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Coexpression cluster:C1827: Difference between revisions

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|tf_chipseq_enrich=E2F1#1869;5:4.90738921487932:0.000351281809925646:0.00352968260023326!EGR1#1958;5:4.98817909481014:0.000323739800059071:0.00330897054006355!NRF1#4899;5:12.2102794477109:3.68220991173981e-06:0.000120705059941053!PAX5#5079;5:6.66956553117783:7.57493746384605e-05:0.00117029422157784!ZEB1#6935;3:10.1330592105263:0.00189555692435707:0.011162676606875!ZNF143#7702;3:8.10052593133674:0.00362487051209098:0.0183339557078924
|tf_chipseq_enrich=E2F1#1869;5:4.90738921487932:0.000351281809925646:0.00352968260023326!EGR1#1958;5:4.98817909481014:0.000323739800059071:0.00330897054006355!NRF1#4899;5:12.2102794477109:3.68220991173981e-06:0.000120705059941053!PAX5#5079;5:6.66956553117783:7.57493746384605e-05:0.00117029422157784!ZEB1#6935;3:10.1330592105263:0.00189555692435707:0.011162676606875!ZNF143#7702;3:8.10052593133674:0.00362487051209098:0.0183339557078924
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}}
}}

Revision as of 15:08, 26 November 2012


Full id: C1827_Mast_CD19_immature_ovary_CD4_CD8_Peripheral



Phase1 CAGE Peaks

Hg19::chr19:54041508..54041527,+p8@ZNF331
Hg19::chr19:54041534..54041545,+p11@ZNF331
Hg19::chr19:54041574..54041589,+p6@ZNF331
Hg19::chr19:54058046..54058053,+p18@ZNF331
Hg19::chr19:54058073..54058088,+p1@ZNF331


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
leukocyte5.74e-21136
classical monocyte3.01e-2042
CD14-positive, CD16-negative classical monocyte3.01e-2042
granulocyte monocyte progenitor cell1.35e-1867
myeloid leukocyte2.40e-1872
defensive cell2.28e-1748
phagocyte2.28e-1748
hematopoietic lineage restricted progenitor cell6.27e-17120
nongranular leukocyte8.98e-16115
myeloid lineage restricted progenitor cell1.55e-1566
macrophage dendritic cell progenitor1.95e-1561
hematopoietic stem cell1.43e-14168
angioblastic mesenchymal cell1.43e-14168
monopoietic cell4.79e-1459
monocyte4.79e-1459
monoblast4.79e-1459
promonocyte4.79e-1459
hematopoietic cell8.81e-14177
hematopoietic oligopotent progenitor cell5.53e-12161
hematopoietic multipotent progenitor cell5.53e-12161
myeloid cell3.72e-10108
common myeloid progenitor3.72e-10108
CD4-positive, alpha-beta T cell1.40e-076
Uber Anatomy
Ontology termp-valuen
adult organism8.54e-21114
hematopoietic system5.11e-1798
blood island5.11e-1798
bone marrow2.43e-1576
bone element1.33e-1482
hemolymphoid system2.33e-14108
immune system6.75e-1493
skeletal element1.80e-1290
skeletal system2.15e-10100
neural tube3.65e-1056
neural rod3.65e-1056
future spinal cord3.65e-1056
neural keel3.65e-1056
regional part of nervous system1.26e-0953
regional part of brain1.26e-0953
regional part of forebrain6.50e-0941
forebrain6.50e-0941
anterior neural tube6.50e-0941
future forebrain6.50e-0941


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)

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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
E2F1#186954.907389214879320.0003512818099256460.00352968260023326
EGR1#195854.988179094810140.0003237398000590710.00330897054006355
NRF1#4899512.21027944771093.68220991173981e-060.000120705059941053
PAX5#507956.669565531177837.57493746384605e-050.00117029422157784
ZEB1#6935310.13305921052630.001895556924357070.011162676606875
ZNF143#770238.100525931336740.003624870512090980.0183339557078924



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.