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Coexpression cluster:C1181: Difference between revisions

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|full_id=C1181_Myoblast_CD14_liposarcoma_mesenchymal_caudate_diencephalon_putamen
|full_id=C1181_Myoblast_CD14_liposarcoma_mesenchymal_caudate_diencephalon_putamen
|id=C1181
|id=C1181
|ontology_enrichment_celltype=CL:0002057!3.85e-25!42;CL:0000738!1.07e-23!140;CL:0000860!1.23e-23!45;CL:0002087!1.76e-20!119;CL:0000766!2.18e-20!76;CL:0002009!6.82e-19!65;CL:0002194!2.55e-18!63;CL:0000576!2.55e-18!63;CL:0000040!2.55e-18!63;CL:0000559!2.55e-18!63;CL:0002031!6.51e-18!124;CL:0000557!7.95e-18!71;CL:0000839!2.59e-15!70;CL:0000037!3.03e-14!172;CL:0000566!3.03e-14!172;CL:0002032!2.81e-13!165;CL:0000837!2.81e-13!165;CL:0000988!1.17e-11!182;CL:0002320!2.97e-10!365;CL:0000763!4.29e-10!112;CL:0000049!4.29e-10!112;CL:0000134!6.06e-10!358;CL:0000048!4.32e-09!430;CL:0000034!1.71e-08!444;CL:0000723!3.44e-08!436;CL:0000219!2.92e-07!390
|ontology_enrichment_celltype=CL:0000860!6.38e-26!42;CL:0002057!6.38e-26!42;CL:0000738!8.04e-23!136;CL:0000473!5.42e-21!48;CL:0000234!5.42e-21!48;CL:0002087!7.27e-20!115;CL:0000766!2.51e-19!72;CL:0002009!2.80e-18!61;CL:0002031!6.23e-18!120;CL:0002194!1.45e-17!59;CL:0000576!1.45e-17!59;CL:0000040!1.45e-17!59;CL:0000559!1.45e-17!59;CL:0000557!1.55e-17!67;CL:0000839!3.40e-15!66;CL:0000037!1.57e-14!168;CL:0000566!1.57e-14!168;CL:0002032!1.10e-13!161;CL:0000837!1.10e-13!161;CL:0000988!1.29e-12!177;CL:0000763!2.08e-10!108;CL:0000049!2.08e-10!108;CL:0002320!7.87e-09!361;CL:0000134!8.37e-09!354;CL:0000048!6.32e-08!427;CL:0000034!1.56e-07!441;CL:0000723!2.89e-07!433;CL:0000219!6.34e-07!386
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!2.60e-16!102;UBERON:0003061!2.60e-16!102;UBERON:0002371!1.98e-15!80;UBERON:0001474!2.66e-13!86;UBERON:0001869!3.10e-13!32;UBERON:0002780!8.86e-13!41;UBERON:0001890!8.86e-13!41;UBERON:0006240!8.86e-13!41;UBERON:0002193!1.49e-12!112;UBERON:0001893!3.94e-12!34;UBERON:0004765!4.82e-12!101;UBERON:0001434!4.82e-12!101;UBERON:0002619!4.94e-12!22;UBERON:0003080!7.76e-12!42;UBERON:0002791!1.41e-11!33;UBERON:0002020!3.60e-11!34;UBERON:0003528!3.60e-11!34;UBERON:0001950!4.68e-11!20;UBERON:0002384!5.49e-11!375;UBERON:0000956!1.37e-09!25;UBERON:0000203!1.37e-09!25;UBERON:0001049!2.62e-09!57;UBERON:0005068!2.62e-09!57;UBERON:0006241!2.62e-09!57;UBERON:0007135!2.62e-09!57;UBERON:0002405!6.61e-09!115;UBERON:0001017!9.96e-09!82;UBERON:0002616!1.01e-08!59;UBERON:0000955!3.06e-08!69;UBERON:0006238!3.06e-08!69;UBERON:0002204!5.23e-08!167;UBERON:0005743!5.48e-08!86;UBERON:0000073!5.73e-08!94;UBERON:0001016!5.73e-08!94
|ontology_enrichment_uberon=UBERON:0002390!4.71e-15!98;UBERON:0003061!4.71e-15!98;UBERON:0002371!5.70e-15!76;UBERON:0001869!1.48e-14!32;UBERON:0002780!9.23e-14!41;UBERON:0001890!9.23e-14!41;UBERON:0003080!9.23e-14!41;UBERON:0006240!9.23e-14!41;UBERON:0001893!1.57e-13!34;UBERON:0002791!8.53e-13!32;UBERON:0003528!1.96e-12!34;UBERON:0002020!1.96e-12!34;UBERON:0002619!2.01e-12!22;UBERON:0001474!2.51e-12!82;UBERON:0002405!9.39e-12!93;UBERON:0001434!1.39e-11!100;UBERON:0002193!1.68e-11!108;UBERON:0001950!2.24e-11!20;UBERON:0004765!2.65e-11!90;UBERON:0000073!8.34e-11!53;UBERON:0002616!8.34e-11!53;UBERON:0000956!1.24e-10!25;UBERON:0000203!1.24e-10!25;UBERON:0001049!3.23e-10!56;UBERON:0005068!3.23e-10!56;UBERON:0006241!3.23e-10!56;UBERON:0007135!3.23e-10!56;UBERON:0001017!1.83e-09!81;UBERON:0002384!2.22e-09!371;UBERON:0001016!3.15e-09!89;UBERON:0000955!3.36e-09!68;UBERON:0006238!3.36e-09!68;UBERON:0002204!4.21e-07!167
|tf_chipseq_enrich=ATF3#467;6:19.2541495937218:5.23155102976118e-08:3.33360560095929e-06!BHLHE40#8553;7:44.8718135469774:2.71655591272133e-12:3.64203315749298e-10!CCNT2#905;7:6.33620157696263:2.43743907326287e-06:8.61759307286733e-05!CHD2#1106;7:10.3440228341169:7.88338195961115e-08:4.72094339724673e-06!CTCF#10664;7:5.36025637307503:7.86114662284756e-06:0.00022237548541267!E2F1#1869;7:4.90738921487932:1.45832274679793e-05:0.000346779984865276!E2F6#1876;7:5.01715573169739:1.24910426162553e-05:0.000308113367926095!EGR1#1958;7:4.98817909481014:1.30079520165561e-05:0.000318084172478834!GATA1#2623;3:5.81156063305733:0.0111931160082029:0.0411271405425239!HDAC2#3066;6:11.4991030599654:1.1228817392662e-06:4.62067162991419e-05!HEY1#23462;7:4.04011104310571:5.68979821988558e-05:0.00094986706567556!JUND#3727;6:5.99542623588945:5.24232039014691e-05:0.000891262736816789!MAX#4149;6:5.53076186486325:8.40673768319711e-05:0.00126184431861946!NFKB1#4790;7:5.48806342419384:6.66568321176054e-06:0.000194674857089782!NRF1#4899;5:8.72162817693636:6.71450045004423e-05:0.00107356967621275!PAX5#5079;7:6.66956553117783:1.7023051190758e-06:6.43456548429814e-05!POLR2A#5430;7:2.14745317655807:0.00474763644761028:0.0223330512094392!SIN3A#25942;7:5.40888472681514:7.3795239773719e-06:0.000211559183275527!TAF1#6872;7:3.34304628574529:0.000214233631962245:0.00246522105426454!TBP#6908;6:3.17723201751119:0.00207411205185266:0.012018986216692!TFAP2C#7022;7:10.8092286098602:5.79365976833206e-08:3.61028659036296e-06!USF1#7391;6:5.45271366617825:9.13505145927422e-05:0.00133136427484669!USF2#7392;7:12.9921973850696:1.59819543071901e-08:1.16641462326249e-06
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886,0.125399,0.043898,7.21552e-05,0.291561,0.0337354,0.146629,0.426032,0.440859,0.177111,0.167984,0.337564,0.394053,0.123448,0.17256,0.126216,0.0947479,0.0787488,0.0883646,0.496336,0.353144,0.407665,0.11039,0.361507,1.76429e-05,0.0754745,0.0190312,0.439214,0.0896836,0.133679,1.07338e-07,0.262768,0.235824,0.23812,0.506939,0.0654706,1.20639e-08,0.00614914,0.0883079,0.192275,0.123717,0.3044,0.494788,0.435034,0.388488,0.27954,0.689314,0.468189,0.187355,0.168686,0.35711,0.180717,0.375467,0.246637,0.000599002,0.299453,0.347601,0.297851,0.195385,0.578705,0.546003,0.106912,0.207535,1.42446e-05,0.283013,0.17144,0.236468,0.274647,0.280244,0.00680262,0.750867,0.1168,0.216736,0.112879,0.138362,0.1674,0.205022,0.304414,0.0775871,0.1646,1.46392e-05,0.820894,0.916686,0.435374,0.190081,0.25636,0.0898474,0.366993,4.07915e-06,0.12921,0.107541,0.00686601,0.136306,0.362226,0.0524702,0.158567,0.446426,0.551931,0.0810658,0.268889,0.361819,2.17592e-06,2.83449e-10,0.417001,0.436925,0.234633,0.150144,0.235575,0.111506,0.209512,0.415762,0.167545,0.1033,0.0310204,1.02793e-06,0.0229455,0.322099,0.0857464,0.282499,0.101873,0.121306,0.246526,0.203595,0.356991,0.227948,0.44271,3.63445e-07,0.463619,0.0150482,1.85063e-06,0.320047,0.397073,0.113603,0.221207,0.603174,0.358,0.621995,0.318595,0.140173,0.390753,0.312917,2.17084e-08,0.326484,0.15977,0.201434,0.134947,0.304849,0.316782,0.212636,0.325012,0.353123,0.394821,0.291345,0.00344244,0.147446,0.547467,0.255995,0.0012226,0.609179,0.244347,0.243363,0.382464,4.87873e-07,0.207462,0.51104,0.487422,0.29768,0.217499,0.154075,0.225368,0.244195,0.0586175,0.348776,0.198885,0.871901,0.00940891,8.52196e-07,0.0011174,0.379465,0.327304,0.581915,0.0892444,0.132491,0.000616953,0.0778828,0.0206668,0.458334,0.00163192,0.895348,0.0821811,0.35171,0.279549,0.0984834,0.284421,0.00952609,0.000862581,0.751141,6.93615e-10,0.458949,0.000638234,0.741039,0.659829,0.726427,0.164056,0.401507,0.0320829,0.648881,0.00815518,0.673541,0.330529,0.0969255,0.380231,0.0329228,0.684866,0.790371,0.00640162,0.00053991,0.822139,0.0598872,3.92158e-08,0.451787,0.244289,0.0270901,0.107763,0.542303,0.226936,0.289067,1.8987e-05,0.54891,0.341975,0.765292,1.3084e-08,0.863925,0.448065,0.615729,0.771117,0.501908,0.74852,0.478352,1.90228e-07,0.685599,9.59122e-05,6.41652e-10,0.337191,6.55877e-08,0.00346315,0.0236217,3.48773e-09,0.0978461,1.25735e-06,0.779967,5.4519e-06,2.96979e-07,1.52729e-07,0.411785,0.00204669,0.415502,0.565657,0.499305,0.726141,0.632958,0.676266,0.327011,0.299176,0.710278,0.210121,0.585578,0.000666047,0.341296,0.457524,0.258349,0.541728,0.854621,0.585566,0.373172,0.538803,8.32671e-05,0.386822,0.706206,0.816529,0.596462,0.041401,0.619962,0.00744292,0.681127,0.821879,0.000160481,0.0103387,0.0217399,0.133209,0.715255,0.765316,0.0937735,0.599651,0.41419,0.0144625,0.294507,1.92345e-05,0.346938,0.40211,0.183851,0.588416,0.198404,0.362009,0.611179,0.664218,0.516101,0.706724,0.654039,0.10637,0.111267,0.651111,0.466416,0.411899,0.525367,0.0995059,0.161827,0.635414,0.528332,1.32529e-06,0.573415,0.474724,0.661532,0.574524,0.570287,0.00600878,0.68023,0.808962,0.490466,0.676249,0.760368,0.22688,0.440345,0.494239,0.400622,0.391073,0.766374,0.883398,0.575489,0.057938,0.540565,0.000889943,0.775603,0.695855,0.171531,0.657348,0.52794,0.67786,0.195343,0.087524,0.620377,0.0154932,0.00190336,0.680876,0.610982,0.256934,0.564763,0.0894143,0.415214,0.364157,0.000980706,0.53064,0.415017,0.0769041,0.387804,0.502902,0.385339,0.159832,0.512288,0.338978,0.0885946,0.339879,0.438999,0.41967,0.197678,0.208523,0.34551,0.4924,0.304359,0.00543266,0.418843,0.402298,0.369586,0.394729,0.441472,0.444932,0.622992,0.580249,0.436618,0.0952884,0.382758,0.264429,0.404954,0.0744027,0.204325,0.265849,0.370442,0.451398,0.533438,0.188364,0.279598,0.420279,0.485091,0.443868,0.150111,0.420451,0.514853,0.244241,0.307495,0.455626,0.3382,0.454846,0.350305,0.0875262,0.147486,0.117583,0.103076,0.166405,0.0979857,0.634608,0.324846,0.25829,0.215261,0.235004,0.133496,0.433115,0.331422,0.440492,0.397558,0.266168,0.504119,0.212491,0.371725,0.334024,0.500457,0.316975,0.435107,0.26559,0.378345,0.380153,0.160696,0.502341,0.507413,0.0999718,0.42955,0.418893,0.0058157,0.393729,0.487504,0.249956,0.447581,0.482721,0.35808,0.406625,0.296254,0.400859,0.473667,0.327684,0.279523,0.499937,0.444635,0.356463,0.364875,0.211724,0.409573,0.579867,0.536787,0.436872,0.181464,1.89204e-05,0.231548,0.120636,0.121001,0.317719,0.172653,0.0924531,0.120918,0.593272,0.0351249,0.425328,0.384398,0.128819,0.387627,0.179489,0.214126,0.143317,0.261663,0.14273,0.227254,0.147968,0.168955,0.274981,0.236422,0.0999117,0.149301,0.196723,0.0836477,0.287028,0.413461,0.558766,0.545381,0.630108,0.299959,0.0356876,0.498355,0.406059,0.452427,0.200877,0.149642,0.366448,0.540845,0.511559,0.280842,4.56296e-06,0.00229313,0.404559,0.545676,0.467154,0.600528,0.249647,0.43669,0.446356,0.248584,0.397145,0.390152,0.537963,0.540199,0.488863,0.342785,0.447064,0.00169253,0.603936,0.449548,0.41929,1.92146e-07,0.189123,0.588995,0.355645,0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}}
}}

Revision as of 10:57, 19 October 2012


Full id: C1181_Myoblast_CD14_liposarcoma_mesenchymal_caudate_diencephalon_putamen



Phase1 CAGE Peaks

Hg19::chr12:90102690..90102701,-p13@ATP2B1
Hg19::chr12:90102773..90102784,-p6@ATP2B1
Hg19::chr12:90102800..90102814,-p4@ATP2B1
Hg19::chr12:90102818..90102829,-p10@ATP2B1
Hg19::chr12:90102935..90102948,-p5@ATP2B1
Hg19::chr12:90102960..90102971,-p7@ATP2B1
Hg19::chr12:90102986..90102998,-p12@ATP2B1


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

No GOStat results

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
classical monocyte6.38e-2642
CD14-positive, CD16-negative classical monocyte6.38e-2642
leukocyte8.04e-23136
defensive cell5.42e-2148
phagocyte5.42e-2148
nongranular leukocyte7.27e-20115
myeloid leukocyte2.51e-1972
macrophage dendritic cell progenitor2.80e-1861
hematopoietic lineage restricted progenitor cell6.23e-18120
monopoietic cell1.45e-1759
monocyte1.45e-1759
monoblast1.45e-1759
promonocyte1.45e-1759
granulocyte monocyte progenitor cell1.55e-1767
myeloid lineage restricted progenitor cell3.40e-1566
hematopoietic stem cell1.57e-14168
angioblastic mesenchymal cell1.57e-14168
hematopoietic oligopotent progenitor cell1.10e-13161
hematopoietic multipotent progenitor cell1.10e-13161
hematopoietic cell1.29e-12177
myeloid cell2.08e-10108
common myeloid progenitor2.08e-10108
connective tissue cell7.87e-09361
mesenchymal cell8.37e-09354
multi fate stem cell6.32e-08427
stem cell1.56e-07441
somatic stem cell2.89e-07433
motile cell6.34e-07386
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.71e-1598
blood island4.71e-1598
bone marrow5.70e-1576
cerebral hemisphere1.48e-1432
regional part of forebrain9.23e-1441
forebrain9.23e-1441
anterior neural tube9.23e-1441
future forebrain9.23e-1441
telencephalon1.57e-1334
regional part of telencephalon8.53e-1332
brain grey matter1.96e-1234
gray matter1.96e-1234
regional part of cerebral cortex2.01e-1222
bone element2.51e-1282
immune system9.39e-1293
skeletal system1.39e-11100
hemolymphoid system1.68e-11108
neocortex2.24e-1120
skeletal element2.65e-1190
regional part of nervous system8.34e-1153
regional part of brain8.34e-1153
cerebral cortex1.24e-1025
pallium1.24e-1025
neural tube3.23e-1056
neural rod3.23e-1056
future spinal cord3.23e-1056
neural keel3.23e-1056
central nervous system1.83e-0981
connective tissue2.22e-09371
nervous system3.15e-0989
brain3.36e-0968
future brain3.36e-0968
musculoskeletal system4.21e-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)

{{{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
ATF3#467619.25414959372185.23155102976118e-083.33360560095929e-06
BHLHE40#8553744.87181354697742.71655591272133e-123.64203315749298e-10
CCNT2#90576.336201576962632.43743907326287e-068.61759307286733e-05
CHD2#1106710.34402283411697.88338195961115e-084.72094339724673e-06
CTCF#1066475.360256373075037.86114662284756e-060.00022237548541267
E2F1#186974.907389214879321.45832274679793e-050.000346779984865276
E2F6#187675.017155731697391.24910426162553e-050.000308113367926095
EGR1#195874.988179094810141.30079520165561e-050.000318084172478834
GATA1#262335.811560633057330.01119311600820290.0411271405425239
HDAC2#3066611.49910305996541.1228817392662e-064.62067162991419e-05
HEY1#2346274.040111043105715.68979821988558e-050.00094986706567556
JUND#372765.995426235889455.24232039014691e-050.000891262736816789
MAX#414965.530761864863258.40673768319711e-050.00126184431861946
NFKB1#479075.488063424193846.66568321176054e-060.000194674857089782
NRF1#489958.721628176936366.71450045004423e-050.00107356967621275
PAX5#507976.669565531177831.7023051190758e-066.43456548429814e-05
POLR2A#543072.147453176558070.004747636447610280.0223330512094392
SIN3A#2594275.408884726815147.3795239773719e-060.000211559183275527
TAF1#687273.343046285745290.0002142336319622450.00246522105426454
TBP#690863.177232017511190.002074112051852660.012018986216692
TFAP2C#7022710.80922860986025.79365976833206e-083.61028659036296e-06
USF1#739165.452713666178259.13505145927422e-050.00133136427484669
USF2#7392712.99219738506961.59819543071901e-081.16641462326249e-06



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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