Coexpression cluster:C1526

Full id: C1526_cervical_chorionic_alveolar_Synoviocyte_oral_CD14_normal

Phase1 CAGE Peaks

Hg19::chr5:137801546..137801573,-	p@chr5:137801546..137801573 -
Hg19::chr5:137802485..137802611,-	p@chr5:137802485..137802611 -
Hg19::chr5:137802624..137802791,-	p@chr5:137802624..137802791 -
Hg19::chr5:137803060..137803134,-	p@chr5:137803060..137803134 -
Hg19::chr5:137803278..137803323,-	p1@CU687283
Hg19::chr5:137804484..137804498,+	p2@EGR1

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

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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

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GO ID	GO name	FDR corrected p-value
GO:0030217	T cell differentiation	0.0328211468267985
GO:0007611	learning and/or memory	0.0328211468267985
GO:0030098	lymphocyte differentiation	0.0328211468267985
GO:0002521	leukocyte differentiation	0.0328211468267985
GO:0042110	T cell activation	0.0328211468267985
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	0.0328211468267985
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	0.0328211468267985
GO:0046649	lymphocyte activation	0.0328211468267985
GO:0030097	hemopoiesis	0.0328211468267985
GO:0048534	hemopoietic or lymphoid organ development	0.0328211468267985
GO:0045321	leukocyte activation	0.0328211468267985
GO:0002520	immune system development	0.0328211468267985
GO:0045892	negative regulation of transcription, DNA-dependent	0.0328211468267985
GO:0001775	cell activation	0.0328211468267985
GO:0045893	positive regulation of transcription, DNA-dependent	0.0328211468267985
GO:0045941	positive regulation of transcription	0.0335360212612067
GO:0045935	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0335360212612067
GO:0016481	negative regulation of transcription	0.0335360212612067
GO:0007610	behavior	0.0335360212612067
GO:0016563	transcription activator activity	0.0335360212612067
GO:0045934	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0335360212612067
GO:0031325	positive regulation of cellular metabolic process	0.0359671199811609
GO:0031324	negative regulation of cellular metabolic process	0.0359671199811609
GO:0009893	positive regulation of metabolic process	0.0359671199811609
GO:0006357	regulation of transcription from RNA polymerase II promoter	0.03702143846969
GO:0009892	negative regulation of metabolic process	0.03702143846969

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><br>uberon_data<br>disease_data<br>

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Uber Anatomy

Ontology term	p-value	n
multi-cellular organism	1.77e-07	656
anatomical group	4.73e-07	625
anatomical system	8.78e-07	624

Disease

Ontology term	p-value	n
cell type cancer	2.23e-07	143
squamous cell carcinoma	9.66e-07	14

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

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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

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

TF	#promoters	Enrichment	p-value	q-value
HEY1#23462	6	4.04011104310571	0.000229896855580751	0.00253459281114726
JUND#3727	6	6.99466394187103	8.53468650061654e-06	0.000232365517058887
POLR2A#5430	6	2.14745317655807	0.0101957067681878	0.0380690507726848
TAF7#6879	6	11.4330694049239	4.47357982339933e-07	2.12854762266971e-05
USF2#7392	6	12.9921973850696	2.07721573629339e-07	1.11366701377179e-05

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

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This analysis result is provided for C0 - C305 clusters.