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Coexpression cluster:C2175: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!1.11e-44!102;UBERON:0003061!1.11e-44!102;UBERON:0002193!2.08e-43!112;UBERON:0002371!1.75e-33!80;UBERON:0003081!8.79e-30!216;UBERON:0001474!5.01e-29!86;UBERON:0002405!9.50e-28!115;UBERON:0004765!3.46e-23!101;UBERON:0001434!3.46e-23!101;UBERON:0002204!1.50e-13!167;UBERON:0002384!4.64e-12!375;UBERON:0000178!2.32e-09!15;UBERON:0000179!2.32e-09!15;UBERON:0000463!2.32e-09!15
|ontology_enrichment_uberon=UBERON:0002390!1.11e-44!102;UBERON:0003061!1.11e-44!102;UBERON:0002193!2.08e-43!112;UBERON:0002371!1.75e-33!80;UBERON:0003081!8.79e-30!216;UBERON:0001474!5.01e-29!86;UBERON:0002405!9.50e-28!115;UBERON:0004765!3.46e-23!101;UBERON:0001434!3.46e-23!101;UBERON:0002204!1.50e-13!167;UBERON:0002384!4.64e-12!375;UBERON:0000178!2.32e-09!15;UBERON:0000179!2.32e-09!15;UBERON:0000463!2.32e-09!15
|tf_chipseq_enrich=HNF4A#3172;2:11.5661451814768:0.0105758568176249:0.0390625233475714
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209692,0.248936,0.0725263,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,0.324236,0.220368,0.258624,0.064656,0.226143,0.460406,0.0438521,0.112715,0.281453,0.0522771,0.0787278,0.515487,0.159873,0.142462,0.143935,0.332403,0.0379537,0.6545,0.187953,0.051459,0.114868,0.0726892,0.18732,0.32305,0.278397,0.245002,0.170848,0.487259,0.051371,0.363016,0.100188,0.223102,0.107653,0.235857,0.419621,0.191914,0.184022,0.216557,0.182956,0.116818,0.389792,0.36316,0.0625685,0.124464,0.544477,0.173134,0.101893,0.142875,0.167635,0.171311,0.787798,0.548036,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.0976639,0.351199,0.535567,0.758305,0.278645,0.365775,0.155708,0.248017,0.22995,0.652972,0.0760151,0.0629459,0.486024,0.0803251,0.226641,0.379174,0.0939463,0.286748,0.367925,0.0471607,0.163865,0.226359,0.832679,0.709625,0.265324,0.279778,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.264432,0.0994829,0.0604041,0.144185,0.0925862,0.289561,0.199201,0.049937,0.172796,0.0595495,0.071232,0.149346,0.121978,0.22302,0.137423,0.284016,0.0754883,0.299492,0.100006,0.362866,0.197817,0.251078,0.279874,0.133127,0.0988568,0.223717,0.426452,0.196838,0.0826805,0.246601,0.193021,0.608002,0.202165,0.0946865,0.120618,0.079499,0.18762,0.195618,0.127688,0.201169,0.220353,0.24948,0.178639,0.291976,0.320355,0.364334,0.15547,0.110256,0.415419,0.14794,0.147307,0.240761,0.225961,0.124417,0.335582,0.317428,0.182843,0.130771,0.327768,0.135777,0.147842,0.0339286,0.217363,0.119015,0.32805,0.21618,0.243266,0.107021,0.0310605,0.20272,0.392453,0.61565,0.0780061,0.315336,0.230477,0.279823,0.295555,0.502112,0.724669,0.0478217,0.507599,0.170854,0.0575231,0.174063,0.514243,0.459091,0.54832,0.502211,0.296013,0.649813,0.537932,0.127256,0.523209,0.548059,0.25423,0.490559,0.45013,0.153911,0.472542,0.685908,0.399934,0.174869,0.509113,0.483077,0.590496,0.23695,0.541914,0.627201,0.526336,0.757308,0.290703,0.622694,0.722684,0.478691,0.360199,0.608176,0.657141,0.824761,0.365494,0.0244211,0.56318,0.364079,0.315494,0.215551,0.421038,0.206595,0.328518,0.545608,0.310552,0.865054,0.483764,0.829658,0.784052,0.209437,0.843495,0.748403,0.232518,0.882403,0.464001,0.871271,0.579004,0.605327,0.839946,0.586133,0.261575,0.257956,0.0384726,0.379063,0.326516,0.522925,0.436016,0.475063,0.202522,0.183837,0.507324,0.126097,0.0912229,0.116739,0.212239,0.048546,0.156999,0.35974,0.301684,0.39549,0.234254,0.357409,0.599068,0.721266,0.50338,0.252827,0.404625,0.416164,0.106633,0.715362,0.479581,0.62689,0.884725,0.642173,0.284496,0.16228,0.162017,0.563206,0.829402,0.321001,0.263302,0.552023,0.180735,0.439629,0.216102,0.254659,0.109605,0.397869,0.582542,0.226491,0.417131,0.463987,0.627953,0.503881,0.454761,0.0840572,0.483658,0.452129,0.301581,0.261657,0.346776,0.466529,0.545655,0.438176,0.349112,0.391754,0.385425,0.307816,0.128211,0.386339,0.382854,0.598787,0.478745,0.611661,0.319747,0.475047,0.0498053,0.608127,0.282281,0.612712,0.2536,0.246827,0.564333,0.70712,0.387134,0.559969,0.358813,0.668972,0.210703,0.148933,0.346636,0.0243196,0.348802,0.476541,0.579645,0.447581,0.42505,0.254628,0.355111,0.479347,0.102411,0.264955,0.378333,0.387805,0.264038,0.22798,0.102495,0.350933,0.263896,0.0446972,0.24452,0.329284,0.242783,0.0947248,0.336551,0.210656,0.246234,0.211271,0.281295,0.267248,0.118257,0.125087,0.215123,0.321224,0.469461,0.325254,0.266651,0.546295,0.231754,0.249415,0.283107,0.285648,0.427316,0.391071,0.279553,0.25563,0.240967,0.160955,0.256687,0.0432189,0.122439,0.16188,0.23235,0.0469743,0.353147,0.112422,0.170886,0.267687,0.315656,0.284866,0.0887542,0.267811,0.338547,0.147872,0.189388,0.293546,0.210125,0.292967,0.218414,0.0509944,0.0871471,0.0689852,0.0602698,0.341188,0.259328,0.437467,0.201057,0.15696,0.129351,0.141936,0.0786166,0.276997,0.205513,0.282389,0.251421,0.162089,0.330223,0.387837,0.233244,0.207281,0.327401,0.195748,0.27845,0.161712,0.237871,0.239139,0.095257,0.328852,0.332769,0.262022,0.274403,0.266687,0.184534,0.248707,0.31749,0.15156,0.287598,0.313858,0.223773,0.25788,0.181895,0.253768,0.30702,0.202977,0.170837,0.327002,0.28543,0.222656,0.228479,0.127111,0.259989,0.390754,0.355805,0.279739,0.108118,0.259901,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.332746,0.271338,0.242121,0.298673,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.373453,0.362662,0.433518,0.184359,0.334474,0.325785,0.257476,0.291176,0.376537,0.322827,0.229571,0.359036,0.335984,0.171704,0.208256,0.265058,0.256405,0.362898,0.302133,0.40806,0.151361,0.279606,0.286696,0.150674,0.251128,0.246177,0.35674,0.35852,0.318525,0.213257,0.287217,0.122782,0.410951,0.289049,0.266974,0.125746,0.112897,0.398354,0.222091,0.205977,0.34423,0.0936726,0.343425,0.132374,0.285122,0.22741,0.203996,0.276721,0.321965,0.264707,0.450113
}}
}}

Revision as of 12:33, 5 September 2012


Full id: C2175_CD14_CD14CD16_splenic_migratory_Peripheral_Basophils_Whole



Phase1 CAGE Peaks

Hg19::chr12:10124110..10124121,+p2@CLEC12A
Hg19::chr4:38080384..38080414,+p@chr4:38080384..38080414
+
Hg19::chr5:54070798..54070804,+p@chr5:54070798..54070804
+
Hg19::chr9:136343729..136343751,-p4@SLC2A6


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:0005355glucose transmembrane transporter activity0.0164759143109795
GO:0015149hexose transmembrane transporter activity0.0164759143109795
GO:0015145monosaccharide transmembrane transporter activity0.0164759143109795
GO:0005351sugar:hydrogen ion symporter activity0.022368731471487
GO:0051119sugar transmembrane transporter activity0.022368731471487
GO:0015144carbohydrate transmembrane transporter activity0.022368731471487
GO:0008643carbohydrate transport0.022368731471487
GO:0015293symporter activity0.0425894721577773



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
leukocyte4.09e-48140
hematopoietic stem cell1.04e-45172
angioblastic mesenchymal cell1.04e-45172
myeloid leukocyte1.36e-4576
hematopoietic cell3.98e-45182
nongranular leukocyte7.56e-43119
hematopoietic oligopotent progenitor cell1.76e-42165
hematopoietic multipotent progenitor cell1.76e-42165
monopoietic cell1.80e-4263
monocyte1.80e-4263
monoblast1.80e-4263
promonocyte1.80e-4263
myeloid lineage restricted progenitor cell5.14e-4170
macrophage dendritic cell progenitor3.09e-4065
granulocyte monocyte progenitor cell5.41e-4071
myeloid cell5.08e-39112
common myeloid progenitor5.08e-39112
hematopoietic lineage restricted progenitor cell1.01e-38124
CD14-positive, CD16-negative classical monocyte1.73e-3642
classical monocyte1.35e-3445
mesenchymal cell2.61e-13358
connective tissue cell1.50e-12365
multi fate stem cell2.85e-11430
stem cell6.75e-11444
somatic stem cell2.05e-10436
motile cell2.27e-10390
intermediate monocyte2.75e-099
CD14-positive, CD16-positive monocyte2.75e-099
lymphocyte of B lineage9.20e-0824
pro-B cell9.20e-0824
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.11e-44102
blood island1.11e-44102
hemolymphoid system2.08e-43112
bone marrow1.75e-3380
lateral plate mesoderm8.79e-30216
bone element5.01e-2986
immune system9.50e-28115
skeletal element3.46e-23101
skeletal system3.46e-23101
musculoskeletal system1.50e-13167
connective tissue4.64e-12375
blood2.32e-0915
haemolymphatic fluid2.32e-0915
organism substance2.32e-0915


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
HNF4A#3172211.56614518147680.01057585681762490.0390625233475714



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.