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Coexpression cluster:C1511: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000475!1.06e-21!365;UBERON:0007023!1.42e-10!115;UBERON:0000033!2.07e-09!123;UBERON:0000062!3.51e-09!511;UBERON:0000153!4.95e-09!129;UBERON:0007811!4.95e-09!129;UBERON:0000481!5.74e-09!347;UBERON:0005743!6.16e-09!86;UBERON:0002616!1.51e-08!59;UBERON:0003075!2.22e-08!86;UBERON:0007284!2.22e-08!86;UBERON:0000955!5.12e-08!69;UBERON:0006238!5.12e-08!69;UBERON:0003102!6.53e-08!95;UBERON:0002346!6.56e-08!90;UBERON:0001049!1.51e-07!57;UBERON:0005068!1.51e-07!57;UBERON:0006241!1.51e-07!57;UBERON:0007135!1.51e-07!57;UBERON:0001017!1.95e-07!82;UBERON:0004121!3.51e-07!169;UBERON:0000483!4.75e-07!309;UBERON:0000468!4.75e-07!659;UBERON:0000119!5.78e-07!312;UBERON:0000924!6.12e-07!173;UBERON:0006601!6.12e-07!173;UBERON:0000073!6.83e-07!94;UBERON:0001016!6.83e-07!94;UBERON:0002100!7.08e-07!216
|ontology_enrichment_uberon=UBERON:0000475!1.06e-21!365;UBERON:0007023!1.42e-10!115;UBERON:0000033!2.07e-09!123;UBERON:0000062!3.51e-09!511;UBERON:0000153!4.95e-09!129;UBERON:0007811!4.95e-09!129;UBERON:0000481!5.74e-09!347;UBERON:0005743!6.16e-09!86;UBERON:0002616!1.51e-08!59;UBERON:0003075!2.22e-08!86;UBERON:0007284!2.22e-08!86;UBERON:0000955!5.12e-08!69;UBERON:0006238!5.12e-08!69;UBERON:0003102!6.53e-08!95;UBERON:0002346!6.56e-08!90;UBERON:0001049!1.51e-07!57;UBERON:0005068!1.51e-07!57;UBERON:0006241!1.51e-07!57;UBERON:0007135!1.51e-07!57;UBERON:0001017!1.95e-07!82;UBERON:0004121!3.51e-07!169;UBERON:0000483!4.75e-07!309;UBERON:0000468!4.75e-07!659;UBERON:0000119!5.78e-07!312;UBERON:0000924!6.12e-07!173;UBERON:0006601!6.12e-07!173;UBERON:0000073!6.83e-07!94;UBERON:0001016!6.83e-07!94;UBERON:0002100!7.08e-07!216
|tf_chipseq_enrich=CEBPB#1051;6:7.97114762582482:3.89609159898068e-06:0.000127038373557897!EP300#2033;6:6.7739417262232:1.03454107484288e-05:0.000269846242046742!HDAC2#3066;6:13.4156202366263:1.71355402088576e-07:9.42897093715953e-06!HEY1#23462;6:4.04011104310571:0.000229896855580751:0.00253405780474913!HNF4A#3172;6:23.1322903629537:6.51490260560877e-09:5.1390476829847e-07!HNF4G#3174;6:28.7534225264468:1.76556713337063e-09:1.541756403362e-07!TBP#6908;5:3.08897557258032:0.00664544827578693:0.0282902202125672
|tfbs_overrepresentation=0.272825,0.113895,0.919872,0.093154,0.359621,0.148479,0.0841651,0.657264,0.0643695,0.0507505,0.259407,0.399944,0.341907,0.236085,0.275252,0.119969,0.000279147,0.18676,0.102909,0.204438,0.341686,0.247578,0.157234,0.180791,0.0814159,0.384547,0.37494,0.173212,0.266831,0.178021,0.3679,0.215086,0.0357376,0.373119,0.128625,0.000803367,0.902769,0.0840902,0.226218,0.128959,0.183651,0.0486174,1.62236e-05,0.334176,0.227213,0.0711697,0.074588,0.330075,0.210181,7.74537e-06,0.284405,0.105423,0.135407,0.177342,0.010449,0.0753565,0.203364,0.380173,0.150513,0.199999,0.0579941,0.276509,0.205409,0.146128,0.10616,0.0984283,0.580456,0.00705583,0.164736,0.3062,0.61426,0.130776,0.170145,0.224513,0.0148962,0.0339424,0.00119733,0.0854797,6.89079e-05,0.0144524,0.182113,0.402334,0.0831938,0.216503,0.000730978,0.440248,0.124542,0.37437,0.290226,0.121557,0.164159,0.0967167,0.181667,0.0925031,0.163486,0.216824,0.827684,0.28366,0.17689,0.473112,0.111667,0.000551659,0.263619,0.0727591,0.390176,0.080182,0.12949,0.561883,0.267635,0.466115,0.331856,0.0668385,0.276738,0.0350582,0.0197817,0.0663658,0.0402636,0.1101,0.258716,0.160649,0.00616773,0.383317,0.260612,0.164207,0.194257,0.322526,0.0159395,0.0293679,0.161604,0.251658,0.115605,0.144069,0.111159,0.045053,0.235761,0.204515,0.125521,0.10761,0.0649881,0.00789487,0.0450332,0.238929,0.366262,0.28766,0.837237,0.133829,0.18788,0.161361,0.0763672,0.227065,0.361034,0.266711,0.328768,0.0524571,0.0835935,0.221281,0.14393,0.40461,0.100724,0.0663128,0.403582,0.181487,0.219679,0.273735,0.472167,0.215506,0.0784618,0.238515,0.0790799,0.0072325,0.327089,0.256483,0.712672,0.10534,0.153476,0.172044,0.260974,0.00799827,0.325054,0.069998,0.0476775,0.229948,0.0540612,0.21779,0.142014,0.0270952,0.332561,0.0787371,0.158872,0.000650235,0.20281,0.339514,0.230757,0.405269,0.212647,0.0919303,0.150381,0.116937,1.43515e-05,0.207318,0.170629,0.117148,0.0607132,0.117534,0.254283,3.90764e-05,0.472314,0.280641,0.370039,0.324906,0.0896296,0.197823,0.22763,0.213053,0.527451,0.309534,0.301442,0.191696,0.122022,0.195373,0.00380771,0.606181,0.287766,0.296123,0.142265,0.237192,0.258424,0.164555,0.00715957,0.116204,0.239261,0.0032423,0.0819301,0.147153,0.18264,0.177704,0.092224,0.45696,0.30027,0.383466,0.331647,0.57619,0.187116,0.15928,0.219044,0.254951,0.156377,0.21083,0.606625,0.220359,0.292806,0.336043,0.336985,0.186448,0.186558,0.293852,0.202983,0.362971,0.134325,0.825612,0.120009,0.319541,0.300061,0.239783,0.0678354,0.155564,0.15574,1.90862e-06,6.7785e-06,0.145331,0.479224,0.122578,0.444637,0.693924,0.165683,0.0746442,0.243403,0.0334856,0.242011,0.952889,0.86741,0.492922,0.269194,0.236143,0.558337,0.319502,0.454695,0.693419,0.607724,0.0391757,0.155098,0.552041,0.0194751,0.55052,0.452242,2.55351e-10,0.469955,0.498953,0.279316,0.00385725,0.00215428,3.43757e-06,7.24432e-05,0.00034614,0.33041,2.71151e-07,0.207878,0.552298,0.000160791,2.19717e-05,0.611777,0.130242,0.875797,0.000936368,0.000148844,0.604085,0.0239001,0.734265,0.0216509,0.477024,0.512499,6.94257e-05,0.53335,0.397052,0.000620337,0.842556,0.486953,0.530428,0.821632,0.000736076,0.000237383,0.820775,0.000875433,0.00555655,0.371535,4.37142e-08,0.0689805,0.000424309,0.847056,0.331481,0.913739,0.968037,0.519866,0.474883,0.417024,0.336852,0.572701,0.78433,0.468536,0.0496988,0.00318529,0.76366,4.74191e-07,0.43545,0.483867,5.73986e-05,0.29984,0.129605,0.000520536,0.335439,0.837308,0.000206693,0.254373,0.00475509,2.15089e-09,0.00125771,0.798903,0.333233,1.31523e-05,0.527767,0.6863,0.0881806,0.143918,0.405564,0.350549,0.00241621,0.165274,0.155199,0.00175316,0.372295,0.494769,0.547216,0.899629,0.47878,0.0196266,0.673583,0.404165,0.198375,0.356202,0.288188,0.0896504,0.29896,0.00238765,0.0979004,3.11345e-06,0.98005,0.557914,0.268648,4.59513e-08,0.0755726,0.610862,0.332296,0.708323,0.440842,0.282051,0.0909735,0.2554,0.451268,0.034645,0.187452,0.794085,0.0335873,5.55266e-07,0.0537079,0.000957853,0.166271,0.000128983,0.753073,0.000154987,0.488244,0.456149,0.589702,0.401321,0.279541,0.000132695,4.46521e-05,4.91993e-05,0.939276,0.369917,0.0181345,0.0629603,0.683229,0.46597,0.563445,0.218543,0.142358,0.263421,0.0351142,0.183661,0.293756,2.29027e-05,0.605969,0.410562,0.343113,0.170331,0.115576,0.774372,0.859607,0.57398,9.68976e-08,0.0566206,0.000383835,0.0042581,0.00028153,4.46091e-05,0.532388,0.134669,0.108266,0.348016,0.149912,0.111821,0.0395767,0.396879,0.365836,0.114065,0.68834,0.346776,0.211334,0.494962,0.0851816,0.514659,0.23696,0.251518,0.202355,0.471945,0.121642,0.617317,0.0354999,0.515499,0.000590393,0.628382,0.0908048,0.310441,0.216037,0.198185,0.171816,0.165877,0.294115,0.202749,0.0858038,0.00776602,0.23191,0.241631,0.376483,0.00966468,0.572771,0.0974547,0.15892,0.128942,0.331179,0.00183595,0.0887944,0.0487777,0.352924,0.246924,0.341783,0.0940377,0.359953,0.64718,0.239194,0.32067,0.00835526,0.309827,0.167604,0.181395,0.0223847,0.00179197,0.202628,0.474729,0.00960329,0.317242,0.262323,0.378417,0.0592343,1.17769e-05,0.0870651,0.101982,0.374106,0.28290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}}
}}

Revision as of 13:51, 5 September 2012


Full id: C1511_Prostate_Smooth_Hepatocyte_liver_Pancreatic_lung_mature



Phase1 CAGE Peaks

Hg19::chr3:123518799..123518836,-p16@MYLK
Hg19::chr3:123518853..123518862,-p48@MYLK
Hg19::chr3:123518869..123518898,-p9@MYLK
Hg19::chr3:123518900..123518913,-p18@MYLK
Hg19::chr3:123518925..123518939,-p29@MYLK
Hg19::chr3:123519062..123519090,-p14@MYLK


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
fat cell8.75e-0915
fibroblast1.93e-0775
skin fibroblast6.31e-0723
Uber Anatomy
Ontology termp-valuen
organism subdivision1.06e-21365
adult organism1.42e-10115
head2.07e-09123
organ3.51e-09511
anterior region of body4.95e-09129
craniocervical region4.95e-09129
multi-tissue structure5.74e-09347
regional part of brain1.51e-0859
neural plate2.22e-0886
presumptive neural plate2.22e-0886
brain5.12e-0869
future brain5.12e-0869
surface structure6.53e-0895
neurectoderm6.56e-0890
neural tube1.51e-0757
neural rod1.51e-0757
future spinal cord1.51e-0757
neural keel1.51e-0757
central nervous system1.95e-0782
ectoderm-derived structure3.51e-07169
epithelium4.75e-07309
multi-cellular organism4.75e-07659
cell layer5.78e-07312
ectoderm6.12e-07173
presumptive ectoderm6.12e-07173
regional part of nervous system6.83e-0794
nervous system6.83e-0794
trunk7.08e-07216


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
CEBPB#105167.971147625824823.89609159898068e-060.000127038373557897
EP300#203366.77394172622321.03454107484288e-050.000269846242046742
HDAC2#3066613.41562023662631.71355402088576e-079.42897093715953e-06
HEY1#2346264.040111043105710.0002298968555807510.00253405780474913
HNF4A#3172623.13229036295376.51490260560877e-095.1390476829847e-07
HNF4G#3174628.75342252644681.76556713337063e-091.541756403362e-07
TBP#690853.088975572580320.006645448275786930.0282902202125672



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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