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Coexpression cluster:C4336: Difference between revisions

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|full_id=C4336_heart_CD14CD16_Alveolar_CD14_Mammary_Renal_left
|full_id=C4336_heart_CD14CD16_Alveolar_CD14_Mammary_Renal_left
|id=C4336
|id=C4336
|ontology_enrichment_celltype=CL:0000763!2.46e-37!112;CL:0000049!2.46e-37!112;CL:0000766!1.94e-35!76;CL:0000557!4.16e-31!71;CL:0002009!4.71e-29!65;CL:0002194!8.42e-29!63;CL:0000576!8.42e-29!63;CL:0000040!8.42e-29!63;CL:0000559!8.42e-29!63;CL:0000839!1.22e-27!70;CL:0002057!3.30e-26!42;CL:0000860!2.99e-25!45;CL:0000037!4.72e-20!172;CL:0000566!4.72e-20!172;CL:0000988!9.08e-20!182;CL:0002032!9.22e-18!165;CL:0000837!9.22e-18!165;CL:0000738!4.59e-15!140;CL:0002031!5.09e-10!124;CL:0002087!6.21e-10!119;CL:0002371!8.77e-08!591;CL:0002393!1.95e-07!9;CL:0002397!1.95e-07!9;CL:0002320!2.78e-07!365;CL:0000134!6.08e-07!358
|ontology_enrichment_celltype=CL:0000763!1.02e-37!108;CL:0000049!1.02e-37!108;CL:0000766!6.70e-37!72;CL:0000557!2.95e-31!67;CL:0002194!1.81e-30!59;CL:0000576!1.81e-30!59;CL:0000040!1.81e-30!59;CL:0000559!1.81e-30!59;CL:0002009!1.31e-29!61;CL:0000839!5.13e-29!66;CL:0000473!2.17e-28!48;CL:0000234!2.17e-28!48;CL:0000860!1.38e-25!42;CL:0002057!1.38e-25!42;CL:0000037!1.19e-20!168;CL:0000566!1.19e-20!168;CL:0000988!1.27e-20!177;CL:0002032!4.65e-18!161;CL:0000837!4.65e-18!161;CL:0000738!1.65e-15!136;CL:0000325!4.74e-14!87;CL:0002087!1.45e-10!115;CL:0002031!4.01e-10!120;CL:0002320!4.04e-08!361;CL:0000134!8.45e-08!354;CL:0002393!1.97e-07!9;CL:0002397!1.97e-07!9;CL:0002371!4.26e-07!588
|ontology_enrichment_disease=DOID:8692!7.61e-07!31
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!7.94e-36!102;UBERON:0003061!7.94e-36!102;UBERON:0002371!2.82e-32!80;UBERON:0002193!1.47e-31!112;UBERON:0001474!1.69e-29!86;UBERON:0004765!3.91e-27!101;UBERON:0001434!3.91e-27!101;UBERON:0003081!4.88e-21!216;UBERON:0002405!1.36e-18!115;UBERON:0002204!1.51e-17!167;UBERON:0000926!8.60e-12!448;UBERON:0004120!8.60e-12!448;UBERON:0006603!8.60e-12!448
|ontology_enrichment_uberon=UBERON:0002390!2.46e-35!98;UBERON:0003061!2.46e-35!98;UBERON:0002371!2.23e-32!76;UBERON:0002193!7.15e-31!108;UBERON:0001474!3.08e-30!82;UBERON:0004765!1.02e-29!90;UBERON:0001434!7.75e-27!100;UBERON:0002405!1.90e-26!93;UBERON:0003081!5.56e-17!203;UBERON:0002204!1.03e-16!167;UBERON:0000926!6.77e-11!315;UBERON:0004120!6.77e-11!315;UBERON:0006603!6.77e-11!315;UBERON:0002384!6.40e-07!371
|tf_chipseq_enrich=E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0323532402916395!HNF4A#3172;2:15.4215269086358:0.00544421048668661:0.0246868660567498
|tf_chipseq_enrich=E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0323532402916395!HNF4A#3172;2:15.4215269086358:0.00544421048668661:0.0246868660567498
|tfbs_overrepresentation=0.147255,0.0586687,0.039404,0.0477154,0.199763,0.000422139,0.0430074,0.414564,0.03272,0.0257057,0.139423,0.225367,0.188771,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.209392,0.0907212,0.143747,0.0933697,0.204953,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.688181,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.212709,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.352278,0.0600088,0.0860723,0.167053,0.378921,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.0425,0.114846,0.291327,0.251834,0.064341,0.209032,0.608896,0.062747,0.00378698,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.58489,0.153631,0.0927458,0.27413,0.0574857,0.276221,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.338096,0.144217,0.269326,0.182599,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.0128549,0.596561,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.273479,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.179689,0.137725,0.12972,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.27358,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.312578,0.169057,0.164202,0.100942,0.062995,0.10299,0.14193,0.0800546,0.15606,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.206862,0.384785,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.163502,0.214803,0.182472,0.348993,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.372804,0.117027,0.159052,0.0183114,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.201859,0.0695832,0.0121776,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.278352,0.063292,0.254773,0.446759,0.0865903,0.0380459,0.130174,0.219944,0.713218,0.0199061,0.635872,0.563047,0.0986134,0.0853552,0.335423,0.629514,0.261553,0.118991,0.373681,0.309233,0.49143,0.330703,0.395854,0.329568,0.53472,0.248224,0.271958,0.0475727,0.405773,0.39729,0.581713,0.597171,0.187251,0.362792,0.181715,0.423979,0.109988,0.330894,0.218329,0.427027,0.376924,0.463191,0.280025,0.173877,0.168255,0.0792797,0.415647,0.484505,0.253571,0.276829,0.301787,0.481778,0.316882,0.223503,0.155672,0.236436,0.283727,0.314747,0.21363,0.291709,0.120054,0.212757,0.416816,0.292835,0.137839,0.439556,0.0807167,0.056723,0.608919,0.18237,0.346458,0.248484,0.161148,0.275351,0.236471,0.185661,0.0684159,0.179399,0.270984,0.258117,0.0340542,0.513852,0.522083,0.248634,0.281576,0.472384,0.163244,0.0670502,0.0730934,0.184794,0.596648,0.176034,0.581837,0.412837,0.102184,0.188159,0.551561,0.448039,0.218623,0.312808,0.695172,0.0451077,0.0747529,0.229003,0.0897888,0.061213,0.50215,0.294698,0.34331,0.0282052,0.289204,0.327108,0.109738,0.278044,0.807485,0.428671,0.228096,0.336314,0.19763,0.15631,0.567452,0.421464,0.141711,0.420626,0.165111,0.135248,0.335105,0.144809,0.145539,0.385517,0.376191,0.447325,0.459928,0.252232,0.152681,0.0465712,0.137098,0.259235,0.134788,0.0985856,0.0460163,0.293698,0.284593,0.343734,0.306556,0.305777,0.00257275,0.503082,0.522888,0.284629,0.262537,0.359455,0.0277799,0.405955,0.41707,0.363685,0.464871,0.40841,0.0228979,0.171685,0.284166,0.437176,0.269226,0.339277,0.552319,0.281425,0.141758,0.0238793,0.168058,0.159617,0.238587,0.372281,0.232251,0.189515,0.0891382,0.0595618,0.171389,0.625309,0.347298,0.539392,0.34988,0.475069,0.404569,0.0204872,0.262389,0.316179,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.223391,0.203656,0.442884,0.441735,0.191777,0.111931,0.28934,0.0435386,0.303336,0.126478,0.134852,0.10689,0.273326,0.0627924,0.381386,0.0179103,0.303939,0.279795,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.210369,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.332809,0.19559,0.132201,0.188694,0.0481795,0.199971,0.406014,0.127758,0.175785,0.184486,0.169234,0.0876426,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.0123828,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.28262,0.517717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}}
}}

Revision as of 15:52, 19 October 2012


Full id: C4336_heart_CD14CD16_Alveolar_CD14_Mammary_Renal_left



Phase1 CAGE Peaks

Hg19::chr3:50654550..50654617,+p1@MAPKAPK3
Hg19::chr3:50654914..50654956,+p3@MAPKAPK3
Hg19::chr3:50655081..50655137,+p4@MAPKAPK3


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
myeloid cell1.02e-37108
common myeloid progenitor1.02e-37108
myeloid leukocyte6.70e-3772
granulocyte monocyte progenitor cell2.95e-3167
monopoietic cell1.81e-3059
monocyte1.81e-3059
monoblast1.81e-3059
promonocyte1.81e-3059
macrophage dendritic cell progenitor1.31e-2961
myeloid lineage restricted progenitor cell5.13e-2966
defensive cell2.17e-2848
phagocyte2.17e-2848
classical monocyte1.38e-2542
CD14-positive, CD16-negative classical monocyte1.38e-2542
hematopoietic stem cell1.19e-20168
angioblastic mesenchymal cell1.19e-20168
hematopoietic cell1.27e-20177
hematopoietic oligopotent progenitor cell4.65e-18161
hematopoietic multipotent progenitor cell4.65e-18161
leukocyte1.65e-15136
stuff accumulating cell4.74e-1487
nongranular leukocyte1.45e-10115
hematopoietic lineage restricted progenitor cell4.01e-10120
connective tissue cell4.04e-08361
mesenchymal cell8.45e-08354
intermediate monocyte1.97e-079
CD14-positive, CD16-positive monocyte1.97e-079
somatic cell4.26e-07588
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.46e-3598
blood island2.46e-3598
bone marrow2.23e-3276
hemolymphoid system7.15e-31108
bone element3.08e-3082
skeletal element1.02e-2990
skeletal system7.75e-27100
immune system1.90e-2693
lateral plate mesoderm5.56e-17203
musculoskeletal system1.03e-16167
mesoderm6.77e-11315
mesoderm-derived structure6.77e-11315
presumptive mesoderm6.77e-11315
connective tissue6.40e-07371


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
E2F6#187635.017155731697390.00791769806886330.0323532402916395
HNF4A#3172215.42152690863580.005444210486686610.0246868660567498



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.