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Coexpression cluster:C2144: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!1.30e-18!102;UBERON:0003061!1.30e-18!102;UBERON:0001474!2.90e-18!86;UBERON:0002371!2.20e-17!80;UBERON:0002193!1.05e-14!112;UBERON:0004765!5.86e-14!101;UBERON:0001434!5.86e-14!101;UBERON:0002384!1.13e-11!375;UBERON:0002405!1.51e-09!115
|ontology_enrichment_uberon=UBERON:0002390!1.30e-18!102;UBERON:0003061!1.30e-18!102;UBERON:0001474!2.90e-18!86;UBERON:0002371!2.20e-17!80;UBERON:0002193!1.05e-14!112;UBERON:0004765!5.86e-14!101;UBERON:0001434!5.86e-14!101;UBERON:0002384!1.13e-11!375;UBERON:0002405!1.51e-09!115
|tf_chipseq_enrich=BATF#10538;2:12.1789008961518:0.00956675880504781:0.0360116317477163!BCL11A#53335;2:14.1847275518035:0.00710832858529874:0.0296125540135626!BCL3#602;2:17.2735514018692:0.00483449420807607:0.0226691393434767!EBF1#1879;3:6.67985013492675:0.00518429411827891:0.0240320680612042!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0160552887826448!EP300#2033;3:5.0804562946674:0.0114429840539824:0.041869944000766!IRF4#3662;2:10.9572563433721:0.0117453018068803:0.0428141277934025!MAX#4149;4:6.45255550900712:0.000576761319564549:0.00484487858553864!MXI1#4601;3:7.47117872156947:0.00374131473855096:0.0186217018529058!NR3C1#2908;3:11.2297674983798:0.00113167206806385:0.00775224315338586!PAX5#5079;3:5.00217414838337:0.0119653317478641:0.0434720407157579!POU2F2#5452;3:6.82959304330689:0.00486047377520374:0.0227521411235939!RXRA#6256;2:10.0373085695666:0.0139170380592011:0.0488696637033455
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282657,0.105411,0.0997542,0.209692,0.248936,0.0725263,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,0.324236,0.220368,0.258624,0.064656,0.226143,0.460406,0.0438521,0.112715,0.281453,0.0522771,0.0787278,0.164404,0.159873,0.142462,0.143935,0.0626466,0.0379537,0.6545,0.187953,0.051459,0.114868,0.0726892,0.18732,0.0589328,0.278397,0.245002,0.170848,0.144756,0.051371,0.363016,0.100188,0.223102,0.107653,0.235857,0.419621,0.191914,0.184022,0.216557,0.182956,0.116818,0.389792,0.36316,0.0625685,0.124464,0.544477,0.173134,0.101893,0.142875,0.167635,0.171311,0.458838,0.548036,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.0976639,0.0705088,0.107849,0.415079,0.278645,0.365775,0.155708,0.000219214,0.22995,0.285695,0.0760151,0.0629459,0.143933,0.0803251,0.226641,0.379174,0.0939463,0.286748,0.367925,0.0471607,0.163865,0.226359,0.22476,0.0792764,0.265324,0.279778,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.264432,0.0994829,0.0604041,0.144185,0.0925862,0.289561,0.199201,0.049937,0.172796,0.0595495,0.071232,0.149346,0.121978,0.22302,0.137423,0.284016,0.0754883,0.299492,0.100006,0.362866,0.197817,0.251078,0.279874,0.133127,0.410303,0.223717,0.426452,0.196838,0.0826805,0.246601,0.193021,0.608002,0.202165,0.0946865,0.120618,0.079499,0.18762,0.195618,0.127688,0.201169,0.220353,0.24948,0.0170013,0.291976,0.320355,0.0110794,0.15547,0.110256,0.415419,0.14794,0.147307,0.240761,0.225961,0.124417,0.335582,0.317428,0.182843,0.130771,0.327768,0.135777,0.147842,0.0339286,0.217363,0.119015,0.690952,0.21618,0.243266,0.107021,0.238657,0.20272,0.0896967,0.0724243,0.0780061,0.315336,0.230477,0.279823,0.00552386,0.154895,0.140541,0.0478217,0.507599,0.170854,0.0575231,0.174063,0.514243,0.459091,0.54832,0.0338476,0.296013,0.282366,0.537932,0.459994,0.170061,0.189126,0.25423,0.490559,0.45013,0.153911,0.472542,0.685908,0.160788,0.529642,0.244786,0.14198,0.000329342,0.23695,0.184287,0.627201,0.0237007,0.757308,0.290703,0.0757071,0.366999,0.478691,0.360199,0.241059,0.657141,0.519564,0.365494,0.212703,0.201391,0.0762097,0.0287777,0.579886,0.421038,0.569409,0.328518,0.545608,0.310552,0.324103,0.142433,0.528161,0.19941,0.209437,0.55323,0.0514874,0.232518,0.361291,0.464001,0.60737,0.0118057,0.605327,0.113944,0.315519,0.261575,0.257956,0.264245,0.379063,0.326516,0.522925,0.436016,0.0277366,0.202522,0.183837,0.507324,0.126097,0.3955,0.0215868,0.212239,0.294954,0.156999,0.35974,0.025886,0.39549,0.0298727,0.0103854,0.146291,0.00204685,0.50338,0.0746831,0.404625,0.759068,0.424691,0.357704,0.479581,0.62689,0.0230743,0.274432,0.284496,0.512545,0.162017,0.201413,0.527709,0.110875,0.263302,0.552023,0.180735,0.439629,0.216102,0.254659,0.109605,0.397869,0.217863,0.226491,0.417131,0.129731,0.627953,0.503881,0.00348879,0.271678,0.483658,0.452129,0.301581,0.261657,0.0686105,0.466529,0.545655,0.438176,0.349112,0.0485429,0.385425,0.307816,0.0250382,0.386339,0.382854,0.598787,0.478745,0.24434,0.319747,0.00431644,0.557967,0.241014,0.282281,0.245336,0.2536,0.246827,0.0519643,0.12664,0.387134,0.559969,0.0738474,0.668972,0.210703,0.493455,0.346636,0.125876,0.0694762,0.476541,0.579645,0.119749,0.42505,0.254628,0.131374,0.479347,0.416962,0.264955,0.378333,0.152547,0.264038,0.22798,0.102495,0.350933,0.263896,0.0446972,0.24452,0.329284,0.242783,0.0947248,0.336551,0.210656,0.246234,0.211271,0.281295,0.267248,0.118257,0.125087,0.215123,0.321224,0.469461,0.325254,0.266651,0.546295,0.231754,0.249415,0.283107,0.285648,0.427316,0.391071,0.279553,0.25563,0.240967,0.160955,0.256687,0.0432189,0.122439,0.16188,0.23235,0.290415,0.353147,0.112422,0.170886,0.267687,0.315656,0.284866,0.0887542,0.267811,0.338547,0.147872,0.189388,0.293546,0.210125,0.292967,0.218414,0.0509944,0.0871471,0.0689852,0.0602698,0.341188,0.259328,0.437467,0.201057,0.15696,0.129351,0.141936,0.0786166,0.276997,0.205513,0.282389,0.251421,0.162089,0.330223,0.387837,0.233244,0.207281,0.327401,0.195748,0.27845,0.161712,0.237871,0.239139,0.095257,0.328852,0.332769,0.262022,0.274403,0.266687,0.184534,0.248707,0.31749,0.15156,0.287598,0.313858,0.223773,0.25788,0.181895,0.253768,0.30702,0.202977,0.170837,0.327002,0.28543,0.222656,0.228479,0.127111,0.259989,0.390754,0.0725176,0.279739,0.108118,0.259901,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.332746,0.271338,0.242121,0.298673,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.373453,0.362662,0.433518,0.184359,0.334474,0.325785,0.257476,0.291176,0.376537,0.322827,0.229571,0.359036,0.335984,0.171704,0.208256,0.265058,0.256405,0.362898,0.302133,0.40806,0.151361,0.279606,0.286696,0.150674,0.251128,0.246177,0.35674,0.35852,0.318525,0.213257,0.287217,0.122782,0.410951,0.289049,0.266974,0.125746,0.112897,0.398354,0.222091,0.205977,0.0675312,0.0936726,0.343425,0.132374,0.285122,0.22741,0.203996,0.276721,0.0585101,0.264707,0.121257
}}
}}

Revision as of 13:47, 5 September 2012


Full id: C2144_Basophils_CD14_Eosinophils_CD4_CD19_Natural_Mast



Phase1 CAGE Peaks

Hg19::chr11:62323170..62323185,+p@chr11:62323170..62323185
+
Hg19::chr12:13254352..13254403,+p@chr12:13254352..13254403
+
Hg19::chr1:156076341..156076364,+p22@LMNA
Hg19::chr8:145026443..145026482,+p@chr8:145026443..145026482
+


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
leukocyte2.05e-35140
nongranular leukocyte7.54e-30119
hematopoietic lineage restricted progenitor cell4.64e-29124
hematopoietic stem cell4.71e-27172
angioblastic mesenchymal cell4.71e-27172
hematopoietic cell2.95e-26182
hematopoietic oligopotent progenitor cell7.06e-25165
hematopoietic multipotent progenitor cell7.06e-25165
CD14-positive, CD16-negative classical monocyte1.35e-2442
classical monocyte3.93e-2345
myeloid leukocyte8.85e-2076
granulocyte monocyte progenitor cell2.59e-1871
macrophage dendritic cell progenitor2.51e-1665
monopoietic cell2.33e-1563
monocyte2.33e-1563
monoblast2.33e-1563
promonocyte2.33e-1563
myeloid lineage restricted progenitor cell2.46e-1570
lymphocyte6.83e-1353
common lymphoid progenitor6.83e-1353
lymphoid lineage restricted progenitor cell1.21e-1252
myeloid cell2.05e-12112
common myeloid progenitor2.05e-12112
connective tissue cell5.84e-12365
mesenchymal cell9.91e-12358
motile cell6.64e-09390
intermediate monocyte4.58e-079
CD14-positive, CD16-positive monocyte4.58e-079
native cell5.50e-07722
B cell9.00e-0714
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.30e-18102
blood island1.30e-18102
bone element2.90e-1886
bone marrow2.20e-1780
hemolymphoid system1.05e-14112
skeletal element5.86e-14101
skeletal system5.86e-14101
connective tissue1.13e-11375
immune system1.51e-09115


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
BATF#10538212.17890089615180.009566758805047810.0360116317477163
BCL11A#53335214.18472755180350.007108328585298740.0296125540135626
BCL3#602217.27355140186920.004834494208076070.0226691393434767
EBF1#187936.679850134926750.005184294118278910.0240320680612042
ELF1#199744.258097958807540.003041525565781240.0160552887826448
EP300#203335.08045629466740.01144298405398240.041869944000766
IRF4#3662210.95725634337210.01174530180688030.0428141277934025
MAX#414946.452555509007120.0005767613195645490.00484487858553864
MXI1#460137.471178721569470.003741314738550960.0186217018529058
NR3C1#2908311.22976749837980.001131672068063850.00775224315338586
PAX5#507935.002174148383370.01196533174786410.0434720407157579
POU2F2#545236.829593043306890.004860473775203740.0227521411235939
RXRA#6256210.03730856956660.01391703805920110.0488696637033455



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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