Coexpression cluster:C2234: Difference between revisions

Revision as of 18:07, 8 August 2012

Full id: C2234_Monocytederived_Dendritic_CD14_Macrophage_CD4_CD14CD16_acute

Phase1 CAGE Peaks

Hg19::chr12:6898674..6898739,+	p1@CD4
Hg19::chr12:6898749..6898763,+	p2@CD4
Hg19::chr12:6927635..6927648,+	p@chr12:6927635..6927648 +
Hg19::chr15:40599895..40599916,-	p4@PLCB2

Enriched pathways on this co-expression clusterSummary: 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. Analyst: Emmanuel Dimont link to source dataset data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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. Analyst: Erik Arner link to source dataset data

GO ID	GO name	FDR corrected p-value
GO:0043085	positive regulation of catalytic activity	0.00280566097991554
GO:0000746	conjugation	0.00280566097991554
GO:0000747	conjugation with cellular fusion	0.00280566097991554
GO:0019932	second-messenger-mediated signaling	0.00280566097991554
GO:0042289	MHC class II protein binding	0.00745842523517691
GO:0050850	positive regulation of calcium-mediated signaling	0.00745842523517691
GO:0050790	regulation of catalytic activity	0.00745842523517691
GO:0001948	glycoprotein binding	0.00745842523517691
GO:0065009	regulation of a molecular function	0.00745842523517691
GO:0050848	regulation of calcium-mediated signaling	0.00745842523517691
GO:0045058	T cell selection	0.00871738324255253
GO:0045086	positive regulation of interleukin-2 biosynthetic process	0.00953192220820685
GO:0042101	T cell receptor complex	0.00953192220820685
GO:0045076	regulation of interleukin-2 biosynthetic process	0.00953192220820685
GO:0007202	phospholipase C activation	0.00953192220820685
GO:0015026	coreceptor activity	0.00953192220820685
GO:0042094	interleukin-2 biosynthetic process	0.00953192220820685
GO:0001772	immunological synapse	0.00953192220820685
GO:0050731	positive regulation of peptidyl-tyrosine phosphorylation	0.00953192220820685
GO:0032623	interleukin-2 production	0.0110461033008635
GO:0042327	positive regulation of phosphorylation	0.0110461033008635
GO:0042287	MHC protein binding	0.0110461033008635
GO:0045937	positive regulation of phosphate metabolic process	0.0110461033008635
GO:0001934	positive regulation of protein amino acid phosphorylation	0.0110461033008635
GO:0033240	positive regulation of amine metabolic process	0.0110461033008635
GO:0045764	positive regulation of amino acid metabolic process	0.0110461033008635
GO:0050730	regulation of peptidyl-tyrosine phosphorylation	0.0110461033008635
GO:0019722	calcium-mediated signaling	0.0128906242346119
GO:0042108	positive regulation of cytokine biosynthetic process	0.0128906242346119
GO:0050870	positive regulation of T cell activation	0.0128906242346119
GO:0030217	T cell differentiation	0.0128906242346119
GO:0018108	peptidyl-tyrosine phosphorylation	0.0128906242346119
GO:0018212	peptidyl-tyrosine modification	0.0128906242346119
GO:0001932	regulation of protein amino acid phosphorylation	0.0128906242346119
GO:0004435	phosphoinositide phospholipase C activity	0.0128906242346119
GO:0004434	inositol or phosphatidylinositol phosphodiesterase activity	0.0128906242346119
GO:0033238	regulation of amine metabolic process	0.0128906242346119
GO:0006521	regulation of amino acid metabolic process	0.0128906242346119
GO:0009897	external side of plasma membrane	0.0135761902533257
GO:0051251	positive regulation of lymphocyte activation	0.0135761902533257
GO:0045727	positive regulation of translation	0.0137640724414414
GO:0007242	intracellular signaling cascade	0.0138868445486009
GO:0004629	phospholipase C activity	0.0138868445486009
GO:0050863	regulation of T cell activation	0.0138868445486009
GO:0042035	regulation of cytokine biosynthetic process	0.0138868445486009
GO:0031328	positive regulation of cellular biosynthetic process	0.0138868445486009
GO:0042325	regulation of phosphorylation	0.0140594504035753
GO:0030098	lymphocyte differentiation	0.0140594504035753
GO:0042089	cytokine biosynthetic process	0.0140594504035753
GO:0042107	cytokine metabolic process	0.0140594504035753
GO:0051174	regulation of phosphorus metabolic process	0.0140594504035753
GO:0019220	regulation of phosphate metabolic process	0.0140594504035753
GO:0009891	positive regulation of biosynthetic process	0.0140594504035753
GO:0051345	positive regulation of hydrolase activity	0.0147081714237988
GO:0051249	regulation of lymphocyte activation	0.0147081714237988
GO:0050865	regulation of cell activation	0.0152049201089264
GO:0019901	protein kinase binding	0.0154976632607284
GO:0051247	positive regulation of protein metabolic process	0.0155970015631685
GO:0007166	cell surface receptor linked signal transduction	0.015608544421815
GO:0007200	G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)	0.015608544421815
GO:0002521	leukocyte differentiation	0.0157011280879805
GO:0042110	T cell activation	0.0167207294086174
GO:0019900	kinase binding	0.0167207294086174
GO:0043235	receptor complex	0.0182853325870361
GO:0001816	cytokine production	0.0184942205328129
GO:0004620	phospholipase activity	0.0191794236901238
GO:0018193	peptidyl-amino acid modification	0.0192101293103155
GO:0005201	extracellular matrix structural constituent	0.0192399133725936
GO:0048015	phosphoinositide-mediated signaling	0.0198842451852989
GO:0008081	phosphoric diester hydrolase activity	0.0207059383359219
GO:0045860	positive regulation of protein kinase activity	0.0207059383359219
GO:0016298	lipase activity	0.0207059383359219
GO:0033674	positive regulation of kinase activity	0.0207059383359219
GO:0016042	lipid catabolic process	0.0207059383359219
GO:0051347	positive regulation of transferase activity	0.0207059383359219
GO:0009986	cell surface	0.0207059383359219
GO:0009967	positive regulation of signal transduction	0.0211259120621586
GO:0046649	lymphocyte activation	0.0211270589636876
GO:0042803	protein homodimerization activity	0.0212624215466013
GO:0030097	hemopoiesis	0.0213943647765682
GO:0048534	hemopoietic or lymphoid organ development	0.0227011416197799
GO:0045321	leukocyte activation	0.023278481821903
GO:0002520	immune system development	0.023278481821903
GO:0006417	regulation of translation	0.023278481821903
GO:0004091	carboxylesterase activity	0.0233786574867989
GO:0031326	regulation of cellular biosynthetic process	0.0245375569140324
GO:0004871	signal transducer activity	0.0245375569140324
GO:0060089	molecular transducer activity	0.0245375569140324
GO:0001775	cell activation	0.0247871288886715
GO:0007169	transmembrane receptor protein tyrosine kinase signaling pathway	0.0247871288886715
GO:0006644	phospholipid metabolic process	0.0250539646838414
GO:0009889	regulation of biosynthetic process	0.0250539646838414
GO:0045859	regulation of protein kinase activity	0.0270608654844422
GO:0043549	regulation of kinase activity	0.0273357959594244
GO:0051338	regulation of transferase activity	0.0276048558785031
GO:0006643	membrane lipid metabolic process	0.0300711054365039
GO:0051239	regulation of multicellular organismal process	0.0303059335980524
GO:0007167	enzyme linked receptor protein signaling pathway	0.0324763465972865
GO:0019899	enzyme binding	0.0325660750257327
GO:0051336	regulation of hydrolase activity	0.0325660750257327
GO:0019953	sexual reproduction	0.0330799505842489
GO:0051704	multi-organism process	0.0346181715556092
GO:0042802	identical protein binding	0.0369436518033426
GO:0031325	positive regulation of cellular metabolic process	0.0369436518033426
GO:0046983	protein dimerization activity	0.0369436518033426
GO:0009893	positive regulation of metabolic process	0.0387476195252912
GO:0007165	signal transduction	0.0387476195252912
GO:0051246	regulation of protein metabolic process	0.0413786854225017
GO:0007154	cell communication	0.0444727613318158
GO:0006520	amino acid metabolic process	0.0455972927344681

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji links to source dataset cell_data uberon_data

Cell Type
Ontology term	p-value	n
hematopoietic stem cell	8.50e-48	172
angioblastic mesenchymal cell	8.50e-48	172
hematopoietic cell	1.83e-47	182
hematopoietic oligopotent progenitor cell	6.97e-44	165
hematopoietic multipotent progenitor cell	6.97e-44	165
leukocyte	2.17e-43	140
myeloid cell	1.47e-41	112
common myeloid progenitor	1.47e-41	112
myeloid leukocyte	5.08e-38	76
granulocyte monocyte progenitor cell	1.53e-35	71
hematopoietic lineage restricted progenitor cell	5.79e-35	124
nongranular leukocyte	8.67e-34	119
myeloid lineage restricted progenitor cell	1.01e-33	70
macrophage dendritic cell progenitor	2.22e-33	65
monopoietic cell	2.19e-32	63
monocyte	2.19e-32	63
monoblast	2.19e-32	63
promonocyte	2.19e-32	63
CD14-positive, CD16-negative classical monocyte	2.64e-26	42
classical monocyte	3.15e-24	45
mesenchymal cell	8.25e-09	358
T cell	1.29e-08	25
pro-T cell	1.29e-08	25
connective tissue cell	2.35e-08	365
mature alpha-beta T cell	1.55e-07	18
alpha-beta T cell	1.55e-07	18
immature T cell	1.55e-07	18
mature T cell	1.55e-07	18
immature alpha-beta T cell	1.55e-07	18
intermediate monocyte	5.83e-07	9
CD14-positive, CD16-positive monocyte	5.83e-07	9
motile cell	8.10e-07	390

Uber Anatomy
Ontology term	p-value	n
hematopoietic system	8.69e-42	102
blood island	8.69e-42	102
hemolymphoid system	4.57e-37	112
bone marrow	3.07e-32	80
immune system	2.09e-27	115
bone element	1.12e-26	86
adult organism	4.40e-23	115
skeletal element	2.29e-20	101
skeletal system	2.29e-20	101
lateral plate mesoderm	8.08e-10	216
blood	1.32e-08	15
haemolymphatic fluid	1.32e-08	15
organism substance	1.32e-08	15
neural tube	1.86e-07	57
neural rod	1.86e-07	57
future spinal cord	1.86e-07	57
neural keel	1.86e-07	57
connective tissue	2.80e-07	375

Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon link to source data Novel motifs data Jaspar motifs data

Novel motifs

JASPAR motifs

Motifs	-log10(p-value)
{{{tfbs_overrepresentation_jaspar}}}

ENCODE TF ChIP-seq peak enrichment analysisSummary: 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. Analyst: Erik Arner link to source dataset data

No analysis results for this cluster

Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. Analyst:NA link to data source data

This analysis result is provided for C0 - C305 clusters.

@@ Line 6: / Line 6: @@
 |ontology_enrichment_disease=
 |ontology_enrichment_uberon=UBERON:0002390!8.69e-42!102;UBERON:0003061!8.69e-42!102;UBERON:0002193!4.57e-37!112;UBERON:0002371!3.07e-32!80;UBERON:0002405!2.09e-27!115;UBERON:0001474!1.12e-26!86;UBERON:0007023!4.40e-23!115;UBERON:0004765!2.29e-20!101;UBERON:0001434!2.29e-20!101;UBERON:0003081!8.08e-10!216;UBERON:0000178!1.32e-08!15;UBERON:0000179!1.32e-08!15;UBERON:0000463!1.32e-08!15;UBERON:0001049!1.86e-07!57;UBERON:0005068!1.86e-07!57;UBERON:0006241!1.86e-07!57;UBERON:0007135!1.86e-07!57;UBERON:0002384!2.80e-07!375
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 }}

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Coexpression cluster:C2234: Difference between revisions

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Revision as of 18:07, 8 August 2012

Phase1 CAGE Peaks

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