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Coexpression cluster:C4026: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!6.55e-29!57;UBERON:0005068!6.55e-29!57;UBERON:0006241!6.55e-29!57;UBERON:0007135!6.55e-29!57;UBERON:0002616!3.34e-27!59;UBERON:0001017!4.44e-26!82;UBERON:0005743!1.27e-25!86;UBERON:0000955!6.24e-25!69;UBERON:0006238!6.24e-25!69;UBERON:0002346!1.87e-24!90;UBERON:0007023!4.45e-24!115;UBERON:0003075!5.10e-24!86;UBERON:0007284!5.10e-24!86;UBERON:0000073!6.71e-24!94;UBERON:0001016!6.71e-24!94;UBERON:0000025!1.67e-23!194;UBERON:0003080!2.96e-21!42;UBERON:0002780!6.48e-21!41;UBERON:0001890!6.48e-21!41;UBERON:0006240!6.48e-21!41;UBERON:0004111!2.01e-20!241;UBERON:0002020!1.69e-18!34;UBERON:0003528!1.69e-18!34;UBERON:0001893!4.39e-18!34;UBERON:0000475!1.07e-17!365;UBERON:0002791!1.48e-17!33;UBERON:0001869!2.39e-17!32;UBERON:0000924!3.62e-17!173;UBERON:0006601!3.62e-17!173;UBERON:0004121!1.33e-16!169;UBERON:0000483!1.36e-16!309;UBERON:0000119!1.47e-16!312;UBERON:0000477!1.48e-16!286;UBERON:0000033!1.10e-15!123;UBERON:0003056!3.41e-15!61;UBERON:0000468!6.41e-15!659;UBERON:0002619!1.01e-14!22;UBERON:0000153!1.30e-14!129;UBERON:0007811!1.30e-14!129;UBERON:0000956!9.57e-14!25;UBERON:0000203!9.57e-14!25;UBERON:0001950!1.72e-13!20;UBERON:0000467!2.84e-12!625;UBERON:0000480!5.10e-12!626;UBERON:0000922!5.27e-10!612;UBERON:0000481!6.10e-10!347;UBERON:0002050!6.23e-10!605;UBERON:0005423!6.23e-10!605;UBERON:0000923!1.20e-09!604;UBERON:0005291!1.20e-09!604;UBERON:0006598!1.20e-09!604;UBERON:0002532!1.20e-09!604;UBERON:0004872!7.24e-09!84;UBERON:0003076!8.95e-09!15;UBERON:0003057!8.95e-09!15;UBERON:0002049!1.11e-08!79;UBERON:0007798!1.11e-08!79;UBERON:0000055!3.44e-08!69;UBERON:0004732!5.81e-08!13;UBERON:0003914!6.57e-08!118;UBERON:0001981!1.33e-07!60;UBERON:0007500!1.33e-07!60;UBERON:0004537!1.33e-07!60;UBERON:0006965!1.33e-07!60;UBERON:0001009!2.11e-07!113;UBERON:0004733!2.42e-07!12;UBERON:0002028!2.42e-07!12;UBERON:0007277!2.42e-07!12;UBERON:0005256!5.20e-07!143;UBERON:0000914!9.41e-07!83;UBERON:0002329!9.41e-07!83;UBERON:0003077!9.41e-07!83;UBERON:0003059!9.41e-07!83;UBERON:0007282!9.41e-07!83;UBERON:0009618!9.41e-07!83;UBERON:0007285!9.41e-07!83
|ontology_enrichment_uberon=UBERON:0001049!6.55e-29!57;UBERON:0005068!6.55e-29!57;UBERON:0006241!6.55e-29!57;UBERON:0007135!6.55e-29!57;UBERON:0002616!3.34e-27!59;UBERON:0001017!4.44e-26!82;UBERON:0005743!1.27e-25!86;UBERON:0000955!6.24e-25!69;UBERON:0006238!6.24e-25!69;UBERON:0002346!1.87e-24!90;UBERON:0007023!4.45e-24!115;UBERON:0003075!5.10e-24!86;UBERON:0007284!5.10e-24!86;UBERON:0000073!6.71e-24!94;UBERON:0001016!6.71e-24!94;UBERON:0000025!1.67e-23!194;UBERON:0003080!2.96e-21!42;UBERON:0002780!6.48e-21!41;UBERON:0001890!6.48e-21!41;UBERON:0006240!6.48e-21!41;UBERON:0004111!2.01e-20!241;UBERON:0002020!1.69e-18!34;UBERON:0003528!1.69e-18!34;UBERON:0001893!4.39e-18!34;UBERON:0000475!1.07e-17!365;UBERON:0002791!1.48e-17!33;UBERON:0001869!2.39e-17!32;UBERON:0000924!3.62e-17!173;UBERON:0006601!3.62e-17!173;UBERON:0004121!1.33e-16!169;UBERON:0000483!1.36e-16!309;UBERON:0000119!1.47e-16!312;UBERON:0000477!1.48e-16!286;UBERON:0000033!1.10e-15!123;UBERON:0003056!3.41e-15!61;UBERON:0000468!6.41e-15!659;UBERON:0002619!1.01e-14!22;UBERON:0000153!1.30e-14!129;UBERON:0007811!1.30e-14!129;UBERON:0000956!9.57e-14!25;UBERON:0000203!9.57e-14!25;UBERON:0001950!1.72e-13!20;UBERON:0000467!2.84e-12!625;UBERON:0000480!5.10e-12!626;UBERON:0000922!5.27e-10!612;UBERON:0000481!6.10e-10!347;UBERON:0002050!6.23e-10!605;UBERON:0005423!6.23e-10!605;UBERON:0000923!1.20e-09!604;UBERON:0005291!1.20e-09!604;UBERON:0006598!1.20e-09!604;UBERON:0002532!1.20e-09!604;UBERON:0004872!7.24e-09!84;UBERON:0003076!8.95e-09!15;UBERON:0003057!8.95e-09!15;UBERON:0002049!1.11e-08!79;UBERON:0007798!1.11e-08!79;UBERON:0000055!3.44e-08!69;UBERON:0004732!5.81e-08!13;UBERON:0003914!6.57e-08!118;UBERON:0001981!1.33e-07!60;UBERON:0007500!1.33e-07!60;UBERON:0004537!1.33e-07!60;UBERON:0006965!1.33e-07!60;UBERON:0001009!2.11e-07!113;UBERON:0004733!2.42e-07!12;UBERON:0002028!2.42e-07!12;UBERON:0007277!2.42e-07!12;UBERON:0005256!5.20e-07!143;UBERON:0000914!9.41e-07!83;UBERON:0002329!9.41e-07!83;UBERON:0003077!9.41e-07!83;UBERON:0003059!9.41e-07!83;UBERON:0007282!9.41e-07!83;UBERON:0009618!9.41e-07!83;UBERON:0007285!9.41e-07!83
|tf_chipseq_enrich=E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0322749490111242!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173104072841199!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0246887340596727!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190578018977537
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211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.28262,0.00662343,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.174921,0.370421,0.0330727,0.348757,0.219556,0.0394698,0.0596469,0.103658,0.122476,0.108872,0.11002,0.00370214,0.0286025,0.000180779,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.0144628,0.237101,0.00501606,0.0761239,0.000982125,0.0818785,0.182701,0.335058,0.000603748,0.141463,0.167267,0.140622,0.0889592,0.0538132,0.28711,0.0473033,0.094881,0.445524,0.132886,0.0774373,0.109194,0.128564,0.131452,0.687347,0.120459,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.153605,0.655293,0.000123443,0.00514993,0.119215,0.192475,0.177967,0.0465298,0.057571,0.047591,0.0899568,0.0608699,0.175319,3.61858e-05,0.0713214,0.00224624,0.291114,0.0355833,0.125606,0.175094,0.226002,0.0225581,0.206454,0.218192,0.108277,5.36187e-05,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.00678942,0.000143882,0.0158019,0.104948,0.221645,0.057168,0.234298,7.75285e-05,7.4568e-08,0.152372,0.194941,0.00207136,0.101607,0.327067,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,9.16892e-05,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.000943322,0.193653,0.00987736,0.00238639,0.00326415,0.288096,0.11903,0.000104984,0.331451,0.113145,0.112651,0.186638,0.174776,0.0948451,0.00382477,0.249049,0.140533,0.0997756,0.0364628,0.103667,0.113069,0.025556,0.16791,0.09066,0.585505,0.166967,0.188651,0.0813902,0.00122372,0.156261,0.311847,0.0362615,0.0590944,0.000216551,0.178389,0.218229,0.231073,0.407281,0.619906,0.0360851,0.0021796,0.131093,0.0434602,0.133616,0.418146,0.36927,0.449036,0.407369,0.231447,0.544776,0.43956,0.37006,0.42622,0.448797,0.197484,0.0919774,0.36145,0.00202987,0.381071,0.057779,0.0863135,0.432035,0.722159,0.390366,0.48809,0.153829,0.443185,0.522904,0.0608227,0.336835,0.227104,0.518585,0.250246,0.38649,0.284625,0.00583062,0.55194,0.00228337,0.28907,0.164197,0.462688,0.287881,0.21103,0.478174,0.336276,0.468444,0.258219,0.446557,0.243383,0.0186777,0.0889613,0.73485,0.00650842,0.161598,0.0527155,0.00422412,0.496032,0.00136122,0.37357,0.00500957,0.477353,0.199161,0.00292516,0.0629574,0.20342,0.200493,0.00171127,0.300504,0.25656,0.425963,0.349197,0.383291,0.156104,0.141318,0.411941,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,0.28424,0.562405,0.314429,0.181415,0.282286,0.000180531,0.616388,0.408413,0.516511,0.322213,0.656109,0.00873429,0.61031,0.387276,0.522605,0.00640674,0.537348,0.222037,0.102227,0.416292,0.0252635,0.148994,0.215157,0.0225745,0.452428,0.138871,0.027191,0.166905,0.19783,0.0833851,0.056391,0.48065,0.175199,0.332919,0.373557,0.0393909,0.0164118,0.365487,0.534741,0.00169836,0.0109626,0.0303438,0.203486,0.273398,0.0123025,0.0223007,0.351067,0.275347,9.09657e-05,0.305885,0.241132,0.371414,0.30666,0.303709,0.495883,0.386538,0.508064,0.250964,0.383276,0.457886,0.504711,0.220231,0.0355483,0.196976,0.191517,0.463751,0.601877,0.307334,0.459728,0.283463,0.000222968,0.472935,0.399569,0.273281,0.0114705,0.275089,0.384593,0.138622,0.359231,0.339729,0.197805,0.000423937,0.0136044,0.332774,0.173874,0.299887,0.634365,0.205413,0.0165618,0.00311629,0.276869,0.00170381,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.0146333,0.252184,0.378361,0.255516,0.20753,0.447185,0.179412,0.193601,0.220904,0.222977,0.341681,0.000593893,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,3.04194e-07,0.00112112,0.226869,0.27872,0.0855609,0.000416591,0.00178627,0.0335483,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.0398662,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.0251995,0.158479,0.220319,0.195218,0.124213,0.00361981,0.30793,0.180606,0.159884,0.000257423,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,8.72774e-05,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,2.67472e-05,0.0537737,0.15113,0.078016,0.0407233,2.69453e-05,0.00717361,4.57541e-11,0.211332,0.187731,1.45062e-11,0.00132285,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.0224775,5.63249e-12,0.0457063,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.0497481,0.253509,0.177664,0.0446853,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.0001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}}
}}

Revision as of 11:49, 5 September 2012


Full id: C4026_pineal_Mesenchymal_brain_Cardiac_amygdala_occipital_hippocampus



Phase1 CAGE Peaks

Hg19::chr20:33146490..33146508,+p3@MAP1LC3A
Hg19::chr20:33146510..33146549,+p1@MAP1LC3A
Hg19::chr20:33146551..33146567,+p2@MAP1LC3A


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>

Cell Type
Ontology termp-valuen
non-terminally differentiated cell3.77e-09180
mesodermal cell5.88e-08119
contractile cell4.55e-0759
Uber Anatomy
Ontology termp-valuen
neural tube6.55e-2957
neural rod6.55e-2957
future spinal cord6.55e-2957
neural keel6.55e-2957
regional part of brain3.34e-2759
central nervous system4.44e-2682
brain6.24e-2569
future brain6.24e-2569
neurectoderm1.87e-2490
adult organism4.45e-24115
neural plate5.10e-2486
presumptive neural plate5.10e-2486
regional part of nervous system6.71e-2494
nervous system6.71e-2494
tube1.67e-23194
anterior neural tube2.96e-2142
regional part of forebrain6.48e-2141
forebrain6.48e-2141
future forebrain6.48e-2141
anatomical conduit2.01e-20241
gray matter1.69e-1834
brain grey matter1.69e-1834
telencephalon4.39e-1834
organism subdivision1.07e-17365
regional part of telencephalon1.48e-1733
cerebral hemisphere2.39e-1732
ectoderm3.62e-17173
presumptive ectoderm3.62e-17173
ectoderm-derived structure1.33e-16169
epithelium1.36e-16309
cell layer1.47e-16312
anatomical cluster1.48e-16286
head1.10e-15123
pre-chordal neural plate3.41e-1561
multi-cellular organism6.41e-15659
regional part of cerebral cortex1.01e-1422
anterior region of body1.30e-14129
craniocervical region1.30e-14129
cerebral cortex9.57e-1425
pallium9.57e-1425
neocortex1.72e-1320
anatomical system2.84e-12625
anatomical group5.10e-12626
embryo5.27e-10612
multi-tissue structure6.10e-10347
embryonic structure6.23e-10605
developing anatomical structure6.23e-10605
germ layer1.20e-09604
embryonic tissue1.20e-09604
presumptive structure1.20e-09604
epiblast (generic)1.20e-09604
splanchnic layer of lateral plate mesoderm7.24e-0984
posterior neural tube8.95e-0915
chordal neural plate8.95e-0915
vasculature1.11e-0879
vascular system1.11e-0879
vessel3.44e-0869
segmental subdivision of nervous system5.81e-0813
epithelial tube6.57e-08118
blood vessel1.33e-0760
epithelial tube open at both ends1.33e-0760
blood vasculature1.33e-0760
vascular cord1.33e-0760
circulatory system2.11e-07113
segmental subdivision of hindbrain2.42e-0712
hindbrain2.42e-0712
presumptive hindbrain2.42e-0712
trunk mesenchyme5.20e-07143
somite9.41e-0783
paraxial mesoderm9.41e-0783
presomitic mesoderm9.41e-0783
presumptive segmental plate9.41e-0783
trunk paraxial mesoderm9.41e-0783
presumptive paraxial mesoderm9.41e-0783


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
E2F6#187635.017155731697390.00791769806886330.0322749490111242
PAX5#507936.669565531177830.003370290999677260.0173104072841199
SP1#666735.69838137814090.005403962701712170.0246887340596727
USF1#739136.361499277207960.00388404057290560.0190578018977537



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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