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Coexpression cluster:C391: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0007602!phototransduction!0.0060343812551513!2793$GO:0050908!detection of light stimulus during visual perception!0.0060343812551513!2793$GO:0050962!detection of light stimulus during sensory perception!0.0060343812551513!2793$GO:0009584!detection of visible light!0.0060343812551513!2793$GO:0009583!detection of light stimulus!0.0060343812551513!2793$GO:0005834!heterotrimeric G-protein complex!0.0060343812551513!2793$GO:0009582!detection of abiotic stimulus!0.0060343812551513!2793$GO:0050906!detection of stimulus during sensory perception!0.0060343812551513!2793$GO:0019897!extrinsic to plasma membrane!0.0060343812551513!2793$GO:0009581!detection of external stimulus!0.0060343812551513!2793$GO:0051606!detection of stimulus!0.00814641469445426!2793$GO:0009416!response to light stimulus!0.00814641469445426!2793$GO:0009314!response to radiation!0.00922398277573127!2793$GO:0019898!extrinsic to membrane!0.00922398277573127!2793$GO:0009628!response to abiotic stimulus!0.0132756387613329!2793$GO:0007601!visual perception!0.0158313767046911!2793$GO:0050953!sensory perception of light stimulus!0.0158313767046911!2793$GO:0003924!GTPase activity!0.0183713384879051!2793$GO:0009605!response to external stimulus!0.0402080351001134!2793
|gostat_on_coexpression_clusters=GO:0007602!phototransduction!0.0060343812551513!2793$GO:0050908!detection of light stimulus during visual perception!0.0060343812551513!2793$GO:0050962!detection of light stimulus during sensory perception!0.0060343812551513!2793$GO:0009584!detection of visible light!0.0060343812551513!2793$GO:0009583!detection of light stimulus!0.0060343812551513!2793$GO:0005834!heterotrimeric G-protein complex!0.0060343812551513!2793$GO:0009582!detection of abiotic stimulus!0.0060343812551513!2793$GO:0050906!detection of stimulus during sensory perception!0.0060343812551513!2793$GO:0019897!extrinsic to plasma membrane!0.0060343812551513!2793$GO:0009581!detection of external stimulus!0.0060343812551513!2793$GO:0051606!detection of stimulus!0.00814641469445426!2793$GO:0009416!response to light stimulus!0.00814641469445426!2793$GO:0009314!response to radiation!0.00922398277573127!2793$GO:0019898!extrinsic to membrane!0.00922398277573127!2793$GO:0009628!response to abiotic stimulus!0.0132756387613329!2793$GO:0007601!visual perception!0.0158313767046911!2793$GO:0050953!sensory perception of light stimulus!0.0158313767046911!2793$GO:0003924!GTPase activity!0.0183713384879051!2793$GO:0009605!response to external stimulus!0.0402080351001134!2793
|id=C391
|id=C391
|ontology_enrichment_celltype=
|ontology_enrichment_celltype=CL:0000082!6.95e-12!19
|ontology_enrichment_disease=
|ontology_enrichment_disease=DOID:4556!2.39e-66!3;DOID:3908!1.48e-40!5;DOID:3905!2.62e-23!9;DOID:1324!1.22e-14!15;DOID:0050615!8.02e-14!16
|ontology_enrichment_uberon=
|ontology_enrichment_uberon=UBERON:0004802!6.95e-12!19;UBERON:0000115!6.95e-12!19;UBERON:0002048!1.80e-10!22;UBERON:0000117!1.80e-10!22;UBERON:0000171!1.80e-10!22;UBERON:0000170!1.80e-10!22;UBERON:0005597!1.80e-10!22;UBERON:0000118!1.80e-10!22;UBERON:0004807!1.52e-08!28;UBERON:0005178!2.74e-07!34;UBERON:0002224!2.74e-07!34;UBERON:0005181!4.03e-07!35;UBERON:0005153!8.21e-07!37
|tf_chipseq_enrich=FOS#2353;8:2.66606083226501:0.00736170601140233:0.0304350096637181
|tf_chipseq_enrich=FOS#2353;8:2.66606083226501:0.00736170601140233:0.0304350096637181
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0.363121,0.822802,0.919746,0.26117,0.740633,0.892583,0.304016,0.0187708,0.992487,0.691447,0.278,0.0895337,0.934616,0.028711,0.999233,0.754714,0.29995,0.199725,0.399143,0.75342,0.489965,0.0250237,0.295475,0.360593,0.988989,0.91246,0.192238,0.509631,0.508001,0.536445,0.837285,0.881258,0.421328,0.0506981,0.490238,0.744344,0.205112,0.964357,0.807596,0.353465,0.59229,0.898976,0.722869,0.515869,0.646778,0.710186,0.718718,0.99811,0.995302,0.0839242,0.610248,0.369968,0.436962,0.5067,0.587279,0.408218,0.0395288,0.0333779,0.558707,0.999928,0.618639,0.378549,0.953747,0.680973,0.302772,0.828603,0.993569,0.413541,0.35522,0.938533,0.43176,0.0984685,0.40143,0.486206,0.664732,0.598088,0.278257,0.340268,0.251345,0.999996,1,0.615526,0.890881,0.643493,0.466081,0.0870695,0.366198,0.230019,0.156286,0.50703,0.0671484,0.282989,0.480977,0.900504,0.442,0.292333,0.366252,0.33928,0.392741,0.29797,0.584415,0.0298253,0.631331,0.0785953,0.41128,0.430985,0.50896,0.952296,0.43809,0.310215,0.89098,0.25112,0.691006,0.819018,0.976539,0.186049,0.441512,0.569463,0.764863,0.998203,0.782273,0.489033,0.580048,0.428306,0.167121,0.431863,0.0665458,0.780432,0.0902456,0.306324,0.383187,0.676145,0.733915,0.365828,0.680368,0.545494,0.701446,0.660631,0.658924,0.554548,0.82252,0.592145,0.936689,0.728287,0.744104,0.244386,0.93149,0.258719,0.0955675,0.207841,0.492439,0.211218,0.536698,0.806821,0.560975,0.534221,0.841266,0.451902,0.965393,0.98827,0.105161,0.92247,0.829393,0.890928,0.906035,0.990971,0.998393,0.28163,0.951556,0.36061,0.0615242,0.724962,0.716813,0.984202,0.995322,0.848567,0.684796,0.993215,0.892053,0.402229,0.734915,0.782031,0.0508693,0.941471,0.573725,0.947649,0.804878,0.98414,0.900795,0.882827,0.989446,0.459156,0.939201,0.985989,0.994855,0.961783,0.995576,0.999988,0.901578,0.959412,0.998321,0.640035,0.356026,0.998208,0.975014,0.9999,0.953608,0.800962,0.996267,0.365222,0.982546,0.997131,0.882789,0.670946,0.503508,0.900141,0.458771,0.999858,0.988473,0.997613,0.991987,0.213112,0.999951,0.983025,0.863103,0.999936,0.79101,0.999892,0.692905,0.999985,0.999943,0.999175,0.336001,0.597727,0.873977,0.62354,0.132398,0.558725,0.979057,0.00183104,0.782929,0.159588,0.855396,0.597397,0.659805,0.980622,0.800169,0.682542,0.684252,0.950693,0.999412,0.441103,0.834966,0.349444,0.982161,0.972355,0.694159,0.998556,0.864144,0.999287,0.886668,0.924819,0.157416,0.898362,0.999703,0.968925,0.895616,0.862156,0.215548,0.917088,0.992058,0.999588,0.610685,0.906573,0.389244,0.999533,0.227933,0.31897,0.185329,0.855874,0.981043,0.517093,0.878533,0.985143,0.655732,0.991185,0.915076,0.967722,0.936955,0.770782,0.0987523,0.870955,0.781289,0.795174,0.777677,0.979592,0.330056,0.994391,0.962599,0.916537,0.786908,0.962973,0.22977,0.944982,0.93358,0.879963,0.732753,0.987093,0.644116,0.951004,0.0767609,0.765274,0.587002,0.570036,0.996333,0.915759,0.238297,0.996078,0.576793,0.995141,0.978769,0.48507,0.781053,0.917571,0.552962,0.987339,0.980271,0.762741,0.513323,0.589546,0.990209,0.449876,0.704558,0.991029,0.621892,0.946866,0.612451,0.825621,0.518054,0.788183,0.873574,0.265567,0.849337,0.932526,0.559741,0.489179,0.93731,0.797443,0.85163,0.475713,0.3852,0.877408,0.572379,0.228253,0.805055,0.267349,0.926826,0.495432,0.876733,0.969455,0.831295,0.306166,0.656644,0.194696,0.976777,0.847191,0.64864,0.863675,0.555079,0.69412,0.594618,0.257861,0.585883,0.69639,0.832177,0.672764,0.563359,0.552912,0.717743,0.877904,0.922713,0.895981,0.130991,0.878043,0.938572,0.0956142,0.757625,0.416017,0.214627,0.90368,0.810506,0.297633,0.459612,0.382756,0.342688,0.534564,0.601076,0.744296,0.780222,0.684155,0.60741,0.276477,0.424597,0.888006,0.788366,0.655034,0.858387,0.696899,0.507716,0.963579,0.534992,0.46465,0.931237,0.770175,0.646133,0.695977,0.547077,0.550361,0.491202,0.932232,0.934858,0.871384,0.636849,0.876774,0.160964,0.854885,0.476123,0.670245,0.898634,0.921332,0.819105,0.597542,0.155773,0.861357,0.707658,0.783765,0.717629,0.930961,0.395591,0.817341,0.82638,0.60054,0.602683,0.964735,0.796072,0.649061,0.538073,0.331865,0.637918,0.390953,0.391928,0.771139,0.518595,0.312148,0.391707,0.456864,0.513925,0.881954,0.846078,0.220185,0.563857,0.533758,0.605214,0.449348,0.689658,0.119932,0.262178,0.46079,0.510243,0.7107,0.646696,0.333698,0.464036,0.570413,0.286047,0.374921,0.872272,0.610803,0.952192,0.533871,0.399686,0.144385,0.277306,0.016908,0.410051,0.617826,0.489411,0.828033,0.577319,0.936947,0.719617,0.793248,0.874914,0.86463,0.952312,0.697639,0.471837,0.303832,0.890705,0.398776,0.667911,0.858013,0.851554,0.571895,0.80038,0.924874,0.801906,0.898267,0.586976,0.692338,0.669785,0.619452,0.596305,0.554522,0.0599949,0.816444,0.461014,0.54194,0.485157,0.77562,0.616519,0.661135,0.253782,0.785623,0.642183,0.927397,0.614052,0.378348
}}
}}

Revision as of 15:30, 19 October 2012


Full id: C391_large_bronchioalveolar_fibrosarcoma_lung_pancreatic_giant_testis



Phase1 CAGE Peaks

Hg19::chr10:4822880..4822903,-p@chr10:4822880..4822903
-
Hg19::chr10:4822908..4822927,-p@chr10:4822908..4822927
-
Hg19::chr10:4822941..4822949,-p@chr10:4822941..4822949
-
Hg19::chr11:75719740..75719766,+p@chr11:75719740..75719766
+
Hg19::chr12:122430653..122430662,+p@chr12:122430653..122430662
+
Hg19::chr12:21815245..21815251,+p1@ENST00000541860
Hg19::chr12:75174802..75174809,+p@chr12:75174802..75174809
+
Hg19::chr13:109644678..109644725,+p@chr13:109644678..109644725
+
Hg19::chr17:47286603..47286624,-p4@GNGT2
Hg19::chr1:33886864..33886872,-p@chr1:33886864..33886872
-
Hg19::chr1:33886874..33886882,-p@chr1:33886874..33886882
-
Hg19::chr1:8251750..8251759,+p@chr1:8251750..8251759
+
Hg19::chr2:33589897..33589917,+p@chr2:33589897..33589917
+
Hg19::chr2:45797888..45797917,-p@chr2:45797888..45797917
-
Hg19::chr2:45797921..45797939,-p@chr2:45797921..45797939
-
Hg19::chr2:75145327..75145329,+p9@ENST00000435984
Hg19::chr3:25894063..25894094,+p@chr3:25894063..25894094
+
Hg19::chr3:26426173..26426176,+p@chr3:26426173..26426176
+
Hg19::chr4:189864076..189864089,+p@chr4:189864076..189864089
+
Hg19::chr5:142638718..142638753,+p@chr5:142638718..142638753
+
Hg19::chr5:92526866..92526914,-p@chr5:92526866..92526914
-
Hg19::chr6:56765635..56765674,-p@chr6:56765635..56765674
-
Hg19::chr6:56765738..56765745,-p@chr6:56765738..56765745
-
Hg19::chr6:707779..707821,+p@chr6:707779..707821
+
Hg19::chr7:100810718..100810739,-p@chr7:100810718..100810739
-
Hg19::chrX:105065622..105065627,+p@chrX:105065622..105065627
+
Hg19::chrX:45474991..45474996,+p@chrX:45474991..45474996
+


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:0007602phototransduction0.0060343812551513
GO:0050908detection of light stimulus during visual perception0.0060343812551513
GO:0050962detection of light stimulus during sensory perception0.0060343812551513
GO:0009584detection of visible light0.0060343812551513
GO:0009583detection of light stimulus0.0060343812551513
GO:0005834heterotrimeric G-protein complex0.0060343812551513
GO:0009582detection of abiotic stimulus0.0060343812551513
GO:0050906detection of stimulus during sensory perception0.0060343812551513
GO:0019897extrinsic to plasma membrane0.0060343812551513
GO:0009581detection of external stimulus0.0060343812551513
GO:0051606detection of stimulus0.00814641469445426
GO:0009416response to light stimulus0.00814641469445426
GO:0009314response to radiation0.00922398277573127
GO:0019898extrinsic to membrane0.00922398277573127
GO:0009628response to abiotic stimulus0.0132756387613329
GO:0007601visual perception0.0158313767046911
GO:0050953sensory perception of light stimulus0.0158313767046911
GO:0003924GTPase activity0.0183713384879051
GO:0009605response to external stimulus0.0402080351001134



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
epithelial cell of lung6.95e-1219
Uber Anatomy
Ontology termp-valuen
respiratory tract epithelium6.95e-1219
lung epithelium6.95e-1219
lung1.80e-1022
respiratory tube1.80e-1022
respiration organ1.80e-1022
pair of lungs1.80e-1022
lung primordium1.80e-1022
lung bud1.80e-1022
respiratory system epithelium1.52e-0828
thoracic cavity element2.74e-0734
thoracic cavity2.74e-0734
thoracic segment organ4.03e-0735
epithelial bud8.21e-0737
Disease
Ontology termp-valuen
lung large cell carcinoma2.39e-663
non-small cell lung carcinoma1.48e-405
lung carcinoma2.62e-239
lung cancer1.22e-1415
respiratory system cancer8.02e-1416


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)

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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
FOS#235382.666060832265010.007361706011402330.0304350096637181



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.