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Coexpression cluster:C272

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Full id: C272_CD19_CD4_CD8_Whole_Peripheral_lymph_tonsil



Phase1 CAGE Peaks

  Short description
Hg19::chr10:111836795..111836820,+ p5@ADD3
Hg19::chr11:10562868..10562896,+ p1@ENST00000529979
Hg19::chr11:64511738..64511759,+ p@chr11:64511738..64511759
+
Hg19::chr11:64512273..64512337,- p3@RASGRP2
Hg19::chr11:94964744..94964758,+ p1@ENST00000540692
Hg19::chr12:103835454..103835475,- p4@C12orf42
Hg19::chr12:103835494..103835510,- p5@C12orf42
Hg19::chr12:12867280..12867310,+ p@chr12:12867280..12867310
+
Hg19::chr12:92539858..92539862,+ p1@uc001tca.2
Hg19::chr12:92539926..92539990,+ p1@ENST00000499685
Hg19::chr12:92540055..92540069,+ p@chr12:92540055..92540069
+
Hg19::chr13:103498907..103498922,- p@chr13:103498907..103498922
-
Hg19::chr15:75081804..75081827,- p@chr15:75081804..75081827
-
Hg19::chr15:89178835..89178856,+ p7@ISG20
Hg19::chr15:89178857..89178898,+ p3@ISG20
Hg19::chr17:26874766..26874781,- p5@UNC119
Hg19::chr17:38020516..38020544,- p5@IKZF3
Hg19::chr17:76128488..76128519,- p4@TMC6
Hg19::chr19:16482478..16482486,- p@chr19:16482478..16482486
-
Hg19::chr19:50004358..50004377,- p2@MIR150
Hg19::chr19:7413915..7413935,+ p@chr19:7413915..7413935
+
Hg19::chr1:157670686..157670730,- p2@FCRL3
Hg19::chr1:157670738..157670753,- p3@FCRL3
Hg19::chr1:207085241..207085281,- p@chr1:207085241..207085281
-
Hg19::chr1:207095279..207095310,- p1@FAIM3
Hg19::chr1:207095324..207095357,- p2@FAIM3
Hg19::chr1:207096529..207096554,- p5@FAIM3
Hg19::chr1:207096713..207096727,+ p@chr1:207096713..207096727
+
Hg19::chr20:57698436..57698458,+ +
p@chr20:57698436..57698458
Hg19::chr20:62266805..62266812,- p@chr20:62266805..62266812
-
Hg19::chr20:62273068..62273079,- p10@STMN3
Hg19::chr20:62273138..62273178,- p5@STMN3
Hg19::chr2:234327537..234327560,+ p6@DGKD
Hg19::chr3:32433154..32433217,+ p3@CMTM7
Hg19::chr3:71355163..71355209,- p5@FOXP1
Hg19::chr5:118668891..118668933,+ p5@TNFAIP8
Hg19::chr6:133084580..133084605,- p2@VNN2
Hg19::chr6:24936227..24936236,- p5@FAM65B
Hg19::chr6:26285304..26285323,- p12@HIST1H4H
Hg19::chr6:31540403..31540430,- p1@LOC100287329
Hg19::chr7:139929994..139930043,+ p@chr7:139929994..139930043
+
Hg19::chr7:99819057..99819097,+ p@chr7:99819057..99819097
+
Hg19::chr8:134511587..134511621,- p6@ST3GAL1
Hg19::chr9:36144997..36145021,- p@chr9:36144997..36145021
-
Hg19::chrX:134429952..134429971,- p3@ZNF75D
Hg19::chrX:78200673..78200687,- p@chrX:78200673..78200687
-
Hg19::chrX:78200857..78200909,+ p1@P2RY10


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


p.valueFDRnGenesnPathwayName
0.0001427065529831310.04516662401916093133T Cell Receptor Signaling Pathway (Wikipathways):WP69
7.05821870032124e-050.04467852437303344295IL-2 down reg. targets (Netpath):NetPath_14



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


No GOStat results

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 termp-valuen
lymphocyte1.33e-5553
common lymphoid progenitor1.33e-5553
lymphoid lineage restricted progenitor cell2.87e-5452
nucleate cell5.17e-5355
leukocyte1.94e-39136
nongranular leukocyte2.02e-37115
hematopoietic lineage restricted progenitor cell2.00e-30120
mature alpha-beta T cell2.36e-2918
alpha-beta T cell2.36e-2918
immature T cell2.36e-2918
mature T cell2.36e-2918
immature alpha-beta T cell2.36e-2918
hematopoietic stem cell4.84e-28168
angioblastic mesenchymal cell4.84e-28168
lymphocyte of B lineage6.02e-2724
pro-B cell6.02e-2724
hematopoietic cell1.34e-25177
hematopoietic oligopotent progenitor cell2.76e-24161
hematopoietic multipotent progenitor cell2.76e-24161
T cell1.15e-2325
pro-T cell1.15e-2325
B cell1.25e-2014
CD8-positive, alpha-beta T cell1.92e-1811
CD4-positive, alpha-beta T cell2.13e-116
intermediate monocyte3.79e-079
CD14-positive, CD16-positive monocyte3.79e-079
naive T cell9.73e-073
Uber Anatomy
Ontology termp-valuen
blood8.76e-1515
haemolymphatic fluid8.76e-1515
organism substance8.76e-1515
hemopoietic organ3.87e-087
immune organ3.87e-087
hematopoietic system1.05e-0798
blood island1.05e-0798
hemolymphoid system1.31e-07108
thymus4.83e-074
hemolymphoid system gland4.83e-074
thymic region4.83e-074
pharyngeal gland4.83e-074
thymus primordium4.83e-074


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)
MA0003.10.017388
MA0004.10.333048
MA0006.10.234536
MA0007.10.876808
MA0009.10.756713
MA0014.10.597102
MA0017.10.312079
MA0019.10.298267
MA0024.10.590327
MA0025.10.982453
MA0027.11.7662
MA0028.10.0460597
MA0029.10.216921
MA0030.10.602396
MA0031.12.21548
MA0038.10.245663
MA0040.10.22078
MA0041.10.653748
MA0042.10.567488
MA0043.10.757231
MA0046.10.267991
MA0048.11.7409
MA0050.10.132387
MA0051.10.0682529
MA0052.10.635267
MA0055.10.560601
MA0056.10
MA0057.10.289703
MA0058.10.187307
MA0059.10.185595
MA0060.10.245515
MA0061.10.441038
MA0063.10
MA0066.10.899742
MA0067.10.529198
MA0068.10.101199
MA0069.10.732638
MA0070.10.257372
MA0071.10.0556134
MA0072.10.707234
MA0073.10.966412
MA0074.10.51581
MA0076.10.98182
MA0077.10.694833
MA0078.10.729893
MA0081.11.26097
MA0083.10.281174
MA0084.10.695499
MA0087.10.703294
MA0088.10.219244
MA0089.10
MA0090.10.229679
MA0091.10.610215
MA0092.10.816938
MA0093.10.420362
MA0095.10
MA0098.10
MA0100.10.075437
MA0101.10.117887
MA0103.11.19122
MA0105.10.788969
MA0106.10.0870163
MA0107.10.125877
MA0108.20.967713
MA0109.10
MA0111.10.470228
MA0113.10.313585
MA0114.10.575644
MA0115.10.464275
MA0116.10.408271
MA0117.10.303182
MA0119.10.0129611
MA0122.10.322548
MA0124.10.429905
MA0125.10.362554
MA0130.10
MA0131.10.384838
MA0132.10
MA0133.10
MA0135.10.297838
MA0136.11.90944
MA0139.10.150236
MA0140.10.44418
MA0141.10.183298
MA0142.10.150759
MA0143.11.59314
MA0144.10.197368
MA0145.10.1252
MA0146.10.226882
MA0147.11.17617
MA0148.11.04091
MA0149.10.0514353
MA0062.21.62199
MA0035.20.44283
MA0039.25.26493
MA0138.20.362512
MA0002.20.717689
MA0137.20.277891
MA0104.20.567911
MA0047.20.988232
MA0112.20.928748
MA0065.20.533795
MA0150.10.0879472
MA0151.10
MA0152.10.208064
MA0153.10.349438
MA0154.10.763515
MA0155.12.85041
MA0156.12.73457
MA0157.11.95087
MA0158.10
MA0159.10.422206
MA0160.10.0477329
MA0161.10
MA0162.10.185583
MA0163.10.353492
MA0164.11.64551
MA0080.22.5118
MA0018.20.295242
MA0099.20.0571009
MA0079.22.26551
MA0102.20.729507
MA0258.10.474019
MA0259.10.448852
MA0442.10



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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
BCL11A#53335116.639659705099525.56664771744241e-072.57473481382626e-05
BCLAF1#977473.224862410018150.00553807199974510.0250700317099986
CHD2#1106102.200855922152520.0130322744598420.0462385416602609
EBF1#1879193.600486597549172.70249283007159e-071.39105790379422e-05
ELF1#1997201.811956578215970.002962197311299230.0157897680291318
GATA1#262392.596654750940510.006727721148173810.0285950052496388
MEF2A#4205114.386713617150742.88179123592645e-050.000603754051933645
MEF2C#420887.031719913638141.58699131059788e-050.000371123568041944
NFKB1#4790232.685648058648051.61968458039418e-066.14673829548646e-05
PAX5#5079141.98667909439340.007381490951806610.0305047298795398
PBX3#509083.730129819020280.001195053091432750.00810718738656347
POLR2A#5430411.873310217848536.97304015138524e-095.43070350761016e-07
POU2F2#5452163.099957126040012.33354936079437e-050.000509115441178197
RAD21#5885102.203198701160920.01294132403334750.0465179466776382
RDBP#793639.806706637661160.003603461139133730.0182424565152684
SPI1#6688254.364001866235491.34287519443163e-111.6558269472402e-09
SREBF2#6721327.88999547306470.0001790788414701220.0021719678462778
TAF1#6872251.778216109438990.0007179730170939880.00573669833465527
TBP#6908221.735084151406820.002814118596580680.0154037595444596
TCF12#6938122.715182528217810.001077559157677460.00760862692641989
ZEB1#693593.233955067189250.001557425405251390.00988850093616934



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