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Coexpression cluster:C3568: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!6.53e-23!102;UBERON:0003061!6.53e-23!102;UBERON:0002193!2.41e-22!112;UBERON:0007023!1.31e-18!115;UBERON:0002371!7.44e-14!80;UBERON:0001474!3.64e-13!86;UBERON:0002405!2.37e-12!115;UBERON:0004765!4.69e-10!101;UBERON:0001434!4.69e-10!101;UBERON:0000178!5.83e-08!15;UBERON:0000179!5.83e-08!15;UBERON:0000463!5.83e-08!15
|ontology_enrichment_uberon=UBERON:0002390!6.53e-23!102;UBERON:0003061!6.53e-23!102;UBERON:0002193!2.41e-22!112;UBERON:0007023!1.31e-18!115;UBERON:0002371!7.44e-14!80;UBERON:0001474!3.64e-13!86;UBERON:0002405!2.37e-12!115;UBERON:0004765!4.69e-10!101;UBERON:0001434!4.69e-10!101;UBERON:0000178!5.83e-08!15;UBERON:0000179!5.83e-08!15;UBERON:0000463!5.83e-08!15
|tf_chipseq_enrich=ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0461426883748348!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.027619740102932!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0328802131221092
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595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.0443426,0.0377931,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.0154037,0.201033,0.0488949,0.174921,0.0117175,0.0330727,0.00956472,0.219556,0.0394698,0.0596469,0.103658,0.122476,0.108872,0.11002,0.26144,0.0286025,0.0470027,0.144567,0.038848,0.0874516,0.0550279,0.0109154,0.253693,0.217069,0.190048,0.131088,0.090504,0.0306378,0.0458068,0.0761239,0.172491,0.0818785,0.182701,0.00836526,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.000417587,0.0473033,0.094881,0.022113,0.132886,0.0774373,0.109194,0.128564,0.131452,0.0306206,0.0226843,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.00264443,0.0232393,0.21727,0.00043197,0.119215,0.192475,0.177967,0.0088427,0.057571,0.047591,0.00174134,0.0608699,0.175319,0.0505407,0.0713214,0.223874,0.291114,0.0355833,0.00824114,0.175094,1.70007e-06,0.000581378,0.206454,0.0257531,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.0158019,0.104948,0.221645,0.057168,0.234298,0.0759837,0.286863,0.152372,0.194941,0.00207136,0.101607,0.327067,0.172982,0.0661495,0.151597,0.0626744,0.191335,0.148574,9.16892e-05,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.00238639,0.00326415,0.0461822,0.11903,0.0838874,0.331451,0.00665699,0.112651,0.186638,0.01625,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.0364628,0.103667,0.113069,0.025556,0.16791,0.09066,0.0125264,0.166967,0.188651,0.0813902,0.0182671,0.156261,0.000604034,0.0062542,0.0590944,0.00309372,0.178389,0.218229,0.000161114,0.0161946,0.000500398,0.0360851,0.0021796,0.131093,0.0434602,0.133616,0.0177337,0.0115948,0.449036,0.0973145,0.231447,0.00858901,0.115047,0.37006,0.10748,0.022688,0.197484,0.0148336,0.0750251,0.406019,0.381071,0.216033,0.276075,0.11074,0.0100497,0.0886602,0.145312,0.0334527,0.117158,0.522904,0.000322406,1.75287e-06,0.227104,0.0380245,7.77002e-06,0.0867545,0.284625,0.504757,0.00143312,6.64072e-05,0.28907,0.164197,0.462688,0.0461094,0.21103,0.0283889,0.336276,0.468444,0.0366482,0.0031948,0.243383,4.14881e-06,0.0889613,1.40974e-06,2.74091e-05,0.161598,0.000101989,0.0868402,0.496032,7.35021e-06,0.37357,5.07251e-06,0.138234,0.00104348,2.35949e-07,0.000153842,0.20342,0.200493,0.20558,0.300504,0.25656,0.107337,0.349197,0.0851996,0.156104,0.141318,0.0997241,0.0961477,0.055627,0.354789,0.163828,0.230581,0.120226,0.28424,0.20075,0.314429,0.181415,0.0442318,0.000180531,0.0727621,0.408413,0.165147,0.0586066,0.656109,0.00873429,0.0700181,0.0871388,0.0391112,0.00640674,0.0433137,0.222037,0.416621,0.416292,0.128937,1.66869e-07,0.057399,0.204817,0.122646,0.138871,0.00583733,0.166905,0.19783,0.0833851,0.056391,0.0289164,0.175199,0.332919,0.373557,0.170369,0.408861,0.0111982,0.178743,0.0889149,0.363192,0.236011,0.203486,0.273398,0.375787,0.4466,0.351067,0.275347,0.000640194,0.0524515,0.241132,0.371414,0.0527347,0.303709,0.00533663,0.386538,0.035296,0.250964,0.383276,0.457886,0.156714,0.220231,0.159791,0.196976,0.191517,0.129584,0.235208,0.307334,0.127092,0.283463,0.00164832,0.135386,0.0932845,0.273281,0.0780405,0.0418805,0.0858306,0.138622,0.359231,0.339729,0.197805,0.0690807,0.387069,0.332774,0.0406989,0.299887,8.64162e-05,0.00170684,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.0192444,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,3.62915e-05,0.219428,0.0233135,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.255516,0.20753,0.447185,0.0171537,0.193601,0.0264253,0.222977,0.0664606,0.310674,0.21801,0.0211771,0.0186488,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.00455899,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.000916623,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.0370716,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.0339803,0.115972,0.224568,0.246105,0.0159159,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.0437875,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.0377035,0.211332,0.187731,0.0297055,0.00132285,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.0488311,0.286691,0.347036,0.141729,0.263159,0.0359756,0.200105,0.227491,0.0497481,0.0352561,0.177664,0.28365,0.264413,0.00908908,0.160658,0.206239,0.19924,0.28689,0.236464,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}}
}}

Revision as of 12:52, 5 September 2012


Full id: C3568_Mast_Eosinophils_CD4_immature_CD8_Neutrophils_Natural



Phase1 CAGE Peaks

Hg19::chr16:50776050..50776074,+p3@CYLD
Hg19::chr1:100818080..100818094,+p2@CDC14A
Hg19::chr9:2017714..2017737,+p@chr9:2017714..2017737
+


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:0007049cell cycle0.0463706779592514
GO:0016788hydrolase activity, acting on ester bonds0.0463706779592514
GO:0005856cytoskeleton0.0469426303635197
GO:0008138protein tyrosine/serine/threonine phosphatase activity0.049963050018113
GO:0043687post-translational protein modification0.049963050018113
GO:0006464protein modification process0.049963050018113
GO:0043412biopolymer modification0.049963050018113
GO:0043232intracellular non-membrane-bound organelle0.049963050018113
GO:0043228non-membrane-bound organelle0.049963050018113
GO:0005813centrosome0.049963050018113
GO:0004221ubiquitin thiolesterase activity0.049963050018113
GO:0004843ubiquitin-specific protease activity0.049963050018113
GO:0019783small conjugating protein-specific protease activity0.049963050018113
GO:0005815microtubule organizing center0.049963050018113



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
leukocyte6.81e-38140
hematopoietic stem cell2.00e-34172
angioblastic mesenchymal cell2.00e-34172
hematopoietic oligopotent progenitor cell1.08e-31165
hematopoietic multipotent progenitor cell1.08e-31165
hematopoietic cell1.75e-31182
hematopoietic lineage restricted progenitor cell2.76e-29124
nongranular leukocyte3.73e-28119
myeloid leukocyte6.53e-1976
myeloid cell7.17e-17112
common myeloid progenitor7.17e-17112
CD14-positive, CD16-negative classical monocyte7.69e-1742
granulocyte monocyte progenitor cell3.68e-1671
lymphoid lineage restricted progenitor cell1.66e-1452
lymphocyte2.03e-1453
common lymphoid progenitor2.03e-1453
classical monocyte2.43e-1445
myeloid lineage restricted progenitor cell8.08e-1470
macrophage dendritic cell progenitor2.59e-1365
mature alpha-beta T cell2.01e-1218
alpha-beta T cell2.01e-1218
immature T cell2.01e-1218
mature T cell2.01e-1218
immature alpha-beta T cell2.01e-1218
monopoietic cell2.25e-1263
monocyte2.25e-1263
monoblast2.25e-1263
promonocyte2.25e-1263
T cell3.75e-0925
pro-T cell3.75e-0925
CD8-positive, alpha-beta T cell4.34e-0811
Uber Anatomy
Ontology termp-valuen
hematopoietic system6.53e-23102
blood island6.53e-23102
hemolymphoid system2.41e-22112
adult organism1.31e-18115
bone marrow7.44e-1480
bone element3.64e-1386
immune system2.37e-12115
skeletal element4.69e-10101
skeletal system4.69e-10101
blood5.83e-0815
haemolymphatic fluid5.83e-0815
organism substance5.83e-0815


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
ELF1#199734.258097958807540.01295179875054610.0461426883748348
SIN3A#2594235.408884726815140.006318961977991520.027619740102932
YY1#752834.911170749853860.008441455341808260.0328802131221092



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.