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Coexpression cluster:C2596: Difference between revisions

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|full_id=C2596_granulocyte_osteosarcoma_rhabdomyosarcoma_embryonic_acute_Saos2_non
|full_id=C2596_granulocyte_osteosarcoma_rhabdomyosarcoma_embryonic_acute_Saos2_non
|id=C2596
|id=C2596
|ontology_enrichment_celltype=CL:0000542!7.09e-10!53;CL:0000051!7.09e-10!53;CL:0000838!1.87e-09!52
|ontology_enrichment_celltype=CL:0002242!2.19e-11!55;CL:0000542!2.18e-10!53;CL:0000051!2.18e-10!53;CL:0000838!6.31e-10!52
|ontology_enrichment_disease=DOID:162!3.09e-65!235;DOID:14566!1.44e-62!239;DOID:0050687!9.10e-37!143;DOID:0050686!1.45e-30!137;DOID:305!3.89e-29!106;DOID:2531!4.36e-21!51;DOID:0060083!4.36e-21!51;DOID:1240!4.49e-18!39;DOID:8692!4.33e-14!31;DOID:7!6.54e-08!39
|ontology_enrichment_disease=DOID:162!9.49e-64!235;DOID:14566!4.01e-61!239;DOID:0050687!7.00e-37!143;DOID:0050686!7.13e-29!137;DOID:305!8.31e-29!106;DOID:2531!1.71e-19!51;DOID:0060083!1.71e-19!51;DOID:1240!1.22e-16!39;DOID:8692!6.83e-13!31;DOID:7!1.02e-07!39
|ontology_enrichment_uberon=
|ontology_enrichment_uberon=
|tf_chipseq_enrich=BCLAF1#9774;2:10.8263238050609:0.0120220381643258:0.0436568026371356!CTBP2#1488;2:31.3585001696641:0.00149267688204723:0.00954120086199465!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106573051778933!E2F4#1874;4:12.6680603152844:3.88145892637771e-05:0.00072739222826478!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0161008610960833!FAM48A#55578;1:288.7921875:0.00345823182072735:0.0175771010864777!GATA1#2623;3:10.1702311078503:0.00151515816849827:0.00966478983447085!GTF2B#2959;2:15.9719149671621:0.00563658572353722:0.025474030740426!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186232911935558!IRF4#3662;2:10.9572563433721:0.0117453018068803:0.0428515187385166!JUNB#3726;3:22.9579744948659:0.000135977250401878:0.00177939206298982!JUND#3727;3:5.24599795640327:0.0104343275174842:0.0386985345027888!MAFF#23764;2:28.1576782449726:0.00184687618036715:0.0109259035573448!MAFK#7975;2:13.550366568915:0.0077720281209805:0.0319580631098501!MAX#4149;3:4.83941663175534:0.0131573713783684:0.0466332748289752!MYC#4609;4:5.2222818716094:0.00134430939527274:0.0088825970475066!NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.00768339477406303!PAX5#5079;3:5.00217414838337:0.0119653317478641:0.0435068510397652!PBX3#5090;2:10.9572563433721:0.0117453018068803:0.0428530157348044!POU2F2#5452;4:9.10612405774252:0.00014539566517493:0.0018846937911387!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00796934846854927!SRF#6722;3:10.3478836966259:0.00143989377840126:0.0092400040751121!STAT2#6773;2:32.6318855932203:0.00137958877512552:0.00898440307322654!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322533517091194!TAF7#6879;4:11.4330694049239:5.85061525419808e-05:0.000970046684447044!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244507095698299!TCF12#6938;3:7.97584867663982:0.00309092039601307:0.0162806453116406!ZNF143#7702;3:10.1256574141709:0.00153486161068818:0.00976899334259634
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66228,0.271849,0.282657,0.105411,0.0997542,0.209692,0.248936,0.0725263,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,0.324236,0.220368,0.258624,0.064656,0.226143,0.0248217,0.0438521,0.435508,0.281453,0.0522771,0.0787278,0.515487,0.159873,0.142462,0.143935,0.332403,0.0379537,0.0230803,0.187953,0.051459,0.114868,0.0726892,0.18732,0.0589328,0.278397,0.245002,0.170848,0.0303627,0.302909,0.363016,0.100188,0.223102,0.107653,0.235857,0.103852,0.191914,0.184022,0.216557,0.182956,0.116818,0.0883765,0.0757944,0.0625685,0.124464,0.544477,0.173134,0.101893,0.142875,0.167635,0.171311,0.787798,0.189107,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.0976639,0.351199,0.107849,0.415079,0.278645,0.365775,0.155708,0.248017,0.22995,0.0227764,0.0760151,0.0629459,0.486024,0.0803251,0.226641,0.379174,0.0939463,0.286748,0.367925,0.0471607,0.163865,0.226359,0.404165,0.0792764,0.265324,0.279778,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.264432,0.0994829,0.0604041,0.144185,0.0925862,0.000433669,0.199201,0.049937,0.0158721,0.0595495,0.071232,0.149346,0.121978,0.22302,0.137423,0.284016,0.0754883,0.299492,0.100006,0.000106752,0.0210009,0.251078,0.0434358,0.133127,0.0988568,0.223717,0.426452,0.0207859,0.0826805,0.246601,0.193021,0.000422824,0.202165,0.0946865,0.120618,0.079499,0.18762,0.195618,0.127688,0.0217469,0.220353,0.24948,0.178639,0.291976,0.320355,0.364334,0.15547,7.06917e-06,0.415419,0.14794,0.147307,0.240761,0.0277041,0.124417,0.335582,0.317428,0.182843,0.130771,0.327768,0.135777,0.147842,0.0339286,0.217363,0.119015,0.32805,0.21618,0.243266,0.107021,0.238657,0.20272,0.392453,0.0724243,0.0780061,0.315336,0.230477,0.043419,0.295555,0.0338237,0.724669,0.0478217,0.158752,0.170854,0.0575231,0.174063,0.514243,0.0245723,0.189333,0.0338476,0.296013,0.649813,0.537932,0.459994,0.523209,0.548059,0.25423,0.00505798,0.121268,0.500698,0.472542,0.685908,0.0510811,0.529642,0.509113,0.483077,0.224887,0.23695,0.541914,0.627201,0.938109,0.0594404,0.290703,0.254935,0.722684,0.478691,0.360199,0.241059,0.657141,0.519564,0.365494,0.212703,0.56318,0.364079,0.680099,0.579886,0.421038,0.569409,0.328518,0.545608,0.310552,0.865054,0.483764,0.528161,0.784052,0.209437,0.843495,0.748403,0.598945,0.882403,0.464001,0.871271,0.579004,0.870272,0.839946,0.860705,0.261575,0.257956,0.264245,0.379063,0.326516,0.522925,0.436016,0.475063,0.202522,0.183837,0.158557,0.126097,0.0912229,0.442469,0.212239,0.294954,0.156999,0.35974,0.667777,0.39549,0.234254,0.357409,0.86719,0.721266,0.50338,0.620526,0.404625,0.416164,0.424691,0.715362,0.479581,0.62689,0.884725,0.0854676,0.284496,0.512545,0.512178,0.563206,0.829402,0.684899,0.00378836,0.192292,0.180735,0.775168,0.216102,0.254659,0.109605,0.397869,0.582542,0.226491,0.417131,0.463987,0.627953,0.503881,0.124057,0.271678,0.483658,0.452129,0.301581,0.261657,0.346776,0.466529,0.187223,0.438176,0.349112,0.391754,0.0862349,0.307816,0.461541,0.386339,0.0849889,0.598787,0.478745,0.611661,0.319747,0.475047,0.197104,0.0690544,0.282281,0.612712,0.2536,0.246827,0.0519643,0.70712,0.387134,0.050476,0.358813,0.0261538,0.574252,0.493455,0.346636,0.457747,0.348802,0.476541,0.215342,0.119749,0.42505,0.254628,0.713293,0.479347,0.416962,0.632833,0.378333,0.738545,0.264038,0.22798,0.102495,0.350933,0.263896,0.0446972,0.24452,0.329284,0.242783,0.0947248,0.336551,0.210656,0.246234,0.211271,0.281295,0.267248,0.118257,0.125087,0.215123,0.0582227,0.469461,0.325254,0.266651,0.546295,0.231754,0.249415,0.283107,0.285648,0.427316,0.391071,0.279553,0.25563,0.240967,0.160955,0.256687,0.0432189,0.00782177,0.16188,0.23235,0.290415,0.353147,0.112422,0.170886,0.267687,0.315656,0.284866,0.00406065,0.267811,0.338547,0.147872,0.189388,0.293546,0.210125,0.292967,0.218414,0.0509944,0.0871471,0.0689852,0.0602698,0.341188,0.259328,0.113839,0.201057,0.15696,0.129351,0.141936,0.0786166,0.276997,0.205513,0.282389,0.251421,0.162089,0.330223,0.0874139,0.233244,0.207281,0.327401,0.195748,0.0429696,0.161712,0.237871,0.239139,0.095257,0.328852,0.332769,0.262022,0.274403,0.266687,0.184534,0.248707,0.31749,0.000654477,0.0460134,0.313858,0.223773,0.25788,0.181895,0.253768,0.30702,0.202977,0.170837,0.327002,0.28543,0.0268645,0.228479,0.127111,0.259989,0.390754,0.355805,0.279739,0.108118,0.259901,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.332746,0.271338,0.242121,0.298673,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.373453,0.362662,0.433518,0.184359,0.0634867,0.325785,0.257476,0.291176,0.376537,0.322827,0.229571,0.359036,0.335984,0.171704,0.208256,0.265058,0.256405,0.362898,0.302133,0.40806,0.151361,0.279606,0.286696,0.150674,0.251128,0.246177,0.35674,0.35852,0.318525,0.213257,0.287217,0.122782,0.410951,0.289049,0.266974,0.00825997,0.112897,0.398354,0.222091,0.205977,0.34423,0.0936726,0.0671916,0.132374,0.285122,0.0280766,0.203996,0.276721,0.321965,0.264707,0.450113
}}
}}

Revision as of 14:12, 19 October 2012


Full id: C2596_granulocyte_osteosarcoma_rhabdomyosarcoma_embryonic_acute_Saos2_non



Phase1 CAGE Peaks

Hg19::chr1:62902687..62902806,+p1@USP1
Hg19::chr8:121457642..121457672,+p1@MTBP
Hg19::chr8:124408630..124408647,-p2@ATAD2
Hg19::chr8:124408652..124408712,-p1@ATAD2


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><br>disease_data<br>

Cell Type
Ontology termp-valuen
nucleate cell2.19e-1155
lymphocyte2.18e-1053
common lymphoid progenitor2.18e-1053
lymphoid lineage restricted progenitor cell6.31e-1052
Disease
Ontology termp-valuen
cancer9.49e-64235
disease of cellular proliferation4.01e-61239
cell type cancer7.00e-37143
organ system cancer7.13e-29137
carcinoma8.31e-29106
hematologic cancer1.71e-1951
immune system cancer1.71e-1951
leukemia1.22e-1639
myeloid leukemia6.83e-1331
disease of anatomical entity1.02e-0739


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
BCLAF1#9774210.82632380506090.01202203816432580.0436568026371356
CTBP2#1488231.35850016966410.001492676882047230.00954120086199465
E2F1#186944.907389214879320.001724022357361790.0106573051778933
E2F4#1874412.66806031528443.88145892637771e-050.00072739222826478
ELF1#199744.258097958807540.003041525565781240.0161008610960833
FAM48A#555781288.79218750.003458231820727350.0175771010864777
GATA1#2623310.17023110785030.001515158168498270.00966478983447085
GTF2B#2959215.97191496716210.005636585723537220.025474030740426
HEY1#2346244.040111043105710.00375304636917980.0186232911935558
IRF4#3662210.95725634337210.01174530180688030.0428515187385166
JUNB#3726322.95797449486590.0001359772504018780.00177939206298982
JUND#372735.245997956403270.01043432751748420.0386985345027888
MAFF#23764228.15767824497260.001846876180367150.0109259035573448
MAFK#7975213.5503665689150.00777202812098050.0319580631098501
MAX#414934.839416631755340.01315737137836840.0466332748289752
MYC#460945.22228187160940.001344309395272740.0088825970475066
NFKB1#479045.488063424193840.001102199566301980.00768339477406303
PAX5#507935.002174148383370.01196533174786410.0435068510397652
PBX3#5090210.95725634337210.01174530180688030.0428530157348044
POU2F2#545249.106124057742520.000145395665174930.0018846937911387
SIN3A#2594245.408884726815140.001168172384885160.00796934846854927
SRF#6722310.34788369662590.001439893778401260.0092400040751121
STAT2#6773232.63188559322030.001379588775125520.00898440307322654
TAF1#687243.343046285745290.008005664898701650.0322533517091194
TAF7#6879411.43306940492395.85061525419808e-050.000970046684447044
TBP#690843.706770687096390.005296377814784350.0244507095698299
TCF12#693837.975848676639820.003090920396013070.0162806453116406
ZNF143#7702310.12565741417090.001534861610688180.00976899334259634



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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