Coexpression cluster:C900

Full id: C900_CD4_thymus_Hodgkin_CD8_CD34_chronic_CD133

Phase1 CAGE Peaks

Hg19::chr13:30951074..30951122,-	p1@LINC00426
Hg19::chr13:30951124..30951135,-	p4@LINC00426
Hg19::chr13:30951150..30951161,-	p5@LINC00426
Hg19::chr14:22309226..22309237,+	p4@uc001wbx.2 p4@uc010tmg.1
Hg19::chr14:81425875..81425889,-	p5@CEP128
Hg19::chr2:38830160..38830206,-	p3@HNRPLL
Hg19::chr3:133209983..133210005,-	p2@AK128281
Hg19::chr4:109087819..109087826,-	p45@LEF1
Hg19::chr6:25042231..25042263,-	p7@FAM65B

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:0021542	dentate gyrus development	0.00788803686016357
GO:0021766	hippocampus development	0.00788803686016357
GO:0048341	paraxial mesoderm formation	0.00788803686016357
GO:0048340	paraxial mesoderm morphogenesis	0.00788803686016357
GO:0048339	paraxial mesoderm development	0.00788803686016357
GO:0021543	pallium development	0.00788803686016357
GO:0021761	limbic system development	0.00788803686016357
GO:0045843	negative regulation of striated muscle development	0.00788803686016357
GO:0008301	DNA bending activity	0.00832491294628465
GO:0021537	telencephalon development	0.00832491294628465
GO:0016202	regulation of striated muscle development	0.00832491294628465
GO:0030879	mammary gland development	0.00832491294628465
GO:0001890	placenta development	0.00832491294628465
GO:0001707	mesoderm formation	0.00832491294628465
GO:0048332	mesoderm morphogenesis	0.00832491294628465
GO:0001704	formation of primary germ layer	0.00832491294628465
GO:0001756	somitogenesis	0.00832491294628465
GO:0042475	odontogenesis of dentine-containing teeth	0.00832491294628465
GO:0042476	odontogenesis	0.00925727956560874
GO:0007369	gastrulation	0.00925727956560874
GO:0003705	RNA polymerase II transcription factor activity, enhancer binding	0.00925727956560874
GO:0035282	segmentation	0.00925727956560874
GO:0030111	regulation of Wnt receptor signaling pathway	0.00925727956560874
GO:0030326	embryonic limb morphogenesis	0.0100597509018366
GO:0035113	embryonic appendage morphogenesis	0.0100597509018366
GO:0060173	limb development	0.0100597509018366
GO:0035107	appendage morphogenesis	0.0100597509018366
GO:0035108	limb morphogenesis	0.0100597509018366
GO:0048736	appendage development	0.0100597509018366
GO:0007498	mesoderm development	0.0113327103941029
GO:0030900	forebrain development	0.0113327103941029
GO:0048732	gland development	0.0113327103941029
GO:0009952	anterior/posterior pattern formation	0.013137632697009
GO:0048729	tissue morphogenesis	0.0166883415293181
GO:0003002	regionalization	0.0191898420490159
GO:0014706	striated muscle development	0.0191898420490159
GO:0048598	embryonic morphogenesis	0.0191898420490159
GO:0009792	embryonic development ending in birth or egg hatching	0.0191898420490159
GO:0043009	chordate embryonic development	0.0191898420490159
GO:0003682	chromatin binding	0.023232030545665
GO:0007389	pattern specification process	0.0238101401826761
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	0.0238101401826761
GO:0007420	brain development	0.0248709738339615
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	0.0248709738339615
GO:0016055	Wnt receptor signaling pathway	0.0253657508702202
GO:0048646	anatomical structure formation	0.0261802979410705
GO:0007517	muscle development	0.0287971716144891
GO:0045892	negative regulation of transcription, DNA-dependent	0.0332640668261998
GO:0005667	transcription factor complex	0.0337053528466996
GO:0032991	macromolecular complex	0.0343816716168921
GO:0045893	positive regulation of transcription, DNA-dependent	0.0343816716168921
GO:0007417	central nervous system development	0.0348583904248288
GO:0009790	embryonic development	0.0348583904248288
GO:0016070	RNA metabolic process	0.0371124061293968
GO:0006397	mRNA processing	0.0384558457409892
GO:0003702	RNA polymerase II transcription factor activity	0.0384558457409892
GO:0045941	positive regulation of transcription	0.0384558457409892
GO:0045935	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0387433320914088
GO:0016481	negative regulation of transcription	0.0387433320914088
GO:0009888	tissue development	0.0397803929901879
GO:0016563	transcription activator activity	0.0397803929901879
GO:0045934	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0403994266050121
GO:0016071	mRNA metabolic process	0.0426102447334929
GO:0009887	organ morphogenesis	0.0440615929370697
GO:0031325	positive regulation of cellular metabolic process	0.0440615929370697
GO:0031324	negative regulation of cellular metabolic process	0.0452854709956637
GO:0009893	positive regulation of metabolic process	0.0457736471972898
GO:0006357	regulation of transcription from RNA polymerase II promoter	0.048768482251992
GO:0009892	negative regulation of metabolic process	0.0493319114072623
GO:0010467	gene expression	0.0493319114072623
GO:0044451	nucleoplasm part	0.049888598166981

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
hematopoietic stem cell	1.96e-42	172
angioblastic mesenchymal cell	1.96e-42	172
hematopoietic cell	1.94e-39	182
hematopoietic oligopotent progenitor cell	6.26e-39	165
hematopoietic multipotent progenitor cell	6.26e-39	165
leukocyte	1.20e-31	140
lymphocyte	1.69e-27	53
common lymphoid progenitor	1.69e-27	53
lymphoid lineage restricted progenitor cell	5.55e-27	52
hematopoietic lineage restricted progenitor cell	1.71e-25	124
nongranular leukocyte	1.13e-24	119
T cell	4.50e-15	25
pro-T cell	4.50e-15	25
myeloid cell	2.57e-14	112
common myeloid progenitor	2.57e-14	112
mature alpha-beta T cell	1.44e-12	18
alpha-beta T cell	1.44e-12	18
immature T cell	1.44e-12	18
mature T cell	1.44e-12	18
immature alpha-beta T cell	1.44e-12	18
lymphocyte of B lineage	2.19e-11	24
pro-B cell	2.19e-11	24
CD8-positive, alpha-beta T cell	2.70e-08	11
B cell	2.24e-07	14

Uber Anatomy

Ontology term	p-value	n
adult organism	1.72e-28	115
hematopoietic system	1.32e-10	102
blood island	1.32e-10	102
hemolymphoid system	2.00e-09	112
neural tube	5.42e-09	57
neural rod	5.42e-09	57
future spinal cord	5.42e-09	57
neural keel	5.42e-09	57
anterior neural tube	6.18e-08	42
regional part of forebrain	9.96e-08	41
forebrain	9.96e-08	41
future forebrain	9.96e-08	41
blood	4.00e-07	15
haemolymphatic fluid	4.00e-07	15
organism substance	4.00e-07	15
regional part of brain	8.51e-07	59

Disease

Ontology term	p-value	n
hematologic cancer	1.52e-13	51
immune system cancer	1.52e-13	51
leukemia	2.21e-11	39
myeloid leukemia	4.81e-08	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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No analysis results for this cluster

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.