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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>

Cell Type
Ontology termp-valuen
T cell2.20e-4325
pro-T cell2.20e-4325
mature alpha-beta T cell3.25e-4318
alpha-beta T cell3.25e-4318
immature T cell3.25e-4318
mature T cell3.25e-4318
immature alpha-beta T cell3.25e-4318
lymphoid lineage restricted progenitor cell8.84e-3052
lymphocyte4.28e-2953
common lymphoid progenitor4.28e-2953
CD8-positive, alpha-beta T cell3.16e-2811
nucleate cell8.41e-2855
CD4-positive, alpha-beta T cell1.86e-196
nongranular leukocyte1.65e-14115
leukocyte2.30e-13136
hematopoietic lineage restricted progenitor cell2.86e-11120
naive T cell2.19e-103
hematopoietic stem cell2.65e-10168
angioblastic mesenchymal cell2.65e-10168
single nucleate cell4.27e-103
mononuclear cell4.27e-103
natural killer cell8.25e-103
pro-NK cell8.25e-103
hematopoietic cell2.06e-09177
hematopoietic oligopotent progenitor cell1.33e-07161
hematopoietic multipotent progenitor cell1.33e-07161
regulatory T cell1.56e-072
CD4-positive, CD25-positive, alpha-beta regulatory T cell1.56e-072
naive regulatory T cell1.56e-072
Uber Anatomy
Ontology termp-valuen
blood2.26e-1215
haemolymphatic fluid2.26e-1215
organism substance2.26e-1215
thymus1.82e-084
hemolymphoid system gland1.82e-084
thymic region1.82e-084
pharyngeal gland1.82e-084
thymus primordium1.82e-084
hemopoietic organ7.13e-087
immune organ7.13e-087


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)
MA0003.10.0137961
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.10.187674
MA0017.10.991615
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.382278
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.0407081
MA0056.10
MA0057.10.744639
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.10.198335
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.946606
MA0069.10.958358
MA0070.10.947018
MA0071.11.39306
MA0072.10.942461
MA0073.10.887754
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.538456
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.332048
MA0105.10.340955
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.11.14351
MA0113.10.665691
MA0114.10.741402
MA0115.11.21667
MA0116.10.760835
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.11.491
MA0139.10.186511
MA0140.10.564957
MA0141.11.04059
MA0142.10.777365
MA0143.10.66587
MA0144.10.708913
MA0145.10.276317
MA0146.10.0610556
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.21.07166
MA0035.20.564239
MA0039.20.0553061
MA0138.20.704862
MA0002.20.611548
MA0137.20.95459
MA0104.20.223944
MA0047.20.636643
MA0112.20.0758925
MA0065.20.282161
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.335384
MA0155.10.534073
MA0156.11.7082
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.10.25944
MA0163.10.942271
MA0164.10.678332
MA0080.20.911393
MA0018.20.650405
MA0099.20.572
MA0079.20.263996
MA0102.21.51913
MA0258.10.245543
MA0259.10.289405
MA0442.10



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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