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Coexpression cluster:C2938: Difference between revisions

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|ontology_enrichment_disease=DOID:1240!1.86e-18!39;DOID:8692!1.26e-16!31;DOID:2531!7.36e-16!51;DOID:0060083!7.36e-16!51
|ontology_enrichment_disease=DOID:1240!1.86e-18!39;DOID:8692!1.26e-16!31;DOID:2531!7.36e-16!51;DOID:0060083!7.36e-16!51
|ontology_enrichment_uberon=UBERON:0002390!5.77e-24!102;UBERON:0003061!5.77e-24!102;UBERON:0002193!1.59e-22!112;UBERON:0007023!2.23e-16!115;UBERON:0002371!2.11e-14!80;UBERON:0001474!3.34e-12!86;UBERON:0002405!5.43e-12!115;UBERON:0000178!9.94e-10!15;UBERON:0000179!9.94e-10!15;UBERON:0000463!9.94e-10!15;UBERON:0003081!3.01e-07!216;UBERON:0004765!3.07e-07!101;UBERON:0001434!3.07e-07!101
|ontology_enrichment_uberon=UBERON:0002390!5.77e-24!102;UBERON:0003061!5.77e-24!102;UBERON:0002193!1.59e-22!112;UBERON:0007023!2.23e-16!115;UBERON:0002371!2.11e-14!80;UBERON:0001474!3.34e-12!86;UBERON:0002405!5.43e-12!115;UBERON:0000178!9.94e-10!15;UBERON:0000179!9.94e-10!15;UBERON:0000463!9.94e-10!15;UBERON:0003081!3.01e-07!216;UBERON:0004765!3.07e-07!101;UBERON:0001434!3.07e-07!101
|tf_chipseq_enrich=EGR1#1958;4:4.98817909481014:0.00161501150007605:0.0101688181139714
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03989,0.171436,0.05892,0.0691994,0.000309443,0.198844,0.104946,0.127738,0.207615,0.161213,0.118999,0.0737069,0.357807,0.0173365,0.178782,0.019419,0.0866228,0.271849,0.282657,0.105411,0.0997542,0.209692,0.248936,0.00269603,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,0.324236,0.220368,0.258624,0.064656,0.0277507,4.52659e-05,0.0438521,0.435508,2.49856e-05,0.0522771,0.0787278,0.00648069,0.159873,0.142462,0.0108948,0.00814638,0.0379537,0.000120758,0.0012877,0.051459,0.114868,6.76981e-05,0.18732,0.0589328,0.278397,0.245002,0.170848,0.487259,0.051371,0.363016,0.100188,0.223102,0.107653,0.235857,0.000253229,0.191914,0.184022,0.0253522,0.182956,0.116818,0.389792,0.0757944,0.0625685,0.124464,0.544477,4.67732e-05,0.101893,0.0107308,0.167635,0.171311,0.00520751,0.548036,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.0976639,0.00103527,0.000107347,0.758305,0.278645,0.0769795,2.82505e-08,0.248017,0.22995,0.0227764,0.0760151,0.0629459,0.0300882,0.0803251,0.226641,0.00147405,0.00455803,0.286748,0.367925,0.0471607,0.163865,0.226359,7.74729e-06,6.22269e-16,0.265324,0.000372329,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.264432,0.0994829,0.0604041,0.144185,0.0925862,0.289561,0.199201,0.049937,0.172796,0.0595495,0.071232,0.149346,0.121978,0.0269564,0.137423,0.284016,0.0754883,0.299492,0.100006,0.0109294,0.197817,0.0345492,0.279874,0.133127,0.410303,0.223717,0.426452,0.196838,0.0826805,0.246601,0.193021,0.240896,0.202165,0.0946865,0.120618,0.079499,0.18762,0.195618,0.127688,0.201169,0.220353,0.00318161,0.178639,0.291976,0.320355,0.364334,0.15547,0.00631475,0.415419,0.14794,0.147307,0.240761,0.225961,0.124417,0.335582,0.317428,0.182843,0.130771,0.327768,0.135777,0.147842,0.0339286,0.00012367,0.119015,0.690952,0.21618,0.243266,0.107021,0.238657,0.20272,0.392453,0.000471212,0.0780061,0.315336,0.230477,0.279823,0.0487563,3.9843e-09,0.000385252,1.89049e-05,9.5926e-06,0.170854,0.0575231,0.174063,0.00640224,0.459091,0.54832,0.00568499,0.296013,0.282366,0.537932,0.459994,0.523209,0.548059,0.25423,0.490559,0.45013,0.500698,0.472542,0.685908,0.00294638,0.529642,0.0943307,0.483077,0.00226518,0.23695,0.541914,0.627201,0.000155182,1.66157e-11,0.290703,0.622694,0.722684,0.139104,0.360199,0.608176,0.657141,0.824761,0.365494,0.212703,0.201391,0.364079,0.00628541,0.00199999,0.421038,0.569409,0.0610883,0.545608,0.310552,2.10702e-07,0.483764,0.000503744,0.0201581,0.209437,0.0118712,9.66019e-05,0.232518,2.71157e-06,4.80168e-05,2.73066e-07,3.39195e-05,0.000276195,0.00283087,0.00100112,0.261575,0.257956,0.264245,0.379063,0.326516,0.0391986,0.436016,0.475063,0.202522,0.183837,0.507324,0.126097,0.3955,0.442469,0.212239,0.294954,0.156999,0.00115593,0.667777,0.39549,0.234254,0.073225,2.30198e-07,0.137737,0.15578,0.0746831,0.404625,0.000119107,0.424691,0.00931622,0.479581,0.0181348,0.884725,0.0854676,0.284496,0.512545,0.512178,0.201413,0.00957951,0.684899,0.263302,0.552023,0.180735,0.0646927,0.216102,0.254659,0.109605,0.00184531,0.582542,0.226491,0.417131,0.463987,0.000560419,0.0342559,0.454761,0.639483,0.0295677,0.452129,0.301581,0.261657,0.346776,0.466529,0.0458396,0.438176,0.349112,0.0124698,1.22036e-05,0.000569773,0.461541,0.0135171,0.382854,0.598787,0.478745,0.611661,0.319747,0.475047,0.557967,0.608127,0.282281,0.612712,0.2536,0.246827,0.564333,0.70712,0.0870695,0.050476,0.358813,0.100705,0.574252,0.493455,0.346636,0.457747,0.348802,5.8853e-05,0.0118751,0.447581,0.42505,0.254628,0.0382032,0.479347,0.102411,0.632833,0.378333,0.738545,0.264038,0.22798,0.102495,0.350933,0.263896,0.0446972,0.24452,0.000772039,0.242783,0.0947248,0.336551,0.210656,0.246234,0.211271,0.281295,0.267248,0.118257,0.125087,0.215123,0.321224,0.469461,0.325254,0.266651,0.546295,0.231754,0.249415,0.283107,0.285648,0.0191181,0.0140903,0.279553,0.25563,0.240967,0.160955,0.256687,0.0432189,0.000336791,0.000804479,0.23235,0.00521493,0.0099749,0.112422,0.170886,0.267687,0.315656,0.284866,0.0887542,0.267811,0.338547,0.147872,0.189388,0.293546,0.210125,0.292967,0.218414,0.0509944,0.0871471,0.0689852,0.0602698,0.341188,0.259328,0.437467,0.201057,0.15696,0.129351,0.141936,0.0786166,0.276997,9.71681e-05,0.282389,0.251421,0.162089,0.00796989,0.387837,0.233244,0.207281,0.000752253,0.195748,0.27845,0.161712,0.000182735,0.239139,0.095257,0.328852,0.332769,0.00372893,0.274403,0.266687,0.184534,0.248707,0.31749,0.15156,0.287598,0.313858,0.000140205,0.25788,0.181895,0.253768,0.30702,0.202977,0.170837,0.00771419,0.000406848,0.222656,0.228479,0.127111,0.259989,0.00169581,0.355805,0.279739,0.108118,0.259901,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.0154764,0.000809519,0.271338,0.242121,0.298673,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.00137371,0.00119976,0.433518,0.184359,0.334474,0.325785,0.257476,0.291176,0.376537,3.49391e-06,0.000156623,0.359036,0.335984,0.171704,0.208256,0.265058,0.256405,0.00120337,0.000524161,0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}}
}}

Revision as of 13:47, 5 September 2012


Full id: C2938_CD4_Peripheral_CD8_Natural_acute_chronic_Renal



Phase1 CAGE Peaks

Hg19::chr9:134152345..134152369,-p1@FAM78A
Hg19::chr9:134152371..134152402,-p2@FAM78A
Hg19::chr9:134152417..134152430,-p6@FAM78A
Hg19::chr9:134152434..134152466,-p@chr9:134152434..134152466
-


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>disease_data<br>

Cell Type
Ontology termp-valuen
hematopoietic stem cell2.31e-62172
angioblastic mesenchymal cell2.31e-62172
hematopoietic cell2.53e-61182
hematopoietic oligopotent progenitor cell3.71e-59165
hematopoietic multipotent progenitor cell3.71e-59165
nongranular leukocyte1.62e-45119
leukocyte2.90e-44140
hematopoietic lineage restricted progenitor cell6.35e-40124
myeloid cell2.66e-34112
common myeloid progenitor2.66e-34112
lymphocyte8.50e-2253
common lymphoid progenitor8.50e-2253
myeloid leukocyte1.45e-2176
lymphoid lineage restricted progenitor cell1.67e-2152
monopoietic cell1.36e-2063
monocyte1.36e-2063
monoblast1.36e-2063
promonocyte1.36e-2063
myeloid lineage restricted progenitor cell2.13e-1970
macrophage dendritic cell progenitor3.63e-1965
granulocyte monocyte progenitor cell6.23e-1871
T cell4.37e-1525
pro-T cell4.37e-1525
CD14-positive, CD16-negative classical monocyte1.49e-1442
mature alpha-beta T cell1.66e-1318
alpha-beta T cell1.66e-1318
immature T cell1.66e-1318
mature T cell1.66e-1318
immature alpha-beta T cell1.66e-1318
classical monocyte2.17e-1345
CD8-positive, alpha-beta T cell7.66e-0911
mesenchymal cell6.67e-07358
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.77e-24102
blood island5.77e-24102
hemolymphoid system1.59e-22112
adult organism2.23e-16115
bone marrow2.11e-1480
bone element3.34e-1286
immune system5.43e-12115
blood9.94e-1015
haemolymphatic fluid9.94e-1015
organism substance9.94e-1015
lateral plate mesoderm3.01e-07216
skeletal element3.07e-07101
skeletal system3.07e-07101
Disease
Ontology termp-valuen
leukemia1.86e-1839
myeloid leukemia1.26e-1631
hematologic cancer7.36e-1651
immune system cancer7.36e-1651


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
EGR1#195844.988179094810140.001615011500076050.0101688181139714



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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