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Coexpression cluster:C3608: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000080!8.38e-22!18;UBERON:0002120!8.38e-22!18;UBERON:0004875!8.38e-22!18;UBERON:0005721!8.38e-22!18;UBERON:0005754!8.38e-22!18;UBERON:0007297!8.38e-22!18;UBERON:0000058!1.07e-21!26;UBERON:0006555!1.13e-19!17;UBERON:0005103!1.13e-19!17;UBERON:0000083!1.13e-19!17;UBERON:0009201!1.13e-19!17;UBERON:0004819!1.13e-19!17;UBERON:0006553!1.13e-19!17;UBERON:0003074!1.13e-19!17;UBERON:0003060!1.13e-19!17;UBERON:0004876!2.96e-19!20;UBERON:0002113!2.94e-18!27;UBERON:0003918!2.94e-18!27;UBERON:0005095!2.94e-18!27;UBERON:0007687!2.94e-18!27;UBERON:0003887!3.64e-18!21;UBERON:0004211!1.21e-17!16;UBERON:0001285!1.21e-17!16;UBERON:0007684!1.21e-17!16;UBERON:0003220!1.21e-17!16;UBERON:0004208!1.21e-17!16;UBERON:0009773!2.40e-16!12;UBERON:0001231!2.40e-16!12;UBERON:0004810!2.40e-16!12;UBERON:0001225!5.30e-15!13;UBERON:0008987!5.30e-15!13;UBERON:0000489!9.79e-15!32;UBERON:0001851!8.61e-12!16;UBERON:0005172!1.01e-11!55;UBERON:0005173!1.01e-11!55;UBERON:0006554!5.43e-11!44;UBERON:0000353!5.64e-11!17;UBERON:0001008!1.19e-10!45;UBERON:0000466!1.36e-10!126;UBERON:0000464!1.92e-10!104;UBERON:0003886!2.21e-10!63;UBERON:0003064!2.94e-10!37;UBERON:0002417!4.59e-10!61;UBERON:0000916!4.59e-10!61;UBERON:0002553!6.87e-10!70;UBERON:0005177!2.11e-09!107;UBERON:0006947!9.95e-09!3;UBERON:0004054!9.95e-09!3;UBERON:0006853!1.07e-08!3;UBERON:0007685!1.07e-08!3;UBERON:0004134!1.07e-08!3;UBERON:0009569!1.54e-08!113;UBERON:0003135!3.17e-07!11
|ontology_enrichment_uberon=UBERON:0000080!8.38e-22!18;UBERON:0002120!8.38e-22!18;UBERON:0004875!8.38e-22!18;UBERON:0005721!8.38e-22!18;UBERON:0005754!8.38e-22!18;UBERON:0007297!8.38e-22!18;UBERON:0000058!1.07e-21!26;UBERON:0006555!1.13e-19!17;UBERON:0005103!1.13e-19!17;UBERON:0000083!1.13e-19!17;UBERON:0009201!1.13e-19!17;UBERON:0004819!1.13e-19!17;UBERON:0006553!1.13e-19!17;UBERON:0003074!1.13e-19!17;UBERON:0003060!1.13e-19!17;UBERON:0004876!2.96e-19!20;UBERON:0002113!2.94e-18!27;UBERON:0003918!2.94e-18!27;UBERON:0005095!2.94e-18!27;UBERON:0007687!2.94e-18!27;UBERON:0003887!3.64e-18!21;UBERON:0004211!1.21e-17!16;UBERON:0001285!1.21e-17!16;UBERON:0007684!1.21e-17!16;UBERON:0003220!1.21e-17!16;UBERON:0004208!1.21e-17!16;UBERON:0009773!2.40e-16!12;UBERON:0001231!2.40e-16!12;UBERON:0004810!2.40e-16!12;UBERON:0001225!5.30e-15!13;UBERON:0008987!5.30e-15!13;UBERON:0000489!9.79e-15!32;UBERON:0001851!8.61e-12!16;UBERON:0005172!1.01e-11!55;UBERON:0005173!1.01e-11!55;UBERON:0006554!5.43e-11!44;UBERON:0000353!5.64e-11!17;UBERON:0001008!1.19e-10!45;UBERON:0000466!1.36e-10!126;UBERON:0000464!1.92e-10!104;UBERON:0003886!2.21e-10!63;UBERON:0003064!2.94e-10!37;UBERON:0002417!4.59e-10!61;UBERON:0000916!4.59e-10!61;UBERON:0002553!6.87e-10!70;UBERON:0005177!2.11e-09!107;UBERON:0006947!9.95e-09!3;UBERON:0004054!9.95e-09!3;UBERON:0006853!1.07e-08!3;UBERON:0007685!1.07e-08!3;UBERON:0004134!1.07e-08!3;UBERON:0009569!1.54e-08!113;UBERON:0003135!3.17e-07!11
|tf_chipseq_enrich=JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156529661153219!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00470778884922955
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0.0876426,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.173708,0.141119,0.0241568,0.0300692,0.131551,0.0445237,0.052362,0.00179985,0.0123828,0.0797897,0.0974211,0.0135691,0.123526,0.0906475,0.0558058,0.28262,0.517717,0.137332,0.0145999,0.0656973,0.211746,0.026334,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.0015938,0.0488949,0.174921,0.370421,0.0330727,0.348757,0.219556,0.0394698,0.0596469,0.419264,0.122476,0.108872,0.11002,0.26144,0.0286025,0.190156,0.0109933,0.038848,0.0874516,0.0550279,0.000558597,0.253693,0.217069,0.00133367,0.131088,0.0144628,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.335058,0.147698,0.141463,0.0148418,0.140622,0.0889592,0.00643528,0.28711,0.0473033,0.094881,0.445524,0.132886,0.0774373,0.109194,0.128564,0.131452,0.323837,0.448776,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.739716,0.0232393,2.43406e-07,0.00514993,0.119215,0.192475,0.177967,0.0465298,0.057571,0.047591,0.392974,0.0608699,0.175319,0.00583965,0.0713214,7.05918e-06,0.291114,0.0355833,0.125606,0.175094,0.696435,0.76084,0.206454,0.000125718,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.0277579,0.000680617,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.00259914,0.0759837,0.286863,0.152372,7.74968e-05,0.218271,0.101607,0.327067,0.0159074,0.00886538,0.151597,0.0626744,0.191335,0.148574,0.504592,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.000642001,0.0973823,0.15503,0.170295,0.193653,0.137219,0.00238639,0.251466,0.288096,0.11903,0.0838874,0.331451,0.113145,0.00659775,0.186638,0.174776,0.0948451,0.00382477,0.249049,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,4.10812e-05,0.09066,0.585505,0.166967,0.188651,0.0813902,0.184948,0.156261,0.311847,0.511859,0.0590944,0.247324,0.178389,0.0020701,0.231073,0.407281,0.619906,0.0360851,0.0998546,0.131093,0.0434602,0.133616,0.00233292,8.98135e-06,0.449036,0.0973145,0.231447,0.0455669,0.0210947,0.37006,0.42622,0.120472,0.197484,0.00182638,0.0750251,0.0160226,0.0129,0.0119618,0.276075,0.0198622,0.722159,0.390366,0.145312,0.50058,0.443185,0.522904,0.875915,0.336835,0.227104,0.518585,0.00310917,0.000154756,0.284625,0.00583062,2.10364e-06,0.00228337,0.28907,0.164197,0.128922,0.287881,0.0556235,6.0419e-05,0.000849258,0.468444,0.0366482,0.446557,0.032364,0.777351,0.390974,0.382874,0.109758,0.161598,0.751174,0.277094,0.496032,0.799185,0.0120582,0.78509,0.0282154,0.452741,0.746954,0.43491,0.20342,0.200493,0.20558,0.300504,0.25656,0.425963,0.349197,0.383291,0.156104,0.141318,0.411941,0.0961477,0.314438,0.354789,0.163828,0.0289012,0.120226,0.28424,0.0101317,0.314429,0.181415,0.282286,0.78,0.24884,0.01635,0.0374737,0.322213,0.0931134,0.33942,0.000436901,0.0871388,0.522605,0.221908,0.537348,0.222037,0.102227,0.416292,0.462712,0.382478,0.0118519,0.204817,3.96668e-05,0.138871,0.103502,0.166905,0.0210039,0.0833851,0.056391,0.00457272,0.175199,5.59614e-10,1.9387e-09,0.00701509,0.0164118,0.365487,0.534741,0.000165487,0.363192,0.236011,0.203486,0.273398,0.375787,0.119167,0.351067,0.275347,0.0830022,0.305885,0.241132,0.371414,0.00623664,0.00604105,0.0323359,0.386538,0.508064,0.250964,0.383276,0.457886,0.0344603,0.220231,0.509064,0.196976,0.191517,0.463751,0.0145214,0.0529819,3.89164e-06,0.0048173,0.00164832,0.472935,0.0151656,0.273281,0.000116083,0.275089,1.28993e-10,0.47795,0.359231,0.339729,0.197805,0.0690807,0.387069,0.0627969,0.52832,0.299887,0.00375452,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.00329437,0.0828367,0.255516,0.20753,0.447185,0.179412,0.193601,0.220904,0.222977,0.341681,0.310674,0.21801,0.198614,0.186804,0.123324,0.0213665,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.20847,0.266544,0.113092,0.0111711,0.229428,0.162145,0.000154811,0.000916623,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,3.79162e-07,0.154941,0.120196,0.000172898,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.00361981,0.30793,0.180606,0.159884,0.00351525,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.000991755,0.00157872,0.139785,0.197112,4.75501e-07,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,4.34104e-05,0.280943,0.218161,0.0822373,0.0219487,0.106739,0.0536053,0.0537737,0.000648679,0.078016,0.0407233,0.0537355,0.00717361,0.261724,0.00186843,0.0012829,0.233626,0.189559,9.53285e-05,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.000980315,0.141729,0.263159,0.00345643,0.200105,0.227491,0.29837,0.253509,0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}}
}}

Revision as of 12:37, 5 September 2012


Full id: C3608_Renal_ductus_bronchioalveolar_retina_kidney_seminal_Alveolar



Phase1 CAGE Peaks

Hg19::chr17:171082..171101,+p@chr17:171082..171101
+
Hg19::chr17:171106..171120,+p@chr17:171106..171120
+
Hg19::chr17:171147..171161,+p@chr17:171147..171161
+


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>

Uber Anatomy
Ontology termp-valuen
mesonephros8.38e-2218
pronephros8.38e-2218
nephrogenic cord8.38e-2218
pronephric mesoderm8.38e-2218
rostral part of nephrogenic cord8.38e-2218
presumptive pronephric mesoderm8.38e-2218
duct1.07e-2126
excretory tube1.13e-1917
mesonephric epithelium1.13e-1917
mesonephric tubule1.13e-1917
nephric duct1.13e-1917
kidney epithelium1.13e-1917
renal duct1.13e-1917
mesonephric duct1.13e-1917
pronephric duct1.13e-1917
urogenital ridge2.96e-1920
kidney2.94e-1827
kidney mesenchyme2.94e-1827
kidney rudiment2.94e-1827
kidney field2.94e-1827
intraembryonic coelom3.64e-1821
nephron epithelium1.21e-1716
nephron1.21e-1716
uriniferous tubule1.21e-1716
metanephric mesenchyme1.21e-1716
nephrogenic mesenchyme1.21e-1716
renal tubule2.40e-1612
nephron tubule2.40e-1612
nephron tubule epithelium2.40e-1612
cortex of kidney5.30e-1513
renal parenchyma5.30e-1513
cavitated compound organ9.79e-1532
cortex8.61e-1216
abdomen element1.01e-1155
abdominal segment element1.01e-1155
urinary system structure5.43e-1144
parenchyma5.64e-1117
renal system1.19e-1045
immaterial anatomical entity1.36e-10126
anatomical space1.92e-10104
body cavity precursor2.21e-1063
intermediate mesoderm2.94e-1037
abdominal segment of trunk4.59e-1061
abdomen4.59e-1061
anatomical cavity6.87e-1070
trunk region element2.11e-09107
male genital duct9.95e-093
internal male genitalia9.95e-093
renal cortex tubule1.07e-083
region of nephron tubule1.07e-083
proximal tubule1.07e-083
subdivision of trunk1.54e-08113
male reproductive organ3.17e-0711


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
JUND#372736.994663941871030.002921845042734990.0156529661153219
NRF1#4899312.21027944771090.0005492172401020010.00470778884922955



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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