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Difference between revisions of "Coexpression cluster:C527"

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|ontology_enrichment_uberon=
 
|ontology_enrichment_uberon=
 
|pathway_enrichment=6.91014427352572e-35;1.7163710643638e-32;14;92;Ribosome (KEGG):03010!0.000120664641274534;0.00763807179267799;3;188;TNF-alpha/NF-kB Signaling Pathway (Wikipathways):WP231!8.13446002068154e-35;1.7163710643638e-32;14;93;Cytoplasmic Ribosomal Proteins (Wikipathways):WP477!1.20547531912621e-30;1.27177646167815e-28;15;296;Metabolism of proteins (Reactome):REACT_17015!1.71339533049491e-33;2.7114481105082e-31;14;114;Regulation of beta-cell development (Reactome):REACT_13698!2.64892183772546e-28;2.3953821761146e-26;15;421;Gene Expression (Reactome):REACT_71!3.84782720500134e-27;3.04459327595731e-25;14;312;Diabetes pathways (Reactome):REACT_15380!4.86641825718034e-32;6.16088551359031e-30;14;143;Influenza Infection (Reactome):REACT_6167!2.93027540557533e-13;2.06096036858798e-11;10;728;TNF alpha/NF-kB up reg. targets (Netpath):NetPath_9!8.39347489466827e-36;5.31306960832501e-33;15;138;{RPS27A,138} (Static Module):NA
 
|pathway_enrichment=6.91014427352572e-35;1.7163710643638e-32;14;92;Ribosome (KEGG):03010!0.000120664641274534;0.00763807179267799;3;188;TNF-alpha/NF-kB Signaling Pathway (Wikipathways):WP231!8.13446002068154e-35;1.7163710643638e-32;14;93;Cytoplasmic Ribosomal Proteins (Wikipathways):WP477!1.20547531912621e-30;1.27177646167815e-28;15;296;Metabolism of proteins (Reactome):REACT_17015!1.71339533049491e-33;2.7114481105082e-31;14;114;Regulation of beta-cell development (Reactome):REACT_13698!2.64892183772546e-28;2.3953821761146e-26;15;421;Gene Expression (Reactome):REACT_71!3.84782720500134e-27;3.04459327595731e-25;14;312;Diabetes pathways (Reactome):REACT_15380!4.86641825718034e-32;6.16088551359031e-30;14;143;Influenza Infection (Reactome):REACT_6167!2.93027540557533e-13;2.06096036858798e-11;10;728;TNF alpha/NF-kB up reg. targets (Netpath):NetPath_9!8.39347489466827e-36;5.31306960832501e-33;15;138;{RPS27A,138} (Static Module):NA
 +
|tf_chipseq_enrich=ATF3#467;5:6.6068160370614:0.000688705274230141:0.00555297538294772!BCL3#602;5:10.1609125893348:9.3771989931945e-05:0.00136152549096377!BCLAF1#9774;9:11.4631663818292:1.64938010205014e-08:1.19541713031239e-06!BRCA1#672;9:10.6857691640596:3.02685895110408e-08:2.0487499805208e-06!CCNT2#905;9:3.35445965839198:0.000436791244356075:0.00407194865386986!CEBPB#1051;7:3.28223725769257:0.00300615955226439:0.0159743715009128!CHD2#1106;8:4.86777545134911:8.28678044676969e-05:0.00124527059435997!CTCF#10664;10:3.15309198416178:0.000272288389173733:0.00290415921945624!E2F1#1869;13:3.7527093996136:1.07464925288554e-06:4.47509144027565e-05!E2F4#1874;10:7.45180018546144:1.08332875404144e-07:6.31724018667414e-06!E2F6#1876;11:3.24639488521596:7.30785949477464e-05:0.00114753501394492!EGR1#1958;11:3.22764529664185:7.72881844422271e-05:0.00119160033878975!ELF1#1997;15:3.75714525777136:3.01093513305367e-08:2.04326870929819e-06!ELK4#2005;12:11.4604811706833:1.36979533911823e-11:1.68504187776406e-09!EP300#2033;9:3.58620444329464:0.000260364373300338:0.0027912332973839!ETS1#2113;12:6.86736065096636:5.21732437064727e-09:4.18182762813531e-07!FOSL2#2355;6:5.97536491925707:0.000297459514596548:0.00310477455975904!GABPB1#2553;15:6.23619162016074:1.85944138102383e-11:2.24247342254905e-09!GATA1#2623;7:5.58365629450606:0.000118669714610486:0.00161146097051158!GATA3#2625;4:6.40859208404847:0.00294238410040412:0.0156985774233515!GTF2B#2959;14:26.3066834753258:5.32024204737651e-19:1.25995637003618e-16!GTF2F1#2962;15:11.2408772441979:3.06871838319925e-15:5.52575653832667e-13!HEY1#23462;15:3.56480386156386:6.42357439240872e-08:3.95794504996327e-06!HMGN3#9324;7:3.36763729785024:0.00258933236757512:0.0143204449871414!IRF1#3659;15:6.73867390020344:5.9464769948207e-12:7.68618949086731e-10!IRF4#3662;5:6.44544490786592:0.000770512874507435:0.0060409574431861!JUND#3727;12:4.93740984132072:2.2224306781037e-07:1.18061260218959e-05!KAT2A#2648;3:108.721764705882:2.8307392927591e-06:9.7699795438357e-05!MAX#4149;14:5.31386924271175:1.9579146541289e-09:1.69133704352827e-07!MEF2A#4205;5:5.51271497342472:0.00155536061245248:0.00987779306804042!MEF2C#4208;3:7.29023902811013:0.00747486284700268:0.0308247335101521!MXI1#4601;9:5.27377321522551:1.18160458251851e-05:0.000299020113868792!MYC#4609;15:4.60789576906712:1.5591047504541e-09:1.37526470466787e-07!NFKB1#4790;15:4.84240890370044:7.5609025131929e-10:7.15913959723802e-08!NR2C2#7182;7:13.4295456668639:3.76445247482019e-07:1.84840456990007e-05!NRF1#4899;9:6.4642655899646:2.18388258131197e-06:7.83788704156842e-05!PAX5#5079;14:5.49258337861704:1.25245751600589e-09:1.14041334362807e-07!POLR2A#5430;15:1.89481162637477:0.00045412137082633:0.00422107350015406!POU2F2#5452;13:6.96350663239134:5.21432763147211e-10:5.02843179596783e-08!RDBP#7936;6:54.2253190553029:8.74207406264564e-10:8.18846164151254e-08!REST#5978;11:6.24413622808284:1.00510740280017e-07:5.90064148628705e-06!RFX5#5993;8:5.66960509515063:2.75176813312189e-05:0.00058508125418387!RXRA#6256;7:8.26601882199605:9.47656767003136e-06:0.000251837977325803!SIN3A#25942;16:5.09071503700248:2.6091191843489e-11:3.07208341030682e-09!SIX5#147912;12:12.0612108391475:7.52951998920128e-12:9.53182470487506e-10!SP1#6667;17:5.6983813781409:1.41488962347743e-13:2.17949347177522e-11!SPI1#6688;12:5.79128718248663:3.65832040474177e-08:2.43047916508159e-06!SRF#6722;11:8.92758593434388:2.36843848361268e-09:2.01759662960869e-07!STAT1#6772;6:7.30820735195266:9.87071454255867e-05:0.00139083588250173!STAT2#6773;3:11.5171360917248:0.00208062454216598:0.012052043625029!TAF1#6872;15:2.94974672271643:9.6669521918546e-07:4.10576177293657e-05!TAF7#6879;14:9.41546892170205:8.03861479186331e-13:1.14691924897187e-10!TBP#6908;15:3.27068001802622:2.21275576192132e-07:1.1760712418285e-05!TCF12#6938;10:6.25556758952142:5.62154679880538e-07:2.59667724953753e-05!TCF7L2#6934;7:4.43477858482126:0.000498305774925007:0.0044032961187404!TRIM28#10155;7:7.65492207746104:1.56494839226159e-05:0.00036646108775652!USF1#7391;12:4.49047007802915:6.43363093087209e-07:2.92013029460821e-05!YY1#7528;14:4.04449355870318:7.60115579236282e-08:4.57290961865542e-06!ZBTB33#10009;6:11.1757853046992:9.06703361730025e-06:0.00024224914913206!ZEB1#6935;7:6.95406024251806:2.9174422587585e-05:0.000610121650105084!ZNF143#7702;9:7.14752288059124:9.38784177277639e-07:4.0215619643437e-05!ZNF263#10127;8:3.86910194682855:0.000418295010921723:0.00391384273836712
 
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}}
 
}}

Revision as of 03:25, 5 September 2012


Full id: C527_CD4_CD8_CD19_CD34_CD133_skeletal_Mesenchymal



Phase1 CAGE Peaks

  Short description
Hg19::chr11:118889041..118889062,- p1@RPS25
Hg19::chr11:17099202..17099230,- p1@RPS13
Hg19::chr11:64889592..64889615,- p1@FAU
Hg19::chr11:75110555..75110574,+ p1@RPS3
Hg19::chr11:809961..809977,+ p1@RPLP2
Hg19::chr17:17287371..17287378,- p1@ENST00000392730
p1@ENST00000396469
Hg19::chr19:39926576..39926593,- p1@RPS16
Hg19::chr19:49999681..49999705,+ p1@RPS11
Hg19::chr1:153963227..153963249,+ p1@RPS27
Hg19::chr2:207024612..207024634,+ p1@EEF1B2
Hg19::chr3:23958632..23958651,+ p2@RPL15
Hg19::chr5:81574161..81574189,- p1@RPS23
Hg19::chr6:133135704..133135711,+ p1@RPS12
Hg19::chr6:153603882..153603892,- p1@ENST00000492974
Hg19::chr8:56987061..56987067,- p1@RPS20
Hg19::chr8:99057769..99057776,- p1@RPL30
Hg19::chr9:19380220..19380245,- p1@RPS6


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
6.91014427352572e-351.7163710643638e-321492Ribosome (KEGG):03010
0.0001206646412745340.007638071792677993188TNF-alpha/NF-kB Signaling Pathway (Wikipathways):WP231
8.13446002068154e-351.7163710643638e-321493Cytoplasmic Ribosomal Proteins (Wikipathways):WP477
1.20547531912621e-301.27177646167815e-2815296Metabolism of proteins (Reactome):REACT_17015
1.71339533049491e-332.7114481105082e-3114114Regulation of beta-cell development (Reactome):REACT_13698
2.64892183772546e-282.3953821761146e-2615421Gene Expression (Reactome):REACT_71
3.84782720500134e-273.04459327595731e-2514312Diabetes pathways (Reactome):REACT_15380
4.86641825718034e-326.16088551359031e-3014143Influenza Infection (Reactome):REACT_6167
2.93027540557533e-132.06096036858798e-1110728TNF alpha/NF-kB up reg. targets (Netpath):NetPath_9
8.39347489466827e-365.31306960832501e-3315138{RPS27A,138} (Static Module):NA



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 IDGO nameFDR corrected p-value
GO:0005830cytosolic ribosome (sensu Eukaryota)1.53717595287726e-28
GO:0005843cytosolic small ribosomal subunit (sensu Eukaryota)2.22911714947442e-26
GO:0044445cytosolic part6.2977514458212e-24
GO:0033279ribosomal subunit3.58722918760839e-23
GO:0003735structural constituent of ribosome1.77922535769504e-21
GO:0006412translation1.77922535769504e-21
GO:0005840ribosome4.47164198772868e-21
GO:0015935small ribosomal subunit5.31479479118266e-21
GO:0009059macromolecule biosynthetic process5.89884984362245e-20
GO:0030529ribonucleoprotein complex1.92857280141859e-19
GO:0005829cytosol1.07577653929725e-18
GO:0044249cellular biosynthetic process1.1174865310891e-18
GO:0009058biosynthetic process3.59966244039392e-17
GO:0003723RNA binding5.75583651685696e-16
GO:0032991macromolecular complex3.09290771796598e-14
GO:0043232intracellular non-membrane-bound organelle6.0665711660925e-14
GO:0043228non-membrane-bound organelle6.0665711660925e-14
GO:0044444cytoplasmic part3.20273086792488e-13
GO:0010467gene expression4.02078380200549e-12
GO:0044267cellular protein metabolic process5.4410593064807e-12
GO:0044260cellular macromolecule metabolic process6.28142478439238e-12
GO:0019538protein metabolic process1.01562353823208e-11
GO:0005737cytoplasm3.82952380538418e-10
GO:0043234protein complex4.26009319663417e-09
GO:0044446intracellular organelle part8.06342440604049e-09
GO:0044422organelle part8.06342440604049e-09
GO:0003676nucleic acid binding6.04178419965562e-08
GO:0043170macromolecule metabolic process1.2447166993263e-07
GO:0005842cytosolic large ribosomal subunit (sensu Eukaryota)1.3911532841307e-06
GO:0043229intracellular organelle2.24095090694968e-06
GO:0043226organelle2.24095090694968e-06
GO:0044237cellular metabolic process3.93747758510936e-06
GO:0044238primary metabolic process4.42357966828784e-06
GO:0044424intracellular part5.74349273900959e-06
GO:0015934large ribosomal subunit2.32336017423447e-05
GO:0005622intracellular6.70743009689029e-05
GO:0006414translational elongation0.000567391746485201
GO:0043284biopolymer biosynthetic process0.00150908021917965
GO:0005515protein binding0.0104877819644371
GO:0042593glucose homeostasis0.0109937085211293
GO:0033500carbohydrate homeostasis0.0109937085211293
GO:0044464cell part0.0127976687206917
GO:0005853eukaryotic translation elongation factor 1 complex0.0156976823336595
GO:0019843rRNA binding0.0229546190419338
GO:0003746translation elongation factor activity0.0329280001100885



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



Cell Type
Ontology termp-valuen
lymphocyte4.47e-2153
common lymphoid progenitor4.47e-2153
lymphoid lineage restricted progenitor cell9.10e-2152
nongranular leukocyte6.97e-19119
hematopoietic stem cell1.15e-15172
angioblastic mesenchymal cell1.15e-15172
hematopoietic lineage restricted progenitor cell1.38e-15124
hematopoietic cell7.64e-15182
leukocyte9.51e-15140
native cell5.96e-14722
hematopoietic oligopotent progenitor cell1.25e-13165
hematopoietic multipotent progenitor cell1.25e-13165
mature alpha-beta T cell4.88e-1218
alpha-beta T cell4.88e-1218
immature T cell4.88e-1218
mature T cell4.88e-1218
immature alpha-beta T cell4.88e-1218
T cell4.29e-1125
pro-T cell4.29e-1125
animal cell1.19e-09679
eukaryotic cell1.19e-09679
lymphocyte of B lineage1.40e-0924
pro-B cell1.40e-0924
somatic cell1.40e-09591
B cell2.45e-0914
CD8-positive, alpha-beta T cell2.69e-0811
stem cell3.69e-08444
CD14-positive, CD16-negative classical monocyte4.42e-0842
multi fate stem cell3.27e-07430
classical monocyte4.29e-0745
somatic stem cell5.93e-07436


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


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

TF#promotersEnrichmentp-valueq-value
ATF3#46756.60681603706140.0006887052742301410.00555297538294772
BCL3#602510.16091258933489.3771989931945e-050.00136152549096377
BCLAF1#9774911.46316638182921.64938010205014e-081.19541713031239e-06
BRCA1#672910.68576916405963.02685895110408e-082.0487499805208e-06
CCNT2#90593.354459658391980.0004367912443560750.00407194865386986
CEBPB#105173.282237257692570.003006159552264390.0159743715009128
CHD2#110684.867775451349118.28678044676969e-050.00124527059435997
CTCF#10664103.153091984161780.0002722883891737330.00290415921945624
E2F1#1869133.75270939961361.07464925288554e-064.47509144027565e-05
E2F4#1874107.451800185461441.08332875404144e-076.31724018667414e-06
E2F6#1876113.246394885215967.30785949477464e-050.00114753501394492
EGR1#1958113.227645296641857.72881844422271e-050.00119160033878975
ELF1#1997153.757145257771363.01093513305367e-082.04326870929819e-06
ELK4#20051211.46048117068331.36979533911823e-111.68504187776406e-09
EP300#203393.586204443294640.0002603643733003380.0027912332973839
ETS1#2113126.867360650966365.21732437064727e-094.18182762813531e-07
FOSL2#235565.975364919257070.0002974595145965480.00310477455975904
GABPB1#2553156.236191620160741.85944138102383e-112.24247342254905e-09
GATA1#262375.583656294506060.0001186697146104860.00161146097051158
GATA3#262546.408592084048470.002942384100404120.0156985774233515
GTF2B#29591426.30668347532585.32024204737651e-191.25995637003618e-16
GTF2F1#29621511.24087724419793.06871838319925e-155.52575653832667e-13
HEY1#23462153.564803861563866.42357439240872e-083.95794504996327e-06
HMGN3#932473.367637297850240.002589332367575120.0143204449871414
IRF1#3659156.738673900203445.9464769948207e-127.68618949086731e-10
IRF4#366256.445444907865920.0007705128745074350.0060409574431861
JUND#3727124.937409841320722.2224306781037e-071.18061260218959e-05
KAT2A#26483108.7217647058822.8307392927591e-069.7699795438357e-05
MAX#4149145.313869242711751.9579146541289e-091.69133704352827e-07
MEF2A#420555.512714973424720.001555360612452480.00987779306804042
MEF2C#420837.290239028110130.007474862847002680.0308247335101521
MXI1#460195.273773215225511.18160458251851e-050.000299020113868792
MYC#4609154.607895769067121.5591047504541e-091.37526470466787e-07
NFKB1#4790154.842408903700447.5609025131929e-107.15913959723802e-08
NR2C2#7182713.42954566686393.76445247482019e-071.84840456990007e-05
NRF1#489996.46426558996462.18388258131197e-067.83788704156842e-05
PAX5#5079145.492583378617041.25245751600589e-091.14041334362807e-07
POLR2A#5430151.894811626374770.000454121370826330.00422107350015406
POU2F2#5452136.963506632391345.21432763147211e-105.02843179596783e-08
RDBP#7936654.22531905530298.74207406264564e-108.18846164151254e-08
REST#5978116.244136228082841.00510740280017e-075.90064148628705e-06
RFX5#599385.669605095150632.75176813312189e-050.00058508125418387
RXRA#625678.266018821996059.47656767003136e-060.000251837977325803
SIN3A#25942165.090715037002482.6091191843489e-113.07208341030682e-09
SIX5#1479121212.06121083914757.52951998920128e-129.53182470487506e-10
SP1#6667175.69838137814091.41488962347743e-132.17949347177522e-11
SPI1#6688125.791287182486633.65832040474177e-082.43047916508159e-06
SRF#6722118.927585934343882.36843848361268e-092.01759662960869e-07
STAT1#677267.308207351952669.87071454255867e-050.00139083588250173
STAT2#6773311.51713609172480.002080624542165980.012052043625029
TAF1#6872152.949746722716439.6669521918546e-074.10576177293657e-05
TAF7#6879149.415468921702058.03861479186331e-131.14691924897187e-10
TBP#6908153.270680018026222.21275576192132e-071.1760712418285e-05
TCF12#6938106.255567589521425.62154679880538e-072.59667724953753e-05
TCF7L2#693474.434778584821260.0004983057749250070.0044032961187404
TRIM28#1015577.654922077461041.56494839226159e-050.00036646108775652
USF1#7391124.490470078029156.43363093087209e-072.92013029460821e-05
YY1#7528144.044493558703187.60115579236282e-084.57290961865542e-06
ZBTB33#10009611.17578530469929.06703361730025e-060.00024224914913206
ZEB1#693576.954060242518062.9174422587585e-050.000610121650105084
ZNF143#770297.147522880591249.38784177277639e-074.0215619643437e-05
ZNF263#1012783.869101946828550.0004182950109217230.00391384273836712



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.