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Coexpression cluster:C3543: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000468!9.59e-17!659;UBERON:0000467!2.43e-14!625;UBERON:0000480!4.83e-14!626;UBERON:0004872!6.07e-12!84;UBERON:0000055!1.02e-11!69;UBERON:0002049!1.24e-11!79;UBERON:0007798!1.24e-11!79;UBERON:0000922!1.63e-11!612;UBERON:0002050!4.69e-11!605;UBERON:0005423!4.69e-11!605;UBERON:0001986!4.79e-11!18;UBERON:0004638!4.79e-11!18;UBERON:0004852!4.79e-11!18;UBERON:0001981!7.54e-11!60;UBERON:0007500!7.54e-11!60;UBERON:0004537!7.54e-11!60;UBERON:0006965!7.54e-11!60;UBERON:0000923!8.85e-11!604;UBERON:0005291!8.85e-11!604;UBERON:0006598!8.85e-11!604;UBERON:0002532!8.85e-11!604;UBERON:0001009!1.58e-10!113;UBERON:0006914!3.70e-10!25;UBERON:0004535!8.99e-10!110;UBERON:0000487!3.29e-09!22;UBERON:0000025!3.49e-09!194;UBERON:0004111!3.66e-09!241;UBERON:0000483!6.51e-09!309;UBERON:0000119!7.97e-09!312;UBERON:0003914!1.18e-08!118;UBERON:0000477!1.28e-08!286;UBERON:0000926!2.97e-08!448;UBERON:0004120!2.97e-08!448;UBERON:0006603!2.97e-08!448;UBERON:0000490!6.14e-07!138
|ontology_enrichment_uberon=UBERON:0000468!9.59e-17!659;UBERON:0000467!2.43e-14!625;UBERON:0000480!4.83e-14!626;UBERON:0004872!6.07e-12!84;UBERON:0000055!1.02e-11!69;UBERON:0002049!1.24e-11!79;UBERON:0007798!1.24e-11!79;UBERON:0000922!1.63e-11!612;UBERON:0002050!4.69e-11!605;UBERON:0005423!4.69e-11!605;UBERON:0001986!4.79e-11!18;UBERON:0004638!4.79e-11!18;UBERON:0004852!4.79e-11!18;UBERON:0001981!7.54e-11!60;UBERON:0007500!7.54e-11!60;UBERON:0004537!7.54e-11!60;UBERON:0006965!7.54e-11!60;UBERON:0000923!8.85e-11!604;UBERON:0005291!8.85e-11!604;UBERON:0006598!8.85e-11!604;UBERON:0002532!8.85e-11!604;UBERON:0001009!1.58e-10!113;UBERON:0006914!3.70e-10!25;UBERON:0004535!8.99e-10!110;UBERON:0000487!3.29e-09!22;UBERON:0000025!3.49e-09!194;UBERON:0004111!3.66e-09!241;UBERON:0000483!6.51e-09!309;UBERON:0000119!7.97e-09!312;UBERON:0003914!1.18e-08!118;UBERON:0000477!1.28e-08!286;UBERON:0000926!2.97e-08!448;UBERON:0004120!2.97e-08!448;UBERON:0006603!2.97e-08!448;UBERON:0000490!6.14e-07!138
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7897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.28262,0.166024,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.000803238,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.000943525,0.201033,0.0488949,0.174921,0.0791124,0.0330727,0.348757,0.219556,0.0394698,0.0596469,0.103658,0.122476,0.108872,0.11002,0.0376172,0.0286025,0.549354,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.090504,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.335058,0.011488,0.000527702,0.167267,0.140622,0.0889592,0.309588,0.28711,0.0473033,0.094881,0.445524,0.132886,0.00307881,0.109194,0.128564,0.131452,0.687347,0.120459,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.0425274,0.153605,0.0232393,0.21727,0.289306,0.119215,0.192475,0.177967,0.188967,0.057571,0.047591,0.0899568,0.0608699,0.175319,0.00583965,0.0713214,0.223874,0.0472142,0.0355833,0.125606,0.175094,0.43617,0.297678,0.00173453,0.0257531,0.108277,5.36187e-05,0.000233345,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.00631005,6.10604e-05,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,3.25328e-05,0.234298,0.0759837,0.286863,0.152372,0.194941,0.218271,0.101607,0.327067,0.172982,0.340936,0.151597,0.0626744,0.191335,0.0116284,0.504592,0.155821,0.0718905,0.0919008,0.00185183,0.000561466,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,3.35636e-07,0.251466,0.288096,0.11903,0.0838874,0.331451,0.113145,0.112651,0.186638,0.174776,0.0948451,0.0384217,0.249049,0.000516956,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.0125264,0.166967,0.188651,0.0813902,0.184948,0.156261,0.0546539,0.161789,0.0590944,0.0334734,0.178389,0.0257622,0.00248603,0.407281,0.0170505,0.0360851,0.412187,0.131093,0.0434602,0.00935312,0.418146,0.0785808,0.449036,0.407369,0.231447,0.544776,0.43956,0.37006,0.10748,0.120472,0.197484,0.396996,0.36145,0.406019,0.0129,0.580441,0.643768,0.432035,8.1243e-06,0.390366,0.48809,0.50058,0.443185,0.522904,0.158867,0.151996,0.227104,0.518585,0.0734371,0.0867545,0.284625,0.504757,0.55194,0.0108655,0.28907,0.164197,0.462688,0.287881,0.574635,0.478174,0.336276,0.0263888,0.258219,0.446557,0.243383,0.0186777,0.390974,0.0115792,0.029557,0.161598,0.0527155,0.644754,0.496032,0.0795555,0.37357,0.0203982,0.477353,0.78384,0.746954,0.0629574,0.0222555,0.200493,0.20558,0.300504,0.25656,0.425963,0.0696455,0.383291,0.156104,0.141318,1.97791e-05,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,0.28424,0.20075,0.0556238,0.00115141,0.282286,0.0674279,0.24884,0.408413,0.516511,0.322213,0.656109,0.0655189,0.0700181,0.387276,0.522605,0.221908,0.00120002,0.222037,0.416621,0.416292,0.0252635,0.000454034,0.579431,0.204817,0.452428,0.0101228,0.103502,0.166905,0.19783,0.0833851,0.316453,0.0289164,0.175199,0.332919,0.373557,0.523625,0.408861,0.365487,0.534741,0.0889149,0.363192,0.236011,0.0222706,0.273398,0.375787,0.0223007,0.0704514,0.275347,0.269604,0.305885,0.241132,0.371414,0.0527347,0.303709,8.00304e-05,0.0135408,9.67605e-05,0.250964,0.0131557,0.0243456,0.504711,0.00213139,0.509064,0.196976,0.00136659,0.463751,0.0145214,0.307334,0.0246928,0.283463,0.563586,0.472935,0.399569,0.273281,0.0114705,0.275089,0.384593,0.138622,0.0105648,0.339729,0.197805,0.00278185,0.387069,0.0627969,0.52832,0.299887,0.0193657,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.255516,0.20753,0.447185,0.179412,0.193601,0.220904,0.222977,7.52509e-05,0.310674,0.21801,0.0015337,0.186804,0.00793786,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.0430576,0.0855609,0.131118,0.0233967,0.247588,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.00242972,0.162145,0.228955,0.000916623,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.0262794,0.195218,0.124213,0.0370716,0.0532009,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,2.67472e-05,0.0537737,0.15113,8.4053e-05,0.0407233,0.0537355,0.319922,0.0377035,0.211332,0.187731,0.0025753,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.00618871,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.00084829,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.000185889,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435
}}
}}

Revision as of 12:53, 5 September 2012


Full id: C3543_heart_Lymphatic_mature_retinoblastoma_medulla_Renal_Endothelial



Phase1 CAGE Peaks

Hg19::chr16:20911978..20911991,+p10@LYRM1
Hg19::chr16:20912007..20912027,+p6@LYRM1
Hg19::chr16:20912031..20912042,+p14@LYRM1


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
multi-cellular organism9.59e-17659
anatomical system2.43e-14625
anatomical group4.83e-14626
splanchnic layer of lateral plate mesoderm6.07e-1284
vessel1.02e-1169
vasculature1.24e-1179
vascular system1.24e-1179
embryo1.63e-11612
embryonic structure4.69e-11605
developing anatomical structure4.69e-11605
endothelium4.79e-1118
blood vessel endothelium4.79e-1118
cardiovascular system endothelium4.79e-1118
blood vessel7.54e-1160
epithelial tube open at both ends7.54e-1160
blood vasculature7.54e-1160
vascular cord7.54e-1160
germ layer8.85e-11604
embryonic tissue8.85e-11604
presumptive structure8.85e-11604
epiblast (generic)8.85e-11604
circulatory system1.58e-10113
squamous epithelium3.70e-1025
cardiovascular system8.99e-10110
simple squamous epithelium3.29e-0922
tube3.49e-09194
anatomical conduit3.66e-09241
epithelium6.51e-09309
cell layer7.97e-09312
epithelial tube1.18e-08118
anatomical cluster1.28e-08286
mesoderm2.97e-08448
mesoderm-derived structure2.97e-08448
presumptive mesoderm2.97e-08448
unilaminar epithelium6.14e-07138


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
ATF3#467322.46317452600878.81932387510763e-050.00129510878261019
BRCA1#672320.18423064322380.0001215704860271640.001641036576217
CCNT2#90536.336201576962630.003930750035764890.0189723450866646
CEBPB#105137.971147625824820.001974187055288560.0115108375316705
CHD2#1106310.34402283411690.0009033701102746880.00659631342704175
E2F1#186934.907389214879320.008460985347239390.0324706712971388
EGR1#195834.988179094810140.008056488137383440.0320013526254208
ELF1#199734.258097958807540.01295179875054610.0461332461276315
ELK4#2005316.2356816584680.0002336043955745990.00255523769055462
EP300#203336.77394172622320.003216880500103790.0167264653266126
FOXA1#3169311.08141974938550.000734755275698670.00580506136914239
GABPB1#255337.067683836182170.002832212825417420.0153898790465021
HMGN3#932438.178547723350590.001827766942164210.0108571352333459
JUN#3725312.51282919233630.0005103313992726250.0044371046460734
JUND#372736.994663941871030.002921845042734990.0156497550858095
MYC#460935.22228187160940.007020843755740150.0294005573779369
NANOG#79923329.24477848101273.99627955670032e-050.000736747468000397
NFKB1#479035.488063424193840.006049381815655430.0269236933199198
REST#597839.650028716128020.001112636247114590.00766508027786284
RFX5#5993312.04791082719510.0005717246050312580.00484072525535951
SIN3A#2594235.408884726815140.006318961977991520.0276139616728506
SIX5#147912317.0867153554590.0002004060546325010.00239448666511426
SMARCB1#6598212.16847718743830.008675002221921740.0329793446802302
SP1#666735.69838137814090.005403962701712170.0246079991543108
SRF#6722313.79717826216780.0003806615025800190.00374631612023696
STAT1#6772320.70658749719920.0001125992441046670.00154692876283179
STAT3#6774310.51946499715420.0008589184530415310.00642214950724545
TFAP2C#7022310.80922860986020.0007916746575753130.00614551133956504
THAP1#55145331.36914460285133.23800758564397e-050.000645987152315321
TRIM28#10155318.59052504526250.0001555969297255280.001967835764544
USF1#739136.361499277207960.00388404057290560.0189988906090435
ZBTB7A#5134137.35190930787590.002516255860282270.0139926119904169
ZNF263#1012738.221841637010680.001799043925565870.0109225874050793



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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