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Coexpression cluster:C1225

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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

p.valueFDRnGenesnPathwayName
8.30998363188652e-050.004383516365820142151Wnt signaling pathway (KEGG):04310
1.9318817157557e-050.0017954580611457273Adherens junction (KEGG):04520
3.70989802916306e-050.002348365452460222101Melanogenesis (KEGG):04916
0.0003894952439578360.01896542226348542327Pathways in cancer (KEGG):05200
1.39045983109694e-050.00176032214616872262Colorectal cancer (KEGG):05210
9.75241122157353e-060.00176032214616872252Endometrial cancer (KEGG):05213
2.8776320508186e-050.00227692636021022289Prostate cancer (KEGG):05215
2.98763831444955e-060.00176032214616872229Thyroid cancer (KEGG):05216
1.09210518403916e-050.00176032214616872255Basal cell carcinoma (KEGG):05217
1.21557119429462e-050.00176032214616872258Acute myeloid leukemia (KEGG):05221
1.98549864581673e-050.0017954580611457274Arrhythmogenic right ventricular cardiomyopathy (ARVC) (KEGG):05412
3.56387285970187e-050.00234836545246022299Wnt Signaling Pathway and Pluripotency (Wikipathways):WP399
4.56530451706939e-050.002627125235731752112{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

GO IDGO nameFDR corrected p-value
GO:0016055Wnt receptor signaling pathway0.00732956552454962
GO:0021542dentate gyrus development0.00732956552454962
GO:0003702RNA polymerase II transcription factor activity0.0092791978354083
GO:0021766hippocampus development0.0092791978354083
GO:0048341paraxial mesoderm formation0.0092791978354083
GO:0048340paraxial mesoderm morphogenesis0.0092791978354083
GO:0006357regulation of transcription from RNA polymerase II promoter0.0092791978354083
GO:0043124negative regulation of I-kappaB kinase/NF-kappaB cascade0.0092791978354083
GO:0048339paraxial mesoderm development0.0092791978354083
GO:0021543pallium development0.0092791978354083
GO:0021761limbic system development0.0092791978354083
GO:0045843negative regulation of striated muscle development0.0092791978354083
GO:0005095GTPase inhibitor activity0.0092791978354083
GO:0008301DNA bending activity0.0092791978354083
GO:0021537telencephalon development0.0092791978354083
GO:0006366transcription from RNA polymerase II promoter0.0092791978354083
GO:0016202regulation of striated muscle development0.0092791978354083
GO:0030879mammary gland development0.0092791978354083
GO:0045449regulation of transcription0.0092791978354083
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0092791978354083
GO:0001890placenta development0.0092791978354083
GO:0001707mesoderm formation0.0092791978354083
GO:0006350transcription0.0092791978354083
GO:0010468regulation of gene expression0.0092791978354083
GO:0048332mesoderm morphogenesis0.0092791978354083
GO:0001704formation of primary germ layer0.0092791978354083
GO:0031323regulation of cellular metabolic process0.0092791978354083
GO:0001756somitogenesis0.0092791978354083
GO:0009966regulation of signal transduction0.0092791978354083
GO:0042475odontogenesis of dentine-containing teeth0.0092791978354083
GO:0019222regulation of metabolic process0.00975554821880159
GO:0042476odontogenesis0.0109859357310693
GO:0007369gastrulation0.0109859357310693
GO:0003705RNA polymerase II transcription factor activity, enhancer binding0.0109859357310693
GO:0035282segmentation0.0109859357310693
GO:0030111regulation of Wnt receptor signaling pathway0.0109859357310693
GO:0017048Rho GTPase binding0.0121943856283063
GO:0030326embryonic limb morphogenesis0.0121943856283063
GO:0035113embryonic appendage morphogenesis0.0121943856283063
GO:0060173limb development0.0121943856283063
GO:0035107appendage morphogenesis0.0121943856283063
GO:0035108limb morphogenesis0.0121943856283063
GO:0048736appendage development0.0121943856283063
GO:0048523negative regulation of cellular process0.0121943856283063
GO:0048513organ development0.0121943856283063
GO:0007165signal transduction0.0125066031817345
GO:0048519negative regulation of biological process0.0125066031817345
GO:0030217T cell differentiation0.0125066031817345
GO:0019210kinase inhibitor activity0.0125498106132522
GO:0007498mesoderm development0.0128837133747608
GO:0030900forebrain development0.0129505224931683
GO:0048732gland development0.0129505224931683
GO:0010467gene expression0.0129542926297452
GO:0007154cell communication0.0134703643460352
GO:0050794regulation of cellular process0.0141377050911073
GO:0009952anterior/posterior pattern formation0.0141377050911073
GO:0002376immune system process0.0141377050911073
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0145933288696284
GO:0030098lymphocyte differentiation0.0158719586635932
GO:0050789regulation of biological process0.0163276894908023
GO:0048729tissue morphogenesis0.0172664430450755
GO:0048731system development0.0173542383735299
GO:0017016Ras GTPase binding0.0178766619077496
GO:0031267small GTPase binding0.0190242123532425
GO:0003002regionalization0.0190242123532425
GO:0014706striated muscle development0.0190242123532425
GO:0065007biological regulation0.0190242123532425
GO:0002521leukocyte differentiation0.0190242123532425
GO:0048598embryonic morphogenesis0.0190242123532425
GO:0048869cellular developmental process0.0190242123532425
GO:0030154cell differentiation0.0190242123532425
GO:0009792embryonic development ending in birth or egg hatching0.0190242123532425
GO:0043009chordate embryonic development0.0190242123532425
GO:0051020GTPase binding0.0190999558344424
GO:0042110T cell activation0.0190999558344424
GO:0009968negative regulation of signal transduction0.0199991029523099
GO:0043122regulation of I-kappaB kinase/NF-kappaB cascade0.0204961650234922
GO:0048856anatomical structure development0.021355071101342
GO:0003682chromatin binding0.0218205910643405
GO:0019207kinase regulator activity0.0222756425717118
GO:0007389pattern specification process0.0223599827367818
GO:0000122negative regulation of transcription from RNA polymerase II promoter0.0226196700769359
GO:0007420brain development0.023874740545571
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.023874740545571
GO:0007249I-kappaB kinase/NF-kappaB cascade0.023874740545571
GO:0007275multicellular organismal development0.0253138317106509
GO:0048646anatomical structure formation0.0256646725829836
GO:0046649lymphocyte activation0.0257031865783457
GO:0030097hemopoiesis0.0263935001485549
GO:0007166cell surface receptor linked signal transduction0.0270167344596765
GO:0007517muscle development0.0274262058508522
GO:0048534hemopoietic or lymphoid organ development0.0274262058508522
GO:0045321leukocyte activation0.0282232723868985
GO:0002520immune system development0.0282316155375702
GO:0045892negative regulation of transcription, DNA-dependent0.0311383540634779
GO:0001775cell activation0.0315401295149648
GO:0005667transcription factor complex0.0315401295149648
GO:0005515protein binding0.0315401295149648
GO:0045893positive regulation of transcription, DNA-dependent0.0328047451772009
GO:0007417central nervous system development0.0338734734758142
GO:0009790embryonic development0.0338734734758142
GO:0045941positive regulation of transcription0.0397697947150819
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0406682165247854
GO:0016481negative regulation of transcription0.0406682165247854
GO:0009888tissue development0.041688517758191
GO:0019899enzyme binding0.041688517758191
GO:0016563transcription activator activity0.041688517758191
GO:0032502developmental process0.041688517758191
GO:0006355regulation of transcription, DNA-dependent0.041688517758191
GO:0045934negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0421147710934597
GO:0006351transcription, DNA-dependent0.0425998123255963
GO:0032774RNA biosynthetic process0.0425998123255963
GO:0003677DNA binding0.0436998503780613
GO:0009887organ morphogenesis0.0460300472641261
GO:0031325positive regulation of cellular metabolic process0.0460300472641261
GO:0007243protein kinase cascade0.0469932102717966
GO:0031324negative regulation of cellular metabolic process0.0472041534735815
GO:0009893positive regulation of metabolic process0.0480183820810827
GO:0004857enzyme inhibitor activity0.0485783853784669
GO:0032501multicellular organismal process0.0485783853784669



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>

Uber Anatomy
Ontology termp-valuen
hematopoietic system3.26e-12102
blood island3.26e-12102
adult organism7.36e-12115
hemolymphoid system5.99e-11112
blood1.55e-0915
haemolymphatic fluid1.55e-0915
organism substance1.55e-0915


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

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

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

This analysis result is provided for C0 - C305 clusters.

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