Coexpression cluster:C920

Full id: C920_anaplastic_adult_hereditary_cord_hairy_immature_xeroderma

Phase1 CAGE Peaks

Hg19::chr17:53535935..53535939,+	p@chr17:53535935..53535939 +
Hg19::chr17:80317121..80317128,+	p1@TEX19
Hg19::chr1:12123219..12123228,+	p6@TNFRSF8
Hg19::chr1:12123317..12123328,+	p8@TNFRSF8
Hg19::chr1:12123343..12123367,+	p1@TNFRSF8
Hg19::chr1:12123379..12123405,+	p2@TNFRSF8
Hg19::chr1:12123414..12123445,+	p3@TNFRSF8
Hg19::chr1:12124073..12124086,+	p@chr1:12124073..12124086 +
Hg19::chr5:129083784..129083814,+	p1@KIAA1024L

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:0045554	regulation of TRAIL biosynthetic process	0.000551925114800424
GO:0032639	TRAIL production	0.000551925114800424
GO:0045556	positive regulation of TRAIL biosynthetic process	0.000551925114800424
GO:0045553	TRAIL biosynthetic process	0.000551925114800424
GO:0042535	positive regulation of tumor necrosis factor biosynthetic process	0.00220770045920169
GO:0042533	tumor necrosis factor biosynthetic process	0.00252308623908765
GO:0042534	regulation of tumor necrosis factor biosynthetic process	0.00252308623908765
GO:0032640	tumor necrosis factor production	0.00358751324620275
GO:0042108	positive regulation of cytokine biosynthetic process	0.0100573020919188
GO:0045727	positive regulation of translation	0.0103026021429412
GO:0042035	regulation of cytokine biosynthetic process	0.0103026021429412
GO:0031328	positive regulation of cellular biosynthetic process	0.0103026021429412
GO:0042089	cytokine biosynthetic process	0.0103026021429412
GO:0042107	cytokine metabolic process	0.0103026021429412
GO:0009891	positive regulation of biosynthetic process	0.0103026021429412
GO:0051247	positive regulation of protein metabolic process	0.011728408689509
GO:0001816	cytokine production	0.0146747148170466
GO:0006417	regulation of translation	0.0225676046940618
GO:0031326	regulation of cellular biosynthetic process	0.0231227574411125
GO:0009889	regulation of biosynthetic process	0.0236539334914467
GO:0008285	negative regulation of cell proliferation	0.0236539334914467
GO:0043065	positive regulation of apoptosis	0.0247646399336538
GO:0043068	positive regulation of programmed cell death	0.0247646399336538
GO:0031325	positive regulation of cellular metabolic process	0.0335754444836924
GO:0009893	positive regulation of metabolic process	0.0345284351819145
GO:0051246	regulation of protein metabolic process	0.035832676683966
GO:0042127	regulation of cell proliferation	0.0383485746431702
GO:0042981	regulation of apoptosis	0.0438494987758682
GO:0043067	regulation of programmed cell death	0.0438494987758682

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
embryonic stem cell	2.10e-18	5
hematopoietic cell	5.72e-13	177
lymphoid lineage restricted progenitor cell	1.46e-12	52
lymphocyte	2.94e-12	53
common lymphoid progenitor	2.94e-12	53
nucleate cell	1.10e-11	55
hematopoietic oligopotent progenitor cell	1.84e-11	161
hematopoietic multipotent progenitor cell	1.84e-11	161
Langerhans cell	2.08e-11	5
lymphocyte of B lineage	4.95e-11	24
pro-B cell	4.95e-11	24
hematopoietic stem cell	1.06e-10	168
angioblastic mesenchymal cell	1.06e-10	168
germ line cell	8.94e-09	7
germ cell	8.94e-09	7
CD1a-positive Langerhans cell	2.70e-08	2
immature CD1a-positive Langerhans cell	2.70e-08	2

Uber Anatomy

Ontology term	p-value	n
testis	1.12e-07	8

Disease

Ontology term	p-value	n
hematologic cancer	4.46e-23	51
immune system cancer	4.46e-23	51
lymphoma	2.18e-13	10
leukemia	2.42e-12	39
chronic leukemia	1.02e-10	8
myeloid leukemia	1.65e-07	31

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
E2F6#1876	7	3.90223223576463	0.000306742359949273	0.00316278658611336
EBF1#1879	6	5.93764456437934	0.000124243650792417	0.00165614328591056
ELF1#1997	6	2.83873197253836	0.00720786312414863	0.0298592684472238
JUND#3727	5	3.88592441215057	0.00454408927040116	0.0214810183909576
MAFK#7975	6	18.0671554252199	1.92160575057211e-07	1.04744563144051e-05
MAX#4149	6	4.30170367267141	0.000759756385172366	0.00596917152719602
SIN3A#25942	5	3.00493595934174	0.0140161881734652	0.0491979793186979
USF1#7391	5	3.53416626511553	0.0069229675408181	0.0293103537779918

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.