Coexpression cluster:C1612

Full id: C1612_cord_CD19_Natural_CD8_CD4_CD34_CD14

Phase1 CAGE Peaks

Hg19::chr11:118661169..118661182,+	p@chr11:118661169..118661182 +
Hg19::chr12:48499252..48499282,+	p7@PFKM
Hg19::chr13:52026730..52026775,-	p3@INTS6
Hg19::chr13:52026782..52026796,-	p8@INTS6
Hg19::chr6:91005071..91005091,+	p@chr6:91005071..91005091 +

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:0006110	regulation of glycolysis	0.0164013210285011
GO:0016073	snRNA metabolic process	0.0164013210285011
GO:0016180	snRNA processing	0.0164013210285011
GO:0032039	integrator complex	0.0164013210285011
GO:0005945	6-phosphofructokinase complex	0.0164013210285011
GO:0003872	6-phosphofructokinase activity	0.0164013210285011
GO:0009894	regulation of catabolic process	0.0181253739246214
GO:0008443	phosphofructokinase activity	0.0181253739246214
GO:0005977	glycogen metabolic process	0.0248503354425738
GO:0006073	glucan metabolic process	0.0248503354425738
GO:0006112	energy reserve metabolic process	0.0254502126700536
GO:0019200	carbohydrate kinase activity	0.0254502126700536
GO:0008022	protein C-terminus binding	0.0294586637349271
GO:0044264	cellular polysaccharide metabolic process	0.0296657322669193
GO:0005976	polysaccharide metabolic process	0.0296657322669193
GO:0016591	DNA-directed RNA polymerase II, holoenzyme	0.0350587479266175
GO:0015980	energy derivation by oxidation of organic compounds	0.0350587479266175
GO:0043234	protein complex	0.0350587479266175
GO:0006096	glycolysis	0.0350587479266175
GO:0006007	glucose catabolic process	0.0350587479266175
GO:0019320	hexose catabolic process	0.0350587479266175
GO:0046365	monosaccharide catabolic process	0.0350587479266175
GO:0046164	alcohol catabolic process	0.0350587479266175
GO:0044275	cellular carbohydrate catabolic process	0.0367372293616739
GO:0044445	cytosolic part	0.0367372293616739
GO:0016052	carbohydrate catabolic process	0.0367372293616739
GO:0006006	glucose metabolic process	0.0367372293616739
GO:0032991	macromolecular complex	0.0410504682800081
GO:0019318	hexose metabolic process	0.047127271035689
GO:0005996	monosaccharide metabolic process	0.047127271035689

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
leukocyte	1.56e-48	136
lymphocyte	1.53e-45	53
common lymphoid progenitor	1.53e-45	53
lymphoid lineage restricted progenitor cell	1.73e-44	52
nucleate cell	2.51e-43	55
hematopoietic cell	3.75e-38	177
hematopoietic stem cell	4.75e-37	168
angioblastic mesenchymal cell	4.75e-37	168
hematopoietic lineage restricted progenitor cell	3.08e-33	120
nongranular leukocyte	1.50e-32	115
hematopoietic oligopotent progenitor cell	1.49e-31	161
hematopoietic multipotent progenitor cell	1.49e-31	161
lymphocyte of B lineage	1.77e-30	24
pro-B cell	1.77e-30	24
B cell	7.85e-18	14
mature alpha-beta T cell	1.26e-14	18
alpha-beta T cell	1.26e-14	18
immature T cell	1.26e-14	18
mature T cell	1.26e-14	18
immature alpha-beta T cell	1.26e-14	18
T cell	1.47e-12	25
pro-T cell	1.47e-12	25
circulating cell	1.13e-10	6
CD8-positive, alpha-beta T cell	2.94e-10	11
dendritic cell	6.77e-10	10
mesenchymal cell	1.23e-08	354
connective tissue cell	4.39e-08	361
Langerhans cell	1.18e-07	5
conventional dendritic cell	1.99e-07	8
CD4-positive, alpha-beta T cell	4.21e-07	6

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	2.51e-08	98
blood island	2.51e-08	98
hemolymphoid system	6.07e-08	108
connective tissue	9.82e-08	371
hemopoietic organ	2.63e-07	7
immune organ	2.63e-07	7

Disease

Ontology term	p-value	n
lymphoma	1.40e-08	10

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
BCL3#602	2	13.8188411214953	0.00790282333228084	0.0324333136592297
GTF2B#2959	2	12.7775319737297	0.0091993608955972	0.0347841154402547
MEF2C#4208	2	16.5245417970496	0.00557985007798205	0.0252372769604767
POU2F2#5452	3	5.46367443464551	0.0111565009446978	0.0409998170999433
RAD21#5885	4	8.28402711636506	0.000401162263912245	0.00386467905919481
RDBP#7936	2	61.45536159601	0.000417819102241031	0.00390974009667154
REST#5978	3	5.79001722967681	0.00946878869443394	0.0356852923808453
SREBF1#6720	2	18.8023397761953	0.00433531272958737	0.0205760384533231
TAL1#6886	2	11.9474466709761	0.010475778180992	0.0387985317722126
ZBTB33#10009	2	12.6658900119925	0.00935701605965159	0.035336734776856

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.