocyte1.03e-079
CD14-positive, CD16-positive monocyte1.03e-079
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.25e-35102
blood island1.25e-35102
hemolymphoid system7.26e-31112
bone element2.56e-2786
bone marrow3.33e-2780
immune system2.91e-26115
skeletal element6.04e-22101
skeletal system6.04e-22101
blood2.96e-1015
haemolymphatic fluid2.96e-1015
organism substance2.96e-1015


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#1066435.360256373075030.0064925092527670.0280391669292368
E2F1#186934.907389214879320.008460985347239390.0326518437970785
GABPB1#255337.067683836182170.002832212825417420.0154525898690717
HNF4A#3172323.13229036295378.07584663437677e-050.00123110983308667
HNF4G#3174328.75342252644684.20470658818262e-050.0007586996395356
SP1#666735.69838137814090.005403962701712170.0247211765485816



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.