Coexpression cluster:C1225

Full id: C1225_thymus_acute_CD4_CD8_Hodgkin_Peripheral_lymph

Phase1 CAGE Peaks

Hg19::chr17:29637535..29637559,+	p@chr17:29637535..29637559 +
Hg19::chr2:95740679..95740695,+	p@chr2:95740679..95740695 +
Hg19::chr4:109089436..109089456,-	p22@LEF1
Hg19::chr4:109089457..109089474,-	p29@LEF1
Hg19::chr4:109092943..109092955,+	p4@ENST00000508266
Hg19::chr4:40192656..40192672,+	p13@RHOH
Hg19::chr5:133451347..133451358,+	p3@TCF7

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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p.value	FDR	nGenes	nPathway	Name
8.30998363188652e-05	0.00438351636582014	2	151	Wnt signaling pathway (KEGG):04310
1.9318817157557e-05	0.0017954580611457	2	73	Adherens junction (KEGG):04520
3.70989802916306e-05	0.00234836545246022	2	101	Melanogenesis (KEGG):04916
0.000389495243957836	0.0189654222634854	2	327	Pathways in cancer (KEGG):05200
1.39045983109694e-05	0.00176032214616872	2	62	Colorectal cancer (KEGG):05210
9.75241122157353e-06	0.00176032214616872	2	52	Endometrial cancer (KEGG):05213
2.8776320508186e-05	0.00227692636021022	2	89	Prostate cancer (KEGG):05215
2.98763831444955e-06	0.00176032214616872	2	29	Thyroid cancer (KEGG):05216
1.09210518403916e-05	0.00176032214616872	2	55	Basal cell carcinoma (KEGG):05217
1.21557119429462e-05	0.00176032214616872	2	58	Acute myeloid leukemia (KEGG):05221
1.98549864581673e-05	0.0017954580611457	2	74	Arrhythmogenic right ventricular cardiomyopathy (ARVC) (KEGG):05412
3.56387285970187e-05	0.00234836545246022	2	99	Wnt Signaling Pathway and Pluripotency (Wikipathways):WP399
4.56530451706939e-05	0.00262712523573175	2	112	{EP300,115} (Static Module):NA

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:0016055	Wnt receptor signaling pathway	0.00732956552454962
GO:0021542	dentate gyrus development	0.00732956552454962
GO:0003702	RNA polymerase II transcription factor activity	0.0092791978354083
GO:0021766	hippocampus development	0.0092791978354083
GO:0048341	paraxial mesoderm formation	0.0092791978354083
GO:0048340	paraxial mesoderm morphogenesis	0.0092791978354083
GO:0006357	regulation of transcription from RNA polymerase II promoter	0.0092791978354083
GO:0043124	negative regulation of I-kappaB kinase/NF-kappaB cascade	0.0092791978354083
GO:0048339	paraxial mesoderm development	0.0092791978354083
GO:0021543	pallium development	0.0092791978354083
GO:0021761	limbic system development	0.0092791978354083
GO:0045843	negative regulation of striated muscle development	0.0092791978354083
GO:0005095	GTPase inhibitor activity	0.0092791978354083
GO:0008301	DNA bending activity	0.0092791978354083
GO:0021537	telencephalon development	0.0092791978354083
GO:0006366	transcription from RNA polymerase II promoter	0.0092791978354083
GO:0016202	regulation of striated muscle development	0.0092791978354083
GO:0030879	mammary gland development	0.0092791978354083
GO:0045449	regulation of transcription	0.0092791978354083
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0092791978354083
GO:0001890	placenta development	0.0092791978354083
GO:0001707	mesoderm formation	0.0092791978354083
GO:0006350	transcription	0.0092791978354083
GO:0010468	regulation of gene expression	0.0092791978354083
GO:0048332	mesoderm morphogenesis	0.0092791978354083
GO:0001704	formation of primary germ layer	0.0092791978354083
GO:0031323	regulation of cellular metabolic process	0.0092791978354083
GO:0001756	somitogenesis	0.0092791978354083
GO:0009966	regulation of signal transduction	0.0092791978354083
GO:0042475	odontogenesis of dentine-containing teeth	0.0092791978354083
GO:0019222	regulation of metabolic process	0.00975554821880159
GO:0042476	odontogenesis	0.0109859357310693
GO:0007369	gastrulation	0.0109859357310693
GO:0003705	RNA polymerase II transcription factor activity, enhancer binding	0.0109859357310693
GO:0035282	segmentation	0.0109859357310693
GO:0030111	regulation of Wnt receptor signaling pathway	0.0109859357310693
GO:0017048	Rho GTPase binding	0.0121943856283063
GO:0030326	embryonic limb morphogenesis	0.0121943856283063
GO:0035113	embryonic appendage morphogenesis	0.0121943856283063
GO:0060173	limb development	0.0121943856283063
GO:0035107	appendage morphogenesis	0.0121943856283063
GO:0035108	limb morphogenesis	0.0121943856283063
GO:0048736	appendage development	0.0121943856283063
GO:0048523	negative regulation of cellular process	0.0121943856283063
GO:0048513	organ development	0.0121943856283063
GO:0007165	signal transduction	0.0125066031817345
GO:0048519	negative regulation of biological process	0.0125066031817345
GO:0030217	T cell differentiation	0.0125066031817345
GO:0019210	kinase inhibitor activity	0.0125498106132522
GO:0007498	mesoderm development	0.0128837133747608
GO:0030900	forebrain development	0.0129505224931683
GO:0048732	gland development	0.0129505224931683
GO:0010467	gene expression	0.0129542926297452
GO:0007154	cell communication	0.0134703643460352
GO:0050794	regulation of cellular process	0.0141377050911073
GO:0009952	anterior/posterior pattern formation	0.0141377050911073
GO:0002376	immune system process	0.0141377050911073
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0145933288696284
GO:0030098	lymphocyte differentiation	0.0158719586635932
GO:0050789	regulation of biological process	0.0163276894908023
GO:0048729	tissue morphogenesis	0.0172664430450755
GO:0048731	system development	0.0173542383735299
GO:0017016	Ras GTPase binding	0.0178766619077496
GO:0031267	small GTPase binding	0.0190242123532425
GO:0003002	regionalization	0.0190242123532425
GO:0014706	striated muscle development	0.0190242123532425
GO:0065007	biological regulation	0.0190242123532425
GO:0002521	leukocyte differentiation	0.0190242123532425
GO:0048598	embryonic morphogenesis	0.0190242123532425
GO:0048869	cellular developmental process	0.0190242123532425
GO:0030154	cell differentiation	0.0190242123532425
GO:0009792	embryonic development ending in birth or egg hatching	0.0190242123532425
GO:0043009	chordate embryonic development	0.0190242123532425
GO:0051020	GTPase binding	0.0190999558344424
GO:0042110	T cell activation	0.0190999558344424
GO:0009968	negative regulation of signal transduction	0.0199991029523099
GO:0043122	regulation of I-kappaB kinase/NF-kappaB cascade	0.0204961650234922
GO:0048856	anatomical structure development	0.021355071101342
GO:0003682	chromatin binding	0.0218205910643405
GO:0019207	kinase regulator activity	0.0222756425717118
GO:0007389	pattern specification process	0.0223599827367818
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	0.0226196700769359
GO:0007420	brain development	0.023874740545571
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	0.023874740545571
GO:0007249	I-kappaB kinase/NF-kappaB cascade	0.023874740545571
GO:0007275	multicellular organismal development	0.0253138317106509
GO:0048646	anatomical structure formation	0.0256646725829836
GO:0046649	lymphocyte activation	0.0257031865783457
GO:0030097	hemopoiesis	0.0263935001485549
GO:0007166	cell surface receptor linked signal transduction	0.0270167344596765
GO:0007517	muscle development	0.0274262058508522
GO:0048534	hemopoietic or lymphoid organ development	0.0274262058508522
GO:0045321	leukocyte activation	0.0282232723868985
GO:0002520	immune system development	0.0282316155375702
GO:0045892	negative regulation of transcription, DNA-dependent	0.0311383540634779
GO:0001775	cell activation	0.0315401295149648
GO:0005667	transcription factor complex	0.0315401295149648
GO:0005515	protein binding	0.0315401295149648
GO:0045893	positive regulation of transcription, DNA-dependent	0.0328047451772009
GO:0007417	central nervous system development	0.0338734734758142
GO:0009790	embryonic development	0.0338734734758142
GO:0045941	positive regulation of transcription	0.0397697947150819
GO:0045935	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0406682165247854
GO:0016481	negative regulation of transcription	0.0406682165247854
GO:0009888	tissue development	0.041688517758191
GO:0019899	enzyme binding	0.041688517758191
GO:0016563	transcription activator activity	0.041688517758191
GO:0032502	developmental process	0.041688517758191
GO:0006355	regulation of transcription, DNA-dependent	0.041688517758191
GO:0045934	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0421147710934597
GO:0006351	transcription, DNA-dependent	0.0425998123255963
GO:0032774	RNA biosynthetic process	0.0425998123255963
GO:0003677	DNA binding	0.0436998503780613
GO:0009887	organ morphogenesis	0.0460300472641261
GO:0031325	positive regulation of cellular metabolic process	0.0460300472641261
GO:0007243	protein kinase cascade	0.0469932102717966
GO:0031324	negative regulation of cellular metabolic process	0.0472041534735815
GO:0009893	positive regulation of metabolic process	0.0480183820810827
GO:0004857	enzyme inhibitor activity	0.0485783853784669
GO:0032501	multicellular organismal process	0.0485783853784669

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><br>

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Cell Type

Ontology term	p-value	n
T cell	2.20e-43	25
pro-T cell	2.20e-43	25
mature alpha-beta T cell	3.25e-43	18
alpha-beta T cell	3.25e-43	18
immature T cell	3.25e-43	18
mature T cell	3.25e-43	18
immature alpha-beta T cell	3.25e-43	18
lymphoid lineage restricted progenitor cell	8.84e-30	52
lymphocyte	4.28e-29	53
common lymphoid progenitor	4.28e-29	53
CD8-positive, alpha-beta T cell	3.16e-28	11
nucleate cell	8.41e-28	55
CD4-positive, alpha-beta T cell	1.86e-19	6
nongranular leukocyte	1.65e-14	115
leukocyte	2.30e-13	136
hematopoietic lineage restricted progenitor cell	2.86e-11	120
naive T cell	2.19e-10	3
hematopoietic stem cell	2.65e-10	168
angioblastic mesenchymal cell	2.65e-10	168
single nucleate cell	4.27e-10	3
mononuclear cell	4.27e-10	3
natural killer cell	8.25e-10	3
pro-NK cell	8.25e-10	3
hematopoietic cell	2.06e-09	177
hematopoietic oligopotent progenitor cell	1.33e-07	161
hematopoietic multipotent progenitor cell	1.33e-07	161
regulatory T cell	1.56e-07	2
CD4-positive, CD25-positive, alpha-beta regulatory T cell	1.56e-07	2
naive regulatory T cell	1.56e-07	2

Uber Anatomy

Ontology term	p-value	n
blood	2.26e-12	15
haemolymphatic fluid	2.26e-12	15
organism substance	2.26e-12	15
thymus	1.82e-08	4
hemolymphoid system gland	1.82e-08	4
thymic region	1.82e-08	4
pharyngeal gland	1.82e-08	4
thymus primordium	1.82e-08	4
hemopoietic organ	7.13e-08	7
immune organ	7.13e-08	7

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.