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Coexpression cluster:C426: Difference between revisions

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{{Coexpression_clusters
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regulation of apoptosis!0.0012626724630421!7128;4790$GO:0043069!negative regulation of programmed cell death!0.0012626724630421!7128;4790$GO:0042981!regulation of apoptosis!0.00476396946754751!7128;4790$GO:0043067!regulation of programmed cell death!0.00476396946754751!7128;4790$GO:0043124!negative regulation of I-kappaB kinase/NF-kappaB cascade!0.00488601741722185!7128$GO:0006915!apoptosis!0.00592300066246309!7128;4790$GO:0012501!programmed cell death!0.00592300066246309!7128;4790$GO:0016265!death!0.00592300066246309!7128;4790$GO:0008219!cell death!0.00592300066246309!7128;4790$GO:0048523!negative regulation of cellular process!0.00836632581832125!7128;4790$GO:0048519!negative regulation of biological process!0.00836632581832125!7128;4790$GO:0048468!cell development!0.00852704727292275!7128;4790$GO:0048869!cellular developmental process!0.0156990917752577!7128;4790$GO:0030154!cell differentiation!0.0156990917752577!7128;4790$GO:0009968!negative regulation of signal transduction!0.030993977189682!7128$GO:0043122!regulation of I-kappaB kinase/NF-kappaB cascade!0.030993977189682!7128$GO:0007249!I-kappaB kinase/NF-kappaB cascade!0.0376570466175902!7128$GO:0032502!developmental process!0.0423912959518589!7128;4790$GO:0003677!DNA binding!0.0441894487628634!7128;4790|id=C426|ontology_enrichment_celltype=CL:0000738!3.95e-58!136;CL:0000988!6.93e-43!177;CL:0002031!1.80e-42!120;CL:0000037!2.34e-42!168;CL:0000566!2.34e-42!168;CL:0002087!1.48e-41!115;CL:0000860!6.40e-41!42;CL:0002057!6.40e-41!42;CL:0002032!1.01e-40!161;CL:0000837!1.01e-40!161;CL:0000766!4.32e-39!72;CL:0000473!2.91e-34!48;CL:0000234!2.91e-34!48;CL:0000557!7.56e-31!67;CL:0002009!3.94e-29!61;CL:0000839!8.15e-28!66;CL:0000763!3.02e-27!108;CL:0000049!3.02e-27!108;CL:0002194!1.03e-26!59;CL:0000576!1.03e-26!59;CL:0000040!1.03e-26!59;CL:0000559!1.03e-26!59;CL:0000134!1.67e-16!354;CL:0002320!1.08e-15!361;CL:0000325!1.11e-14!87;CL:0000094!3.32e-13!8;CL:0000219!7.21e-13!386;CL:0000838!2.06e-12!52;CL:0000542!4.84e-12!53;CL:0000051!4.84e-12!53;CL:0000081!1.95e-11!11;CL:0002242!2.42e-11!55;CL:0000048!5.60e-11!427;CL:0000723!6.20e-11!433;CL:0000034!8.15e-11!441;CL:0000624!1.71e-10!6;CL:0000080!2.75e-09!6;CL:0000791!8.66e-08!18;CL:0000789!8.66e-08!18;CL:0002420!8.66e-08!18;CL:0002419!8.66e-08!18;CL:0000790!8.66e-08!18;CL:0000453!8.98e-08!5;CL:0000084!4.28e-07!25;CL:0000827!4.28e-07!25|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0002390!1.35e-30!98;UBERON:0003061!1.35e-30!98;UBERON:0002193!1.68e-27!108;UBERON:0002371!1.24e-25!76;UBERON:0002405!1.44e-25!93;UBERON:0001474!8.32e-23!82;UBERON:0004765!1.21e-19!90;UBERON:0001434!1.76e-17!100;UBERON:0002384!1.36e-14!371;UBERON:0003081!7.37e-10!203;UBERON:0002204!6.15e-07!167|pathway_enrichment=4.19956876000442e-06;0.0026583270250828;2;59;NOD-like receptor signaling pathway (KEGG):04621!2.18716290008179e-05;0.00405227851947455;2;134;Measles (KEGG):05162!0.000770550915555693;0.0487758729546754;1;11;Osteopontin Signaling (Wikipathways):WP1434!2.38818258532104e-05;0.00405227851947455;2;140;Regulation of toll-like receptor signaling pathway (Wikipathways):WP1449!0.00056043011929242;0.0443440331890127;1;8;TFs Regulate miRNAs related to cardiac hypertrophy (Wikipathways):WP1559!4.31443715156972e-05;0.00455173119490606;2;188;TNF-alpha/NF-kB Signaling Pathway (Wikipathways):WP231!0.000319827473566556;0.0289215415382328;2;511;Signaling in Immune system (Reactome):REACT_6900!0.00064951693852861;0.0456826913431789;2;728;TNF alpha/NF-kB up reg. targets (Netpath):NetPath_9!3.20085191111734e-05;0.00405227851947455;2;162;TNF alpha/NF-kB down reg. targets (Netpath):NetPath_9!2.92938943019595e-05;0.00405227851947455;2;155;IL-1 up reg. targets 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05,0.098514,0.505382,0.0187224,0.0192914,0.00938199,0.421597,0.0555372,0.544336,0.0431443,0.0051251,2.59011e-05,0.00932376,0.162352,1.9032e-05,0.192882,0.162614,0.920474,0.445744,0.247632,0.055183,4.92102e-05,0.0718162,0.159039,0.578557,0.0100243,0.0115944,0.0723066|tfbs_overrepresentation_for_novel_motifs=0.0799767,0.0280497,0.0765276,0.155501,1.71306,0.469,0.204171,0.700835,0.422589,0.0101458,0.136211,0.23459,0.0561986,0.196345,0.210549,0.0676505,0.372343,0.150422,0.33879,0.196115,0.264528,0.173527,0.149707,0.45317,0.325988,0.251049,1.31683,0.453775,0.215908,0.0350552,0.123558,0.402677,0.0283618,0.0118701,0.172304,0.603565,0.04405,0.155199,0.0362139,0.0160107,0.686612,0.367003,0.210123,0.458076,0.0677786,0.30533,0.204918,0.129869,0.301516,0.471649,0.261519,0.213054,0.426683,0.467708,0.602614,0.198331,0.831117,0.523348,0.21737,0.175903,0.437087,0.206544,0.424001,0.349892,0.21901,0.32251,1.63511,1.032,1.02068,0.876356,0.107303,0.44639,0.00295624,0.600809,0.145148,0.127377,0.109933,0.336375,0.39137,0.65413,0.178296,0.34903,0.218762,0.230083,0.554704,5.25008e-05,0.0402656,0.0961528,0.281033,1.1284,0.769994,0.530777,0.416714,2.18462,0.0586689,0.923294,0.334865,0.452776,0.284531,0.0255382,0.337363,0.41198,0.448017,0.375338,0.313482,0.133549,0.36244,0.194019,0.0988322,0.193397,0.279145,0.445659,0.546997,0.437263,0.725188,0.0434964,0.0371499,0.122878,0.32067,0.127576,0.593343,0.279196,0.464757,0.226712,0.828974,0.33698,0.579525,0.420907,0.631927,0.927484,0.531386,0.788377,0.645033,0.224354,0.782074,0.0295274,0.120181,0.454639,0.742365,1.57584,1.1795,0.707679,0.201014,1.14167,1.52702,0.171082,1.48051,1.41836,0.362226,0.029465,0.0146612,0.000592115,0.531723,0.657888,0.20621,0.90553,0.268853,0.759153,1.11066,0.286826,0.706553,0.515425,0.390719,0.0861239,0.873572,0.218208,0.498853,0.20326,0.000519759|tfbs_overrepresentation_jaspar=MA0003.1;0.00111053,MA0004.1;0.13931,MA0006.1;0.0576274,MA0007.1;0.402704,MA0009.1;0.495012,MA0014.1;0.000357442,MA0017.1;0.259379,MA0019.1;0.238234,MA0024.1;1.04423,MA0025.1;1.49174,MA0027.1;2.05626,MA0028.1;0.0643724,MA0029.1;1.89676,MA0030.1;0.41146,MA0031.1;0.357843,MA0038.1;0.206085,MA0040.1;0.426128,MA0041.1;0.150655,MA0042.1;0.131332,MA0043.1;0.495289,MA0046.1;0.485466,MA0048.1;0.0637366,MA0050.1;0.817596,MA0051.1;1.11081,MA0052.1;0.429421,MA0055.1;0.143182,MA0056.1;0,MA0057.1;0.0582452,MA0058.1;0.292964,MA0059.1;0.0861568,MA0060.1;0.0198514,MA0061.1;0.346364,MA0063.1;0,MA0066.1;0.206381,MA0067.1;0.78548,MA0068.1;0.0418736,MA0069.1;0.482095,MA0070.1;0.472333,MA0071.1;0.179775,MA0072.1;0.468422,MA0073.1;1.08971e-10,MA0074.1;1.10877,MA0076.1;0.094817,MA0077.1;2.03358,MA0078.1;0.755792,MA0081.1;0.0862369,MA0083.1;0.501617,MA0084.1;0.964138,MA0087.1;0.466297,MA0088.1;0.114595,MA0089.1;0,MA0090.1;0.685053,MA0091.1;0.434924,MA0092.1;0.118775,MA0093.1;0.0588752,MA0095.1;0,MA0098.1;0,MA0100.1;0.61748,MA0101.1;0.821369,MA0103.1;0.439733,MA0105.1;0.111879,MA0106.1;0.235406,MA0107.1;2.27015,MA0108.2;0.355343,MA0109.1;0,MA0111.1;0.109681,MA0113.1;0.69147,MA0114.1;0.129654,MA0115.1;0.71383,MA0116.1;0.138337,MA0117.1;0.528241,MA0119.1;1.43809,MA0122.1;0.551352,MA0124.1;0.675302,MA0125.1;0.598285,MA0130.1;0,MA0131.1;0.289284,MA0132.1;0,MA0133.1;0,MA0135.1;0.521813,MA0136.1;0.211008,MA0139.1;0.0119363,MA0140.1;0.526893,MA0141.1;0.288855,MA0142.1;0.88389,MA0143.1;0.691772,MA0144.1;0.824604,MA0145.1;0.000993802,MA0146.1;0.000198722,MA0147.1;0.0356084,MA0148.1;0.469347,MA0149.1;0.17166,MA0062.2;0.0131657,MA0035.2;0.525759,MA0039.2;2.31726e-07,MA0138.2;2.13017,MA0002.2;0.20101,MA0137.2;0.237908,MA0104.2;0.0196756,MA0047.2;0.226642,MA0112.2;0.0595931,MA0065.2;0.0277639,MA0150.1;0.326793,MA0151.1;0,MA0152.1;0.537486,MA0153.1;0.583009,MA0154.1;0.107659,MA0155.1;0.0527191,MA0156.1;0.0681959,MA0157.1;1.51094,MA0158.1;0,MA0159.1;0.332094,MA0160.1;0.493256,MA0161.1;0,MA0162.1;0.00132146,MA0163.1;0.164934,MA0164.1;0.712784,MA0080.2;0.0589108,MA0018.2;0.236412,MA0099.2;0.182613,MA0079.2;2.7815e-09,MA0102.2;1.00004,MA0258.1;0.260331,MA0259.1;0.150791,MA0442.1;0}}
|full_id=C426_CD4_CD14_Neutrophils_CD8_Natural_Mast_Eosinophils
|id=C426
}}

Latest revision as of 11:22, 17 September 2013


Full id: C426_CD4_CD14_Neutrophils_CD8_Natural_Mast_Eosinophils



Phase1 CAGE Peaks

Hg19::chr14:35871591..35871602,-p@chr14:35871591..35871602
-
Hg19::chr4:103480333..103480371,+p@chr4:103480333..103480371
+
Hg19::chr4:103496453..103496481,+p@chr4:103496453..103496481
+
Hg19::chr4:103498478..103498489,+p12@NFKB1
Hg19::chr4:103498623..103498650,+p9@NFKB1
Hg19::chr6:138189104..138189115,+p@chr6:138189104..138189115
+
Hg19::chr6:138189215..138189247,+p@chr6:138189215..138189247
+
Hg19::chr6:138190239..138190250,+p@chr6:138190239..138190250
+
Hg19::chr6:138192331..138192343,+p10@TNFAIP3
Hg19::chr6:138192345..138192366,+p11@TNFAIP3
Hg19::chr6:138192426..138192438,+p12@TNFAIP3
Hg19::chr6:138192543..138192555,+p13@TNFAIP3
Hg19::chr6:138196020..138196034,+p8@TNFAIP3
Hg19::chr6:138196838..138196867,+p16@TNFAIP3
Hg19::chr6:138197180..138197238,+p9@TNFAIP3
Hg19::chr6:138198202..138198217,+p@chr6:138198202..138198217
+
Hg19::chr6:138198297..138198311,+p@chr6:138198297..138198311
+
Hg19::chr6:138198346..138198366,+p@chr6:138198346..138198366
+
Hg19::chr6:138199895..138199908,+p@chr6:138199895..138199908
+
Hg19::chr6:138199945..138199956,+p@chr6:138199945..138199956
+
Hg19::chr6:138201273..138201294,+p@chr6:138201273..138201294
+
Hg19::chr6:138204018..138204028,+p@chr6:138204018..138204028
+
Hg19::chr6:138204056..138204068,+p@chr6:138204056..138204068
+
Hg19::chr7:138766106..138766122,-p@chr7:138766106..138766122
-


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
4.19956876000442e-060.0026583270250828259NOD-like receptor signaling pathway (KEGG):04621
2.18716290008179e-050.004052278519474552134Measles (KEGG):05162
0.0007705509155556930.0487758729546754111Osteopontin Signaling (Wikipathways):WP1434
2.38818258532104e-050.004052278519474552140Regulation of toll-like receptor signaling pathway (Wikipathways):WP1449
0.000560430119292420.044344033189012718TFs Regulate miRNAs related to cardiac hypertrophy (Wikipathways):WP1559
4.31443715156972e-050.004551731194906062188TNF-alpha/NF-kB Signaling Pathway (Wikipathways):WP231
0.0003198274735665560.02892154153823282511Signaling in Immune system (Reactome):REACT_6900
0.000649516938528610.04568269134317892728TNF alpha/NF-kB up reg. targets (Netpath):NetPath_9
3.20085191111734e-050.004052278519474552162TNF alpha/NF-kB down reg. targets (Netpath):NetPath_9
2.92938943019595e-050.004052278519474552155IL-1 up reg. targets (Netpath):NetPath_13



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:0006916anti-apoptosis0.0012626724630421
GO:0043066negative regulation of apoptosis0.0012626724630421
GO:0043069negative regulation of programmed cell death0.0012626724630421
GO:0042981regulation of apoptosis0.00476396946754751
GO:0043067regulation of programmed cell death0.00476396946754751
GO:0043124negative regulation of I-kappaB kinase/NF-kappaB cascade0.00488601741722185
GO:0006915apoptosis0.00592300066246309
GO:0012501programmed cell death0.00592300066246309
GO:0016265death0.00592300066246309
GO:0008219cell death0.00592300066246309
GO:0048523negative regulation of cellular process0.00836632581832125
GO:0048519negative regulation of biological process0.00836632581832125
GO:0048468cell development0.00852704727292275
GO:0048869cellular developmental process0.0156990917752577
GO:0030154cell differentiation0.0156990917752577
GO:0009968negative regulation of signal transduction0.030993977189682
GO:0043122regulation of I-kappaB kinase/NF-kappaB cascade0.030993977189682
GO:0007249I-kappaB kinase/NF-kappaB cascade0.0376570466175902
GO:0032502developmental process0.0423912959518589
GO:0003677DNA binding0.0441894487628634



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
leukocyte3.95e-58136
hematopoietic cell6.93e-43177
hematopoietic lineage restricted progenitor cell1.80e-42120
hematopoietic stem cell2.34e-42168
angioblastic mesenchymal cell2.34e-42168
nongranular leukocyte1.48e-41115
classical monocyte6.40e-4142
CD14-positive, CD16-negative classical monocyte6.40e-4142
hematopoietic oligopotent progenitor cell1.01e-40161
hematopoietic multipotent progenitor cell1.01e-40161
myeloid leukocyte4.32e-3972
defensive cell2.91e-3448
phagocyte2.91e-3448
granulocyte monocyte progenitor cell7.56e-3167
macrophage dendritic cell progenitor3.94e-2961
myeloid lineage restricted progenitor cell8.15e-2866
myeloid cell3.02e-27108
common myeloid progenitor3.02e-27108
monopoietic cell1.03e-2659
monocyte1.03e-2659
monoblast1.03e-2659
promonocyte1.03e-2659
mesenchymal cell1.67e-16354
connective tissue cell1.08e-15361
stuff accumulating cell1.11e-1487
granulocyte3.32e-138
motile cell7.21e-13386
lymphoid lineage restricted progenitor cell2.06e-1252
lymphocyte4.84e-1253
common lymphoid progenitor4.84e-1253
blood cell1.95e-1111
nucleate cell2.42e-1155
multi fate stem cell5.60e-11427
somatic stem cell6.20e-11433
stem cell8.15e-11441
CD4-positive, alpha-beta T cell1.71e-106
circulating cell2.75e-096
mature alpha-beta T cell8.66e-0818
alpha-beta T cell8.66e-0818
immature T cell8.66e-0818
mature T cell8.66e-0818
immature alpha-beta T cell8.66e-0818
Langerhans cell8.98e-085
T cell4.28e-0725
pro-T cell4.28e-0725
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.35e-3098
blood island1.35e-3098
hemolymphoid system1.68e-27108
bone marrow1.24e-2576
immune system1.44e-2593
bone element8.32e-2382
skeletal element1.21e-1990
skeletal system1.76e-17100
connective tissue1.36e-14371
lateral plate mesoderm7.37e-10203
musculoskeletal system6.15e-07167


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)
MA0003.10.00111053
MA0004.10.13931
MA0006.10.0576274
MA0007.10.402704
MA0009.10.495012
MA0014.10.000357442
MA0017.10.259379
MA0019.10.238234
MA0024.11.04423
MA0025.11.49174
MA0027.12.05626
MA0028.10.0643724
MA0029.11.89676
MA0030.10.41146
MA0031.10.357843
MA0038.10.206085
MA0040.10.426128
MA0041.10.150655
MA0042.10.131332
MA0043.10.495289
MA0046.10.485466
MA0048.10.0637366
MA0050.10.817596
MA0051.11.11081
MA0052.10.429421
MA0055.10.143182
MA0056.10
MA0057.10.0582452
MA0058.10.292964
MA0059.10.0861568
MA0060.10.0198514
MA0061.10.346364
MA0063.10
MA0066.10.206381
MA0067.10.78548
MA0068.10.0418736
MA0069.10.482095
MA0070.10.472333
MA0071.10.179775
MA0072.10.468422
MA0073.11.08971e-10
MA0074.11.10877
MA0076.10.094817
MA0077.12.03358
MA0078.10.755792
MA0081.10.0862369
MA0083.10.501617
MA0084.10.964138
MA0087.10.466297
MA0088.10.114595
MA0089.10
MA0090.10.685053
MA0091.10.434924
MA0092.10.118775
MA0093.10.0588752
MA0095.10
MA0098.10
MA0100.10.61748
MA0101.10.821369
MA0103.10.439733
MA0105.10.111879
MA0106.10.235406
MA0107.12.27015
MA0108.20.355343
MA0109.10
MA0111.10.109681
MA0113.10.69147
MA0114.10.129654
MA0115.10.71383
MA0116.10.138337
MA0117.10.528241
MA0119.11.43809
MA0122.10.551352
MA0124.10.675302
MA0125.10.598285
MA0130.10
MA0131.10.289284
MA0132.10
MA0133.10
MA0135.10.521813
MA0136.10.211008
MA0139.10.0119363
MA0140.10.526893
MA0141.10.288855
MA0142.10.88389
MA0143.10.691772
MA0144.10.824604
MA0145.10.000993802
MA0146.10.000198722
MA0147.10.0356084
MA0148.10.469347
MA0149.10.17166
MA0062.20.0131657
MA0035.20.525759
MA0039.22.31726e-07
MA0138.22.13017
MA0002.20.20101
MA0137.20.237908
MA0104.20.0196756
MA0047.20.226642
MA0112.20.0595931
MA0065.20.0277639
MA0150.10.326793
MA0151.10
MA0152.10.537486
MA0153.10.583009
MA0154.10.107659
MA0155.10.0527191
MA0156.10.0681959
MA0157.11.51094
MA0158.10
MA0159.10.332094
MA0160.10.493256
MA0161.10
MA0162.10.00132146
MA0163.10.164934
MA0164.10.712784
MA0080.20.0589108
MA0018.20.236412
MA0099.20.182613
MA0079.22.7815e-09
MA0102.21.00004
MA0258.10.260331
MA0259.10.150791
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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