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Coexpression cluster:C4118: Difference between revisions

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|full_id=C4118_thyroid_clear_kidney_anaplastic_Renal_serous_endometrioid
|full_id=C4118_thyroid_clear_kidney_anaplastic_Renal_serous_endometrioid
|id=C4118
|id=C4118
|ontology_enrichment_celltype=CL:1000497!3.98e-18!18;CL:0002518!3.98e-18!18;CL:1000507!1.22e-15!12;CL:1000494!1.22e-15!12;CL:1000449!1.89e-15!16;CL:0002681!2.48e-11!13;CL:0002584!2.48e-11!13;CL:0000128!1.59e-07!7;CL:0000126!1.59e-07!7;CL:0000127!1.59e-07!7;CL:0002453!1.59e-07!7;CL:0002149!2.00e-07!6;CL:0002255!2.00e-07!6
|ontology_enrichment_celltype=CL:1000507!1.05e-30!10;CL:1000494!1.05e-30!10;CL:1000497!1.37e-30!17;CL:0002518!1.37e-30!17;CL:1000449!2.02e-24!15;CL:0002149!2.70e-16!6;CL:0002255!2.70e-16!6;CL:0002681!2.56e-15!12;CL:0002584!2.56e-15!12;CL:0000239!1.50e-12!3;CL:1000615!1.50e-12!3;CL:0002306!1.50e-12!3;CL:0000669!2.35e-09!4;CL:0000159!3.24e-09!2;CL:0000650!3.38e-09!2;CL:1000500!3.38e-09!2;CL:1000618!3.38e-09!2;CL:1001318!3.38e-09!2;CL:0002173!3.38e-09!2
|ontology_enrichment_disease=DOID:120!4.28e-15!27;DOID:193!4.42e-15!29;DOID:2394!3.73e-09!14;DOID:3001!2.00e-07!6
|ontology_enrichment_disease=DOID:120!3.44e-21!27;DOID:193!1.61e-19!29;DOID:3001!2.70e-16!6;DOID:299!2.86e-11!25;DOID:4468!4.63e-09!2
|ontology_enrichment_uberon=UBERON:0000489!2.87e-21!32;UBERON:0002113!3.42e-18!27;UBERON:0003918!3.42e-18!27;UBERON:0005095!3.42e-18!27;UBERON:0007687!3.42e-18!27;UBERON:0000080!4.03e-18!18;UBERON:0002120!4.03e-18!18;UBERON:0004875!4.03e-18!18;UBERON:0005721!4.03e-18!18;UBERON:0005754!4.03e-18!18;UBERON:0007297!4.03e-18!18;UBERON:0004876!6.40e-18!20;UBERON:0003133!2.25e-17!48;UBERON:0006555!8.60e-17!17;UBERON:0005103!8.60e-17!17;UBERON:0000083!8.60e-17!17;UBERON:0009201!8.60e-17!17;UBERON:0004819!8.60e-17!17;UBERON:0006553!8.60e-17!17;UBERON:0003074!8.60e-17!17;UBERON:0003060!8.60e-17!17;UBERON:0005156!6.59e-16!59;UBERON:0000990!6.59e-16!59;UBERON:0001008!9.46e-16!45;UBERON:0009773!1.22e-15!12;UBERON:0001231!1.22e-15!12;UBERON:0004810!1.22e-15!12;UBERON:0004211!1.89e-15!16;UBERON:0001285!1.89e-15!16;UBERON:0007684!1.89e-15!16;UBERON:0003220!1.89e-15!16;UBERON:0004208!1.89e-15!16;UBERON:0003887!7.94e-15!21;UBERON:0006554!8.46e-15!44;UBERON:0003886!1.17e-13!63;UBERON:0003064!1.79e-13!37;UBERON:0003134!4.72e-13!37;UBERON:0000474!4.72e-13!37;UBERON:0000058!8.56e-13!26;UBERON:0002553!2.29e-12!70;UBERON:0001225!2.48e-11!13;UBERON:0008987!2.48e-11!13;UBERON:0003100!3.68e-11!41;UBERON:0003103!6.54e-11!69;UBERON:0004175!1.78e-09!25;UBERON:0000991!3.47e-09!21;UBERON:0009196!3.47e-09!21;UBERON:0009117!3.47e-09!21;UBERON:0005564!3.47e-09!21;UBERON:0003076!4.34e-09!15;UBERON:0003057!4.34e-09!15;UBERON:0001851!1.08e-08!16;UBERON:0004176!1.30e-08!22;UBERON:0000992!4.10e-08!13;UBERON:0000353!5.04e-08!17;UBERON:0005172!2.20e-07!55;UBERON:0005173!2.20e-07!55;UBERON:0000464!2.27e-07!104
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0.0300692,0.131551,0.0445237,0.052362,0.0235128,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.28262,0.166024,0.137332,0.0145999,0.0656973,0.0241929,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.00340073,0.170307,0.201033,0.0488949,0.174921,0.370421,0.0330727,0.0694567,0.219556,0.0394698,0.0596469,0.419264,0.122476,0.108872,0.11002,0.26144,0.0286025,0.190156,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.0353101,0.217069,0.190048,0.131088,0.0144628,0.237101,0.0458068,0.0761239,0.172491,0.0818785,0.182701,0.0637246,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.0458479,0.0473033,0.094881,0.022113,0.132886,0.0774373,0.00619136,0.128564,0.131452,0.0306206,0.0226843,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.047822,0.655293,0.21727,0.289306,0.119215,0.192475,0.177967,0.188967,0.057571,0.047591,0.0143259,0.0608699,0.175319,0.300597,0.0713214,0.00224624,0.291114,0.0355833,0.125606,0.175094,0.696435,0.297678,0.206454,0.00206897,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.0158019,0.104948,0.221645,0.057168,0.0298844,0.0759837,0.286863,0.152372,0.194941,0.218271,0.101607,0.327067,0.172982,0.340936,0.151597,0.0626744,0.191335,0.0116284,0.504592,0.155821,0.0718905,0.0919008,0.0602373,0.0109522,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.228144,0.251466,0.0461822,0.11903,0.0838874,0.331451,0.113145,0.112651,0.186638,0.174776,0.0948451,0.0384217,0.0339656,0.140533,0.0997756,0.0364628,0.103667,0.113069,0.025556,0.16791,0.09066,0.220462,0.166967,0.188651,0.0813902,0.184948,0.156261,0.0546539,0.511859,0.0590944,0.00309372,0.00109188,0.218229,0.231073,0.407281,0.252227,0.0360851,0.0168763,0.131093,0.0434602,0.133616,0.000247895,0.36927,0.449036,0.0162067,0.231447,0.00858901,0.0210947,0.37006,0.10748,0.022688,0.197484,0.396996,0.0750251,0.0160226,0.0841307,0.216033,0.0863135,0.11074,0.138468,0.390366,0.0049331,0.000757632,0.0217093,0.00696618,0.0608227,0.60734,0.227104,0.0380245,0.617852,0.0867545,0.284625,0.504757,0.192225,0.144318,0.28907,0.164197,0.000461108,0.0461094,0.0113427,0.0283889,0.0642229,0.132529,0.0366482,0.446557,0.243383,0.0186777,0.390974,0.0458848,0.109758,0.161598,0.164332,0.021206,0.0323708,0.21803,0.0805771,0.0203982,0.0282154,0.199161,0.0508568,0.0629574,0.20342,0.200493,0.20558,0.300504,0.25656,0.00254768,0.349197,0.383291,0.156104,0.141318,0.411941,0.0961477,0.314438,0.0101316,0.163828,0.230581,0.120226,0.28424,0.20075,0.314429,0.181415,0.282286,0.0674279,0.00047615,0.0978616,0.00654592,0.322213,0.0234043,0.0655189,0.61031,0.0871388,0.169614,0.221908,0.180745,0.0267088,0.416621,0.416292,0.128937,0.734551,0.000280804,0.204817,0.122646,0.138871,0.103502,0.166905,0.19783,0.0833851,0.00691922,0.000585352,0.175199,0.0628556,0.373557,0.00701509,0.0980968,0.0111982,0.0425451,0.0889149,0.0109626,0.236011,0.203486,0.273398,0.375787,0.119167,0.0704514,0.275347,0.0830022,0.305885,0.241132,0.0795725,0.30666,0.303709,0.15059,0.0867777,0.508064,0.250964,0.383276,0.457886,0.00582796,0.220231,0.00608438,0.196976,0.191517,0.000467747,0.0663581,0.307334,0.127092,0.283463,0.201728,0.472935,0.399569,0.273281,0.0780405,0.275089,0.0858306,0.138622,0.359231,0.0656472,0.197805,0.0690807,0.387069,0.332774,0.00734059,0.299887,0.0814305,0.205413,0.17639,0.0779009,0.276869,0.022685,0.0337138,0.18966,0.036838,0.188263,0.0719199,0.264884,0.162568,7.10854e-05,0.163057,0.219428,0.000102347,0.00418416,0.0953646,0.166124,0.252184,0.378361,0.255516,0.20753,0.447185,0.179412,0.193601,0.220904,0.0269454,0.0664606,0.310674,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.0430576,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.0139199,0.0284767,0.0151141,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.000701257,0.120196,0.0986735,0.108462,0.0595618,0.0251995,0.158479,0.0262794,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.0331281,0.173026,0.200432,0.139785,0.0208458,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.0541163,0.0437875,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.00618871,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993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}}
}}

Revision as of 15:41, 19 October 2012


Full id: C4118_thyroid_clear_kidney_anaplastic_Renal_serous_endometrioid



Phase1 CAGE Peaks

Hg19::chr2:113984760..113984792,+p@chr2:113984760..113984792
+
Hg19::chr2:113999199..113999214,+p@chr2:113999199..113999214
+
Hg19::chr2:114036488..114036504,-p1@PAX8


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
kidney2.14e-3426
kidney mesenchyme2.14e-3426
upper urinary tract2.14e-3426
kidney rudiment2.14e-3426
kidney field2.14e-3426
nephron tubule epithelium1.05e-3010
cavitated compound organ3.35e-2831
excretory tube2.07e-2716
kidney epithelium2.07e-2716
nephron epithelium2.02e-2415
renal tubule2.02e-2415
nephron tubule2.02e-2415
nephron2.02e-2415
uriniferous tubule2.02e-2415
nephrogenic mesenchyme2.02e-2415
urinary system structure1.59e-1947
renal system4.95e-1948
reproductive organ3.52e-1848
female reproductive organ1.49e-1637
female reproductive system1.49e-1637
cortex of kidney2.56e-1512
renal parenchyma2.56e-1512
female organism1.26e-1441
abdomen element1.61e-1454
abdominal segment element1.61e-1454
reproductive structure4.86e-1459
reproductive system4.86e-1459
thyroid gland2.28e-135
pharyngeal pouch2.28e-135
thyroid diverticulum2.28e-135
pharyngeal pouch 22.28e-135
thyroid primordium2.28e-135
internal genitalia5.12e-1325
abdominal segment of trunk1.09e-1260
abdomen1.09e-1260
renal cortex tubule1.50e-123
region of nephron tubule1.50e-123
proximal tubule1.50e-123
cortex4.83e-1215
parenchyma4.83e-1215
compound organ9.34e-1168
mesonephros1.63e-109
pronephros1.63e-109
nephrogenic cord1.63e-109
pronephric mesoderm1.63e-109
rostral part of nephrogenic cord1.63e-109
presumptive pronephric mesoderm1.63e-109
uterus3.43e-1021
gonad5.94e-1021
indifferent external genitalia5.94e-1021
indifferent gonad5.94e-1021
gonad primordium5.94e-1021
female gonad9.44e-1013
embryonic uterus1.14e-0922
internal female genitalia1.14e-0922
external genitalia1.92e-0922
abdomen connective tissue3.38e-092
abdominal segment connective tissue3.38e-092
trunk connective tissue3.38e-092
interstitial tissue3.38e-092
extraglomerular mesangium3.38e-092
kidney interstitium3.38e-092
juxtaglomerular apparatus3.38e-092
mesangium3.38e-092
urogenital ridge1.53e-0811
mesonephric epithelium6.10e-088
mesonephric tubule6.10e-088
nephric duct6.10e-088
renal duct6.10e-088
mesonephric duct6.10e-088
pronephric duct6.10e-088
intraembryonic coelom8.39e-0812
body cavity precursor2.01e-0754


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

No analysis results for this cluster

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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