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Coexpression cluster:C1590: Difference between revisions

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|ontology_enrichment_disease=DOID:2531!1.05e-12!51;DOID:0060083!1.05e-12!51;DOID:1240!3.97e-10!39;DOID:8692!5.61e-09!31
|ontology_enrichment_disease=DOID:2531!1.05e-12!51;DOID:0060083!1.05e-12!51;DOID:1240!3.97e-10!39;DOID:8692!5.61e-09!31
|ontology_enrichment_uberon=UBERON:0002390!1.09e-31!102;UBERON:0003061!1.09e-31!102;UBERON:0002193!3.47e-27!112;UBERON:0002371!1.32e-21!80;UBERON:0001474!1.64e-18!86;UBERON:0002405!8.57e-16!115;UBERON:0002384!3.27e-12!375;UBERON:0004765!5.22e-12!101;UBERON:0001434!5.22e-12!101;UBERON:0000178!2.00e-08!15;UBERON:0000179!2.00e-08!15;UBERON:0000463!2.00e-08!15
|ontology_enrichment_uberon=UBERON:0002390!1.09e-31!102;UBERON:0003061!1.09e-31!102;UBERON:0002193!3.47e-27!112;UBERON:0002371!1.32e-21!80;UBERON:0001474!1.64e-18!86;UBERON:0002405!8.57e-16!115;UBERON:0002384!3.27e-12!375;UBERON:0004765!5.22e-12!101;UBERON:0001434!5.22e-12!101;UBERON:0000178!2.00e-08!15;UBERON:0000179!2.00e-08!15;UBERON:0000463!2.00e-08!15
|tf_chipseq_enrich=BHLHE40#8553;3:26.9230881281864:0.000106941952374384:0.00148918807520377!E2F4#1874;3:7.60083618917066:0.00435414736037571:0.0206466649793543!EBF1#1879;4:7.1251734772552:0.000723053104677421:0.00576890322378955!GTF2B#2959;2:12.7775319737297:0.0091993608955972:0.0347828561499991!IRF3#3661;2:18.7927808845958:0.00433962977712151:0.0205843670766097!JUNB#3726;2:12.2442530639285:0.00999049059334596:0.037464877812512!NFYB#4801;3:10.0558759521219:0.00193816560672546:0.0113859870514569!POU2F2#5452;3:5.46367443464551:0.0111565009446978:0.040996931922286!RFX5#5993;3:7.22874649631706:0.0050291827895866:0.0234630046172445!SMARCB1#6598;3:10.9516294686944:0.00151187284834318:0.00964972733655892!SP2#6668;2:10.4614121975379:0.0135319118334714:0.0477726849871858!SREBF1#6720;2:18.8023397761953:0.00433531272958737:0.0205751034338533
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749,0.0686325,0.0569043,0.0639461,0.387306,0.267408,0.312064,0.080156,0.0415903,0.180885,0.0545112,0.510703,0.33844,0.0649137,0.0974216,0.229627,0.195675,0.0162521,0.176557,0.396547,0.0472148,0.735114,0.229138,0.0639045,0.141461,0.0900204,0.228387,0.0134722,0.334921,0.296227,0.208788,0.566117,0.36304,0.0196869,0.123626,0.270619,0.132705,0.285556,0.493429,0.233835,0.224471,0.262929,0.223204,0.143824,0.460679,0.431098,0.0775891,0.153079,0.62577,0.211515,0.125701,0.175283,0.204954,0.209341,0.855975,0.629422,0.084895,0.160115,0.0819954,0.10091,0.122658,0.151161,0.228398,0.056055,0.120552,0.41771,0.893893,0.830533,0.335207,0.434016,0.190688,0.299739,0.278645,0.733648,0.0940982,0.0780533,0.564811,0.0993772,0.274769,0.448923,0.11602,0.344528,0.436413,0.0585992,0.20045,0.274438,0.76735,0.672453,0.319826,0.336512,0.173868,0.109708,0.174594,0.0809806,0.154589,0.318794,0.122767,0.0749261,0.176858,0.114361,0.347759,0.242462,0.0620267,0.211111,0.0738743,0.0882327,0.183058,0.0118708,0.270522,0.16872,0.341388,0.0934526,0.359135,0.123404,0.110025,0.240825,0.3033,0.336623,0.163542,0.483244,0.27134,0.500871,0.239667,0.10226,0.29809,0.235147,0.689826,0.245965,0.116923,0.148426,0.0983658,0.228743,0.238223,0.156976,0.244789,0.267391,0.301441,0.21807,0.350528,0.382904,0.432408,0.190404,0.135865,0.488841,0.18137,0.180609,0.291283,0.273972,0.153023,0.400137,0.37958,0.22307,0.160699,0.391307,0.166736,0.181253,0.0422294,0.263877,0.146486,0.769574,0.262486,0.294204,0.131936,0.288826,0.246621,0.463617,0.697373,0.0965376,0.377203,0.279263,0.336564,0.35463,0.581771,0.800557,0.0594155,0.587524,0.208795,0.0713793,0.212621,0.594469,0.53612,0.629713,0.581874,0.355154,0.730614,0.251388,0.537088,0.603804,0.0789735,0.306963,0.569605,0.526495,0.215897,0.550495,0.178116,0.820986,0.24322,0.881697,0.561689,0.672416,0.321844,0.623136,0.708698,0.96913,0.855024,0.349068,0.344004,0.798758,0.557035,0.427789,0.326931,0.737642,0.639789,0.433702,0.258394,0.0869065,0.432123,0.759415,0.661773,0.149969,0.651196,0.392155,0.626931,0.371758,0.91821,0.562417,0.890566,0.85279,0.254547,0.901563,0.821811,0.680843,0.746881,0.541378,0.922893,0.660884,0.723387,0.898765,0.705225,0.315485,0.311289,0.318577,0.4488,0.389888,0.0670531,0.161355,0.553178,0.246387,0.224252,0.587237,0.0126953,0.466978,0.518234,0.257848,0.353942,0.192234,0.427276,0.747776,0.466967,0.283682,0.424668,0.462212,0.474058,0.583101,0.702164,0.477016,0.831202,0.498956,0.792095,0.55798,0.127604,0.932831,0.723248,0.34194,0.592696,0.226514,0.644904,0.89036,0.423117,0.0567843,0.633504,0.220564,0.556368,0.262394,0.307462,0.135076,0.469588,0.664443,0.274593,0.490712,0.541363,0.709432,0.218812,0.531474,0.720644,0.562305,0.174119,0.361524,0.31558,0.412744,0.54408,0.62698,0.163034,0.415367,0.503942,0.45585,0.36864,0.538745,0.456862,0.453004,0.680686,0.196391,0.693441,0.382214,0.553161,0.639572,0.68995,0.339393,0.694478,0.306231,0.298354,0.646049,0.784543,0.457741,0.641611,0.10749,0.401917,0.289012,0.572661,0.412586,0.534679,0.41502,0.55475,0.66153,0.170461,0.0331565,0.307426,0.462582,0.557732,0.490527,0.356232,0.44799,0.813041,0.318338,0.276338,0.126433,0.417412,0.318174,0.0555558,0.295666,0.393022,0.293641,0.116969,0.401231,0.255983,0.297663,0.256708,0.338258,0.322052,0.145568,0.153833,0.261242,0.38389,0.54721,0.388459,0.321362,0.0780866,0.280757,0.301366,0.340343,0.343265,0.501812,0.462092,0.336254,0.308589,0.291523,0.19697,0.309816,0.0537285,0.0119616,0.198077,0.281455,0.348739,0.419895,0.138495,0.208834,0.32256,0.377566,0.342366,0.109684,0.322704,0.0952935,0.181288,0.230841,0.352328,0.255358,0.351665,0.265112,0.0633313,0.10772,0.0854747,0.0747609,0.406458,0.312881,0.512825,0.244656,0.192188,0.158985,0.174153,0.0972854,0.333309,0.249919,0.339517,0.303699,0.198326,0.394084,0.126349,0.282501,0.252005,0.390891,0.238377,0.334983,0.197875,0.287909,0.289389,0.117618,0.392533,0.396962,0.316002,0.330317,0.321404,0.225079,0.300542,0.379651,0.185715,0.345505,0.375521,0.271405,0.311201,0.221943,0.306427,0.367733,0.246925,0.208775,0.390438,0.343014,0.270094,0.276922,0.156279,0.313647,0.461742,0.422872,0.336468,0.13327,0.313545,0.17149,0.0877361,0.0880065,0.238969,0.126615,0.0669467,0.0879453,0.474066,0.396935,0.326779,0.292869,0.358198,0.29552,0.131776,0.158116,0.104606,0.194814,0.104167,0.168186,0.108081,0.123829,0.205215,0.175247,0.0724304,0.109077,0.144842,0.0604892,0.214671,0.316879,0.442567,0.430541,0.508546,0.224871,0.398887,0.088016,0.310732,0.349611,0.445995,0.385709,0.278202,0.426488,0.400591,0.209809,0.253154,0.319519,0.309489,0.430805,0.362154,0.480785,0.185476,0.336314,0.344469,0.184651,0.303359,0.297596,0.42392,0.425912,0.0840133,0.259046,0.345068,0.151046,0.483953,0.347171,0.321735,0.15463,0.13907,0.470121,0.269432,0.250466,0.409882,0.115686,0.0981568,0.162633,0.342661,0.27567,0.248127,0.0628839,0.384731,0.319112,0.526476
}}
}}

Revision as of 13:55, 5 September 2012


Full id: C1590_Mast_CD19_Basophils_CD4_Natural_Eosinophils_CD8



Phase1 CAGE Peaks

Hg19::chr10:63806474..63806496,+p@chr10:63806474..63806496
+
Hg19::chr11:73694239..73694253,-p2@UCP2
Hg19::chr11:73694257..73694289,-p3@UCP2
Hg19::chr12:25539261..25539297,+p@chr12:25539261..25539297
+
Hg19::chr22:32188667..32188693,+p2@DEPDC5


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


No results for this coexpression

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:0000303response to superoxide0.00735856827869091
GO:0000305response to oxygen radical0.00735856827869091
GO:0000302response to reactive oxygen species0.0264822674140548
GO:0006839mitochondrial transport0.0352987719354742
GO:0007005mitochondrion organization and biogenesis0.0495752912277362
GO:0006979response to oxidative stress0.0495752912277362
GO:0015992proton transport0.0495752912277362
GO:0006818hydrogen transport0.0495752912277362



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>disease_data<br>


Cell Type
Ontology termp-valuen
hematopoietic stem cell9.68e-73172
angioblastic mesenchymal cell9.68e-73172
hematopoietic cell4.54e-70182
hematopoietic oligopotent progenitor cell1.52e-68165
hematopoietic multipotent progenitor cell1.52e-68165
leukocyte1.69e-61140
hematopoietic lineage restricted progenitor cell3.38e-52124
nongranular leukocyte2.57e-49119
myeloid cell2.14e-40112
common myeloid progenitor2.14e-40112
myeloid leukocyte4.38e-3076
granulocyte monocyte progenitor cell1.01e-2671
myeloid lineage restricted progenitor cell3.95e-2670
lymphocyte3.21e-2453
common lymphoid progenitor3.21e-2453
lymphoid lineage restricted progenitor cell1.11e-2352
macrophage dendritic cell progenitor5.99e-2365
monopoietic cell3.46e-2263
monocyte3.46e-2263
monoblast3.46e-2263
promonocyte3.46e-2263
classical monocyte7.39e-1845
CD14-positive, CD16-negative classical monocyte9.62e-1842
mesenchymal cell1.24e-13358
connective tissue cell8.67e-13365
lymphocyte of B lineage1.14e-1224
pro-B cell1.14e-1224
motile cell2.87e-11390
mature alpha-beta T cell1.59e-1018
alpha-beta T cell1.59e-1018
immature T cell1.59e-1018
mature T cell1.59e-1018
immature alpha-beta T cell1.59e-1018
T cell1.91e-1025
pro-T cell1.91e-1025
B cell4.74e-1014
CD8-positive, alpha-beta T cell9.54e-0711
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.09e-31102
blood island1.09e-31102
hemolymphoid system3.47e-27112
bone marrow1.32e-2180
bone element1.64e-1886
immune system8.57e-16115
connective tissue3.27e-12375
skeletal element5.22e-12101
skeletal system5.22e-12101
blood2.00e-0815
haemolymphatic fluid2.00e-0815
organism substance2.00e-0815
Disease
Ontology termp-valuen
hematologic cancer1.05e-1251
immune system cancer1.05e-1251
leukemia3.97e-1039
myeloid leukemia5.61e-0931


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


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

TF#promotersEnrichmentp-valueq-value
BHLHE40#8553326.92308812818640.0001069419523743840.00148918807520377
E2F4#187437.600836189170660.004354147360375710.0206466649793543
EBF1#187947.12517347725520.0007230531046774210.00576890322378955
GTF2B#2959212.77753197372970.00919936089559720.0347828561499991
IRF3#3661218.79278088459580.004339629777121510.0205843670766097
JUNB#3726212.24425306392850.009990490593345960.037464877812512
NFYB#4801310.05587595212190.001938165606725460.0113859870514569
POU2F2#545235.463674434645510.01115650094469780.040996931922286
RFX5#599337.228746496317060.00502918278958660.0234630046172445
SMARCB1#6598310.95162946869440.001511872848343180.00964972733655892
SP2#6668210.46141219753790.01353191183347140.0477726849871858
SREBF1#6720218.80233977619530.004335312729587370.0205751034338533



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.