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Coexpression cluster:C4509: Difference between revisions

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|ontology_enrichment_disease=DOID:305!2.43e-11!106;DOID:0050687!2.40e-08!143
|ontology_enrichment_disease=DOID:305!2.43e-11!106;DOID:0050687!2.40e-08!143
|ontology_enrichment_uberon=UBERON:0007023!3.77e-36!115;UBERON:0001049!3.81e-21!57;UBERON:0005068!3.81e-21!57;UBERON:0006241!3.81e-21!57;UBERON:0007135!3.81e-21!57;UBERON:0005743!1.41e-17!86;UBERON:0003080!6.94e-17!42;UBERON:0002616!8.08e-17!59;UBERON:0003075!1.07e-16!86;UBERON:0007284!1.07e-16!86;UBERON:0002780!1.81e-16!41;UBERON:0001890!1.81e-16!41;UBERON:0006240!1.81e-16!41;UBERON:0000073!2.60e-16!94;UBERON:0001016!2.60e-16!94;UBERON:0001017!7.87e-16!82;UBERON:0000955!1.11e-15!69;UBERON:0006238!1.11e-15!69;UBERON:0002346!1.43e-15!90;UBERON:0000062!1.97e-15!511;UBERON:0003056!1.05e-13!61;UBERON:0002020!1.37e-13!34;UBERON:0003528!1.37e-13!34;UBERON:0001893!1.79e-13!34;UBERON:0002791!5.28e-13!33;UBERON:0000922!2.06e-12!612;UBERON:0004121!2.28e-12!169;UBERON:0001869!2.59e-12!32;UBERON:0000924!7.89e-12!173;UBERON:0006601!7.89e-12!173;UBERON:0000033!1.07e-11!123;UBERON:0000153!2.68e-11!129;UBERON:0007811!2.68e-11!129;UBERON:0002050!6.89e-11!605;UBERON:0005423!6.89e-11!605;UBERON:0000923!9.14e-11!604;UBERON:0005291!9.14e-11!604;UBERON:0006598!9.14e-11!604;UBERON:0002532!9.14e-11!604;UBERON:0002619!9.26e-10!22;UBERON:0000468!3.16e-09!659;UBERON:0000467!4.02e-09!625;UBERON:0000480!6.29e-09!626;UBERON:0000956!8.25e-09!25;UBERON:0000203!8.25e-09!25;UBERON:0001950!9.04e-09!20
|ontology_enrichment_uberon=UBERON:0007023!3.77e-36!115;UBERON:0001049!3.81e-21!57;UBERON:0005068!3.81e-21!57;UBERON:0006241!3.81e-21!57;UBERON:0007135!3.81e-21!57;UBERON:0005743!1.41e-17!86;UBERON:0003080!6.94e-17!42;UBERON:0002616!8.08e-17!59;UBERON:0003075!1.07e-16!86;UBERON:0007284!1.07e-16!86;UBERON:0002780!1.81e-16!41;UBERON:0001890!1.81e-16!41;UBERON:0006240!1.81e-16!41;UBERON:0000073!2.60e-16!94;UBERON:0001016!2.60e-16!94;UBERON:0001017!7.87e-16!82;UBERON:0000955!1.11e-15!69;UBERON:0006238!1.11e-15!69;UBERON:0002346!1.43e-15!90;UBERON:0000062!1.97e-15!511;UBERON:0003056!1.05e-13!61;UBERON:0002020!1.37e-13!34;UBERON:0003528!1.37e-13!34;UBERON:0001893!1.79e-13!34;UBERON:0002791!5.28e-13!33;UBERON:0000922!2.06e-12!612;UBERON:0004121!2.28e-12!169;UBERON:0001869!2.59e-12!32;UBERON:0000924!7.89e-12!173;UBERON:0006601!7.89e-12!173;UBERON:0000033!1.07e-11!123;UBERON:0000153!2.68e-11!129;UBERON:0007811!2.68e-11!129;UBERON:0002050!6.89e-11!605;UBERON:0005423!6.89e-11!605;UBERON:0000923!9.14e-11!604;UBERON:0005291!9.14e-11!604;UBERON:0006598!9.14e-11!604;UBERON:0002532!9.14e-11!604;UBERON:0002619!9.26e-10!22;UBERON:0000468!3.16e-09!659;UBERON:0000467!4.02e-09!625;UBERON:0000480!6.29e-09!626;UBERON:0000956!8.25e-09!25;UBERON:0000203!8.25e-09!25;UBERON:0001950!9.04e-09!20
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0906475,0.0558058,0.00477066,1.15329e-05,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.00340073,0.170307,0.201033,0.0488949,0.174921,0.0791124,0.0330727,0.348757,0.02609,0.0394698,0.0596469,0.103658,0.122476,0.108872,0.11002,1.65628e-05,0.0286025,2.02725e-05,0.000564671,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.090504,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.335058,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.28711,0.0473033,0.094881,0.118532,0.132886,0.0774373,0.109194,0.128564,0.131452,0.00128046,0.00327218,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.00447267,0.00264443,0.655293,0.21727,0.289306,0.119215,0.192475,0.177967,0.000176812,0.057571,0.047591,0.392974,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.00525614,0.0355833,0.125606,0.175094,0.000216899,1.88644e-11,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.00500888,0.152372,0.194941,0.218271,0.101607,0.327067,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.504592,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.0154015,0.193653,0.00987736,0.228144,0.251466,0.288096,0.11903,0.0838874,0.331451,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.0364628,0.103667,0.113069,0.025556,0.16791,0.09066,0.585505,0.166967,0.188651,0.0813902,0.184948,0.156261,0.311847,0.0062542,0.0590944,0.247324,0.178389,0.218229,0.231073,0.0020598,0.0743925,0.0360851,0.412187,0.131093,0.0434602,0.133616,0.0177337,0.0115948,0.449036,0.407369,0.231447,0.544776,0.43956,0.37006,0.10748,0.448797,0.197484,0.396996,0.36145,0.0160226,0.381071,0.216033,0.643768,0.0198622,0.0100497,0.390366,0.48809,0.0334527,0.443185,0.522904,0.875915,6.79659e-10,0.227104,0.518585,0.0167433,0.38649,0.284625,0.504757,0.04783,0.0437169,0.28907,0.164197,0.462688,0.287881,0.574635,0.478174,0.336276,0.468444,0.258219,0.446557,0.243383,0.0659137,0.390974,0.382874,0.109758,0.161598,1.54935e-05,0.00422412,0.0323708,7.35021e-06,0.37357,0.200632,0.477353,0.00492096,0.0132585,0.185744,0.00165472,0.200493,0.20558,0.300504,0.0361545,0.425963,0.349197,0.383291,0.156104,0.141318,0.0997241,0.0961477,0.314438,0.00108466,0.163828,0.230581,0.120226,0.28424,0.20075,0.314429,0.181415,0.282286,0.0674279,0.0727621,0.408413,0.516511,0.322213,0.28903,0.33942,0.0700181,0.387276,0.522605,0.0248202,0.0433137,0.222037,0.416621,0.416292,0.462712,0.382478,0.215157,0.204817,0.452428,0.138871,0.00583733,0.166905,0.19783,0.0833851,0.316453,0.140384,0.175199,0.332919,0.373557,0.523625,0.408861,0.0768488,0.534741,0.39088,0.363192,0.236011,0.203486,0.273398,0.375787,0.4466,0.351067,0.275347,0.0830022,0.305885,0.241132,0.371414,0.30666,0.303709,0.495883,0.386538,0.508064,0.250964,0.383276,0.457886,0.504711,0.220231,0.509064,0.196976,0.191517,0.463751,0.601877,0.307334,0.459728,0.283463,0.0517073,0.472935,0.399569,0.273281,0.368095,0.275089,0.384593,0.47795,0.359231,0.339729,0.197805,0.608187,0.387069,0.332774,0.52832,0.299887,0.634365,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.255516,0.20753,0.0224033,0.179412,0.193601,0.220904,0.222977,0.0664606,0.310674,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.0430576,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.000284685,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.036274,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.00553696,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.00501043,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0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}}
}}

Revision as of 13:05, 5 September 2012


Full id: C4509_CD14_renal_Whole_serous_signet_small_optic



Phase1 CAGE Peaks

Hg19::chr5:60140009..60140050,-p2@ELOVL7
Hg19::chr5:60140059..60140075,-p3@ELOVL7
Hg19::chr5:60140089..60140118,-p1@ELOVL7


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>

Cell Type
Ontology termp-valuen
epithelial cell1.37e-08254
endo-epithelial cell2.21e-0743
endodermal cell3.72e-0759
Uber Anatomy
Ontology termp-valuen
adult organism3.77e-36115
neural tube3.81e-2157
neural rod3.81e-2157
future spinal cord3.81e-2157
neural keel3.81e-2157
anterior neural tube6.94e-1742
regional part of brain8.08e-1759
neural plate1.07e-1686
presumptive neural plate1.07e-1686
regional part of forebrain1.81e-1641
forebrain1.81e-1641
future forebrain1.81e-1641
regional part of nervous system2.60e-1694
nervous system2.60e-1694
central nervous system7.87e-1682
brain1.11e-1569
future brain1.11e-1569
neurectoderm1.43e-1590
organ1.97e-15511
pre-chordal neural plate1.05e-1361
gray matter1.37e-1334
brain grey matter1.37e-1334
telencephalon1.79e-1334
regional part of telencephalon5.28e-1333
embryo2.06e-12612
ectoderm-derived structure2.28e-12169
cerebral hemisphere2.59e-1232
ectoderm7.89e-12173
presumptive ectoderm7.89e-12173
head1.07e-11123
anterior region of body2.68e-11129
craniocervical region2.68e-11129
embryonic structure6.89e-11605
developing anatomical structure6.89e-11605
germ layer9.14e-11604
embryonic tissue9.14e-11604
presumptive structure9.14e-11604
epiblast (generic)9.14e-11604
regional part of cerebral cortex9.26e-1022
multi-cellular organism3.16e-09659
anatomical system4.02e-09625
anatomical group6.29e-09626
cerebral cortex8.25e-0925
pallium8.25e-0925
neocortex9.04e-0920
Disease
Ontology termp-valuen
carcinoma2.43e-11106
cell type cancer2.40e-08143


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
CCNT2#90536.336201576962630.003930750035764890.0190896816082422
CTCF#1066435.360256373075030.0064925092527670.0280937675608938
E2F1#186934.907389214879320.008460985347239390.0327195485866751
E2F6#187635.017155731697390.00791769806886330.0323937974933997
FOSL1#8061339.7135797163731.59554825631833e-050.000372291028466556
GATA3#2625327.2365163572064.94721007899563e-050.000853737067812664
HMGN3#932438.178547723350590.001827766942164210.0109080086670108
JUN#3725312.51282919233630.0005103313992726250.00445937926779064
JUND#372736.994663941871030.002921845042734990.0157458500731785
MYC#460935.22228187160940.007020843755740150.0295712978305269
PAX5#507936.669565531177830.003370290999677260.0173547885669704
RAD21#5885310.35503389545630.0009004912073565420.00667469135593398
SMC3#9126315.04493284493280.0002935825420371870.00310432996940586
TCF12#6938310.63446490218640.0008313523990202070.00631459005100155
USF1#739136.361499277207960.00388404057290560.0190981785966896
ZBTB7A#5134137.35190930787590.002516255860282270.014075803202572
ZEB1#6935316.88843201754390.0002075486917327580.00243579928260226
ZNF143#7702313.50087655222790.0004062804962997170.0039035445035001



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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