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Coexpression cluster:C4144: Difference between revisions

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|full_id=C4144_Mesenchymal_Smooth_Renal_hepatic_Lens_epithelioid_Endothelial
|full_id=C4144_Mesenchymal_Smooth_Renal_hepatic_Lens_epithelioid_Endothelial
|id=C4144
|id=C4144
|ontology_enrichment_celltype=CL:0000055!1.37e-31!180;CL:0000222!4.31e-31!119;CL:0002321!3.10e-20!248;CL:0000220!4.44e-20!246;CL:0000183!1.42e-18!59;CL:0000680!1.34e-17!57;CL:0000056!1.34e-17!57;CL:0000355!1.34e-17!57;CL:0000187!2.46e-16!54;CL:0000393!3.32e-15!60;CL:0000211!3.32e-15!60;CL:0000192!4.05e-15!42;CL:0000514!4.05e-15!42;CL:0000057!9.57e-15!75;CL:0002078!7.06e-13!44;CL:0000359!2.16e-12!32;CL:0000213!3.27e-12!57;CL:0000215!3.27e-12!57;CL:0000115!1.27e-11!35;CL:0002139!4.40e-11!24;CL:0000144!2.08e-08!625;CL:0000071!1.81e-07!18;CL:0002546!1.81e-07!18;CL:1000449!2.89e-07!16;CL:0002371!5.32e-07!591
|ontology_enrichment_celltype=CL:0000222!4.19e-32!121;CL:0002321!3.33e-21!250;CL:0000183!8.50e-18!59;CL:0000680!1.62e-17!58;CL:0000056!1.62e-17!58;CL:0000355!1.62e-17!58;CL:0000187!2.72e-16!55;CL:0000055!9.61e-16!106;CL:0000393!3.26e-15!61;CL:0000211!3.26e-15!61;CL:0000192!3.61e-15!43;CL:0000514!3.61e-15!43;CL:0000057!4.14e-15!76;CL:0002078!1.08e-13!45;CL:0000213!6.62e-13!58;CL:0000215!6.62e-13!58;CL:0000115!3.24e-12!36;CL:0000359!4.90e-12!32;CL:0002139!6.12e-11!24;CL:0002371!1.91e-07!588;CL:1000449!2.23e-07!15;CL:0000071!2.30e-07!18;CL:0002546!2.30e-07!18
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002049!6.76e-29!79;UBERON:0007798!6.76e-29!79;UBERON:0000055!8.24e-25!69;UBERON:0004872!4.89e-24!84;UBERON:0001981!6.31e-21!60;UBERON:0007500!6.31e-21!60;UBERON:0004537!6.31e-21!60;UBERON:0006965!6.31e-21!60;UBERON:0003914!2.37e-20!118;UBERON:0004535!3.07e-20!110;UBERON:0001009!6.60e-20!113;UBERON:0000914!1.14e-17!83;UBERON:0002329!1.14e-17!83;UBERON:0003077!1.14e-17!83;UBERON:0003059!1.14e-17!83;UBERON:0007282!1.14e-17!83;UBERON:0009618!1.14e-17!83;UBERON:0007285!1.14e-17!83;UBERON:0005256!1.77e-17!143;UBERON:0001134!2.15e-17!61;UBERON:0002036!2.15e-17!61;UBERON:0003082!2.15e-17!61;UBERON:0002385!4.84e-17!63;UBERON:0001015!4.84e-17!63;UBERON:0000383!4.84e-17!63;UBERON:0004290!2.24e-16!70;UBERON:0000486!6.93e-16!82;UBERON:0000490!3.33e-15!138;UBERON:0001637!3.45e-15!42;UBERON:0003509!3.45e-15!42;UBERON:0004572!3.45e-15!42;UBERON:0000119!6.03e-15!312;UBERON:0000477!1.35e-14!286;UBERON:0000483!1.55e-14!309;UBERON:0000475!7.05e-14!365;UBERON:0004573!2.15e-12!33;UBERON:0004571!2.15e-12!33;UBERON:0002100!2.64e-12!216;UBERON:0000468!3.83e-11!659;UBERON:0004111!4.12e-11!241;UBERON:0000481!4.03e-10!347;UBERON:0003104!2.77e-08!238;UBERON:0009142!2.77e-08!238;UBERON:0000947!3.42e-08!21;UBERON:0010191!3.42e-08!21;UBERON:0000025!3.66e-08!194;UBERON:0000353!8.61e-08!17;UBERON:0001986!1.81e-07!18;UBERON:0004638!1.81e-07!18;UBERON:0004852!1.81e-07!18;UBERON:0004211!2.89e-07!16;UBERON:0001285!2.89e-07!16;UBERON:0007684!2.89e-07!16;UBERON:0003220!2.89e-07!16;UBERON:0004208!2.89e-07!16;UBERON:0003103!5.80e-07!69;UBERON:0006555!8.51e-07!17;UBERON:0005103!8.51e-07!17;UBERON:0000083!8.51e-07!17;UBERON:0009201!8.51e-07!17;UBERON:0004819!8.51e-07!17;UBERON:0006553!8.51e-07!17;UBERON:0003074!8.51e-07!17;UBERON:0003060!8.51e-07!17;UBERON:0006914!8.82e-07!25;UBERON:0000480!9.81e-07!626
|ontology_enrichment_uberon=UBERON:0002049!9.65e-28!78;UBERON:0007798!9.65e-28!78;UBERON:0000055!2.05e-23!68;UBERON:0004872!3.45e-23!83;UBERON:0003914!4.87e-20!117;UBERON:0007503!9.40e-20!78;UBERON:0004535!1.31e-19!109;UBERON:0007500!1.32e-19!59;UBERON:0001981!1.32e-19!59;UBERON:0004537!1.32e-19!59;UBERON:0006965!1.32e-19!59;UBERON:0001009!2.90e-19!112;UBERON:0001134!1.94e-17!62;UBERON:0002036!1.94e-17!62;UBERON:0003082!1.94e-17!62;UBERON:0002385!3.96e-17!64;UBERON:0001015!3.96e-17!64;UBERON:0000383!3.96e-17!64;UBERON:0003104!6.82e-17!160;UBERON:0009142!6.82e-17!160;UBERON:0007524!1.71e-16!73;UBERON:0002329!2.16e-16!71;UBERON:0003059!2.16e-16!71;UBERON:0007282!2.16e-16!71;UBERON:0004290!2.16e-16!71;UBERON:0009618!2.16e-16!71;UBERON:0000477!4.23e-16!373;UBERON:0003077!5.57e-16!72;UBERON:0007285!5.57e-16!72;UBERON:0000486!7.24e-16!83;UBERON:0000490!1.49e-15!148;UBERON:0000119!2.46e-15!309;UBERON:0000483!5.05e-15!306;UBERON:0001637!9.01e-15!42;UBERON:0003509!9.01e-15!42;UBERON:0004572!9.01e-15!42;UBERON:0000475!2.56e-14!264;UBERON:0005256!1.17e-13!122;UBERON:0000481!8.25e-12!342;UBERON:0004573!9.14e-12!33;UBERON:0004571!9.14e-12!33;UBERON:0000468!3.41e-11!656;UBERON:0004111!6.74e-11!240;UBERON:0002100!8.19e-11!199;UBERON:0000947!6.33e-08!21;UBERON:0010191!6.33e-08!21;UBERON:0000025!1.15e-07!192;UBERON:0004211!2.23e-07!15;UBERON:0009773!2.23e-07!15;UBERON:0001231!2.23e-07!15;UBERON:0001285!2.23e-07!15;UBERON:0007684!2.23e-07!15;UBERON:0004208!2.23e-07!15;UBERON:0004638!2.30e-07!18;UBERON:0001986!2.30e-07!18;UBERON:0004852!2.30e-07!18;UBERON:0000480!2.79e-07!625;UBERON:0000467!3.77e-07!624;UBERON:0000353!4.23e-07!15;UBERON:0006555!6.98e-07!16;UBERON:0004819!6.98e-07!16;UBERON:0006914!9.94e-07!25
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326168923918623!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00471902092464113!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109633766216696
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326168923918623!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00471902092464113!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109633766216696
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37332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.00340073,0.170307,0.201033,0.0488949,0.174921,0.370421,0.0330727,0.0694567,0.219556,0.0394698,0.0596469,0.419264,0.122476,0.108872,0.11002,0.00370214,0.0286025,0.00896808,0.0109933,0.038848,0.0874516,0.0550279,0.144067,0.000242011,0.217069,0.190048,0.131088,0.0144628,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.0637246,0.147698,0.141463,0.167267,0.140622,0.0889592,4.27652e-05,0.28711,0.0473033,0.094881,0.118532,0.132886,0.0774373,0.109194,0.128564,0.131452,0.687347,0.120459,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.000356768,0.047822,0.655293,0.21727,0.0465945,0.119215,0.192475,0.177967,0.188967,0.057571,0.047591,0.392974,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,0.0121461,3.18684e-05,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.0457643,0.152372,0.194941,0.00207136,0.101607,0.327067,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.504592,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.228144,0.251466,0.288096,0.11903,0.0838874,0.331451,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.585505,0.166967,0.188651,0.0813902,0.184948,0.156261,0.311847,0.511859,0.0590944,0.247324,0.178389,0.218229,0.231073,0.407281,0.0743925,0.0360851,0.0998546,0.131093,0.0434602,0.133616,0.418146,0.00130397,0.449036,0.000211816,0.231447,0.544776,0.43956,0.37006,0.42622,0.448797,0.197484,0.396996,0.36145,0.406019,0.381071,0.580441,0.276075,0.432035,0.366326,0.390366,0.48809,0.50058,0.443185,0.522904,0.0199034,0.00516504,0.227104,0.518585,0.250246,0.38649,0.284625,0.504757,0.192225,0.729153,0.28907,0.164197,0.462688,0.287881,0.574635,0.478174,0.336276,0.468444,0.258219,0.446557,0.243383,0.191695,0.390974,0.73485,0.683217,0.161598,0.164332,0.277094,0.496032,0.0239796,0.37357,0.0704414,0.477353,0.00492096,0.160298,0.185744,0.20342,0.200493,0.20558,0.300504,0.25656,0.425963,0.349197,0.383291,0.156104,0.141318,0.411941,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,2.64048e-05,0.562405,0.314429,0.181415,0.282286,0.78,0.616388,0.408413,0.000926901,0.322213,0.656109,0.33942,0.61031,0.387276,0.522605,4.99296e-05,0.180745,0.222037,0.416621,0.416292,0.128937,0.0457685,0.215157,0.204817,0.452428,0.138871,0.103502,0.166905,0.19783,0.0833851,0.316453,0.48065,0.175199,0.332919,0.373557,0.523625,0.408861,0.365487,0.534741,0.39088,0.363192,0.236011,0.203486,0.273398,0.375787,0.4466,0.351067,0.275347,0.0830022,0.305885,0.241132,0.371414,0.30666,0.303709,0.495883,0.386538,0.508064,0.250964,0.383276,0.457886,0.504711,0.220231,0.509064,0.196976,0.191517,0.463751,0.601877,0.307334,0.459728,0.283463,0.00164832,0.472935,0.399569,0.273281,0.368095,0.275089,0.384593,0.47795,0.359231,0.339729,0.197805,0.608187,0.387069,0.332774,0.52832,0.299887,0.634365,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.00358475,0.188263,0.0719199,0.00386277,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.255516,0.20753,0.0224033,0.179412,0.193601,0.220904,2.88613e-07,0.341681,0.310674,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.00376943,0.131118,0.20837,0.0335483,0.0267847,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.00160819,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.0367308,0.261744,0.203781,0.0246892,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.00899301,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.0404514,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205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}}
}}

Revision as of 15:43, 19 October 2012


Full id: C4144_Mesenchymal_Smooth_Renal_hepatic_Lens_epithelioid_Endothelial



Phase1 CAGE Peaks

Hg19::chr2:1748276..1748295,-p1@PXDN
Hg19::chr2:1748302..1748326,-p2@PXDN
Hg19::chr2:1748343..1748352,-p3@PXDN


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
vasculature9.65e-2878
vascular system9.65e-2878
vessel2.05e-2368
splanchnic layer of lateral plate mesoderm3.45e-2383
epithelial tube4.87e-20117
epithelial vesicle9.40e-2078
cardiovascular system1.31e-19109
epithelial tube open at both ends1.32e-1959
blood vessel1.32e-1959
blood vasculature1.32e-1959
vascular cord1.32e-1959
circulatory system2.90e-19112
skeletal muscle tissue1.94e-1762
striated muscle tissue1.94e-1762
myotome1.94e-1762
muscle tissue3.96e-1764
musculature3.96e-1764
musculature of body3.96e-1764
mesenchyme6.82e-17160
entire embryonic mesenchyme6.82e-17160
dense mesenchyme tissue1.71e-1673
somite2.16e-1671
presomitic mesoderm2.16e-1671
presumptive segmental plate2.16e-1671
dermomyotome2.16e-1671
trunk paraxial mesoderm2.16e-1671
anatomical cluster4.23e-16373
paraxial mesoderm5.57e-1672
presumptive paraxial mesoderm5.57e-1672
multilaminar epithelium7.24e-1683
unilaminar epithelium1.49e-15148
cell layer2.46e-15309
epithelium5.05e-15306
artery9.01e-1542
arterial blood vessel9.01e-1542
arterial system9.01e-1542
organism subdivision2.56e-14264
trunk mesenchyme1.17e-13122
multi-tissue structure8.25e-12342
systemic artery9.14e-1233
systemic arterial system9.14e-1233
multi-cellular organism3.41e-11656
anatomical conduit6.74e-11240
trunk8.19e-11199
aorta6.33e-0821
aortic system6.33e-0821
tube1.15e-07192
nephron epithelium2.23e-0715
renal tubule2.23e-0715
nephron tubule2.23e-0715
nephron2.23e-0715
uriniferous tubule2.23e-0715
nephrogenic mesenchyme2.23e-0715
blood vessel endothelium2.30e-0718
endothelium2.30e-0718
cardiovascular system endothelium2.30e-0718
anatomical group2.79e-07625
anatomical system3.77e-07624
parenchyma4.23e-0715
excretory tube6.98e-0716
kidney epithelium6.98e-0716
squamous epithelium9.94e-0725


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
E2F1#186934.907389214879320.008460985347239390.0326168923918623
NRF1#4899312.21027944771090.0005492172401020010.00471902092464113
ZNF263#1012738.221841637010680.001799043925565870.0109633766216696



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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