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Coexpression cluster:C4673: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005743!8.34e-39!86;UBERON:0000073!2.25e-38!94;UBERON:0001016!2.25e-38!94;UBERON:0001017!4.61e-37!82;UBERON:0001049!1.21e-34!57;UBERON:0005068!1.21e-34!57;UBERON:0006241!1.21e-34!57;UBERON:0007135!1.21e-34!57;UBERON:0007023!1.16e-29!115;UBERON:0000955!3.23e-29!69;UBERON:0006238!3.23e-29!69;UBERON:0002780!3.09e-27!41;UBERON:0001890!3.09e-27!41;UBERON:0006240!3.09e-27!41;UBERON:0002616!5.76e-27!59;UBERON:0003080!5.48e-26!42;UBERON:0003075!4.22e-25!86;UBERON:0007284!4.22e-25!86;UBERON:0002020!4.39e-24!34;UBERON:0003528!4.39e-24!34;UBERON:0001893!4.52e-24!34;UBERON:0002346!7.96e-24!90;UBERON:0000153!1.17e-23!129;UBERON:0007811!1.17e-23!129;UBERON:0000033!1.18e-23!123;UBERON:0002791!2.17e-23!33;UBERON:0004121!1.33e-22!169;UBERON:0001869!1.55e-22!32;UBERON:0000924!5.62e-22!173;UBERON:0006601!5.62e-22!173;UBERON:0000922!9.96e-19!612;UBERON:0003056!2.33e-18!61;UBERON:0000956!8.42e-18!25;UBERON:0000203!8.42e-18!25;UBERON:0000468!2.44e-17!659;UBERON:0002050!3.11e-16!605;UBERON:0005423!3.11e-16!605;UBERON:0000467!4.25e-16!625;UBERON:0000923!6.54e-16!604;UBERON:0005291!6.54e-16!604;UBERON:0006598!6.54e-16!604;UBERON:0002532!6.54e-16!604;UBERON:0000480!7.00e-16!626;UBERON:0002619!1.50e-15!22;UBERON:0004111!2.64e-15!241;UBERON:0001950!2.67e-14!20;UBERON:0000062!7.68e-12!511;UBERON:0000477!8.12e-12!286;UBERON:0000025!1.42e-11!194;UBERON:0003076!1.13e-09!15;UBERON:0003057!1.13e-09!15;UBERON:0000481!2.21e-08!347;UBERON:0004732!2.45e-08!13;UBERON:0002308!9.86e-08!9;UBERON:0000125!9.86e-08!9;UBERON:0004733!1.35e-07!12;UBERON:0002028!1.35e-07!12;UBERON:0007277!1.35e-07!12;UBERON:0002420!1.70e-07!9;UBERON:0007245!1.70e-07!9;UBERON:0010009!1.70e-07!9;UBERON:0010011!1.70e-07!9;UBERON:0000454!1.70e-07!9;UBERON:0000475!4.48e-07!365
|ontology_enrichment_uberon=UBERON:0005743!8.34e-39!86;UBERON:0000073!2.25e-38!94;UBERON:0001016!2.25e-38!94;UBERON:0001017!4.61e-37!82;UBERON:0001049!1.21e-34!57;UBERON:0005068!1.21e-34!57;UBERON:0006241!1.21e-34!57;UBERON:0007135!1.21e-34!57;UBERON:0007023!1.16e-29!115;UBERON:0000955!3.23e-29!69;UBERON:0006238!3.23e-29!69;UBERON:0002780!3.09e-27!41;UBERON:0001890!3.09e-27!41;UBERON:0006240!3.09e-27!41;UBERON:0002616!5.76e-27!59;UBERON:0003080!5.48e-26!42;UBERON:0003075!4.22e-25!86;UBERON:0007284!4.22e-25!86;UBERON:0002020!4.39e-24!34;UBERON:0003528!4.39e-24!34;UBERON:0001893!4.52e-24!34;UBERON:0002346!7.96e-24!90;UBERON:0000153!1.17e-23!129;UBERON:0007811!1.17e-23!129;UBERON:0000033!1.18e-23!123;UBERON:0002791!2.17e-23!33;UBERON:0004121!1.33e-22!169;UBERON:0001869!1.55e-22!32;UBERON:0000924!5.62e-22!173;UBERON:0006601!5.62e-22!173;UBERON:0000922!9.96e-19!612;UBERON:0003056!2.33e-18!61;UBERON:0000956!8.42e-18!25;UBERON:0000203!8.42e-18!25;UBERON:0000468!2.44e-17!659;UBERON:0002050!3.11e-16!605;UBERON:0005423!3.11e-16!605;UBERON:0000467!4.25e-16!625;UBERON:0000923!6.54e-16!604;UBERON:0005291!6.54e-16!604;UBERON:0006598!6.54e-16!604;UBERON:0002532!6.54e-16!604;UBERON:0000480!7.00e-16!626;UBERON:0002619!1.50e-15!22;UBERON:0004111!2.64e-15!241;UBERON:0001950!2.67e-14!20;UBERON:0000062!7.68e-12!511;UBERON:0000477!8.12e-12!286;UBERON:0000025!1.42e-11!194;UBERON:0003076!1.13e-09!15;UBERON:0003057!1.13e-09!15;UBERON:0000481!2.21e-08!347;UBERON:0004732!2.45e-08!13;UBERON:0002308!9.86e-08!9;UBERON:0000125!9.86e-08!9;UBERON:0004733!1.35e-07!12;UBERON:0002028!1.35e-07!12;UBERON:0007277!1.35e-07!12;UBERON:0002420!1.70e-07!9;UBERON:0007245!1.70e-07!9;UBERON:0010009!1.70e-07!9;UBERON:0010011!1.70e-07!9;UBERON:0000454!1.70e-07!9;UBERON:0000475!4.48e-07!365
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432,0.107043,1.17401e-06,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.28262,0.517717,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,2.37346e-08,0.161801,0.193215,0.0549034,8.39064e-05,0.00160873,0.0417636,0.0345419,0.0388736,0.0355977,0.170307,0.201033,0.0488949,0.174921,0.0791124,0.0330727,0.348757,0.02609,0.0394698,0.0596469,0.419264,0.122476,0.108872,0.11002,0.26144,0.0286025,0.549354,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.0144628,0.237101,0.00501606,0.0761239,0.172491,0.0818785,0.182701,0.335058,0.011488,0.141463,0.167267,0.140622,0.0889592,0.309588,0.28711,0.0473033,0.094881,0.445524,0.132886,0.0774373,0.109194,0.128564,9.64595e-09,0.687347,0.448776,0.051838,0.0993999,2.16924e-05,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.739716,0.0232393,0.21727,0.289306,0.119215,0.192475,0.177967,0.0088427,0.057571,0.047591,0.0899568,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.291114,0.0355833,0.125606,1.87632e-06,0.43617,0.76084,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.286863,0.152372,0.194941,0.218271,0.101607,0.060512,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.504592,0.155821,0.0718905,0.0919008,0.0602373,0.000561466,0.15063,0.0973823,0.000702525,0.170295,0.193653,0.137219,0.228144,0.251466,0.0050797,0.11903,0.0838874,0.0622625,0.113145,0.112651,0.0186145,0.01625,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.0364628,0.103667,0.113069,0.025556,0.16791,0.09066,0.00213659,0.166967,0.0190329,0.0813902,0.184948,0.156261,0.311847,0.161789,0.0590944,0.247324,0.178389,0.218229,0.231073,0.407281,0.619906,0.0360851,0.412187,0.131093,0.0434602,0.133616,0.418146,0.36927,0.449036,0.0162067,0.231447,0.0455669,0.115047,0.00131691,0.42622,0.448797,0.197484,0.396996,0.0107863,0.00202987,0.381071,0.580441,0.000101057,0.432035,0.366326,0.390366,0.0305485,0.50058,0.00308025,0.522904,0.3468,0.336835,0.00235168,0.000113758,0.250246,0.000154756,0.284625,0.00583062,0.55194,0.729153,0.00513616,0.164197,0.0252589,0.287881,3.31949e-06,0.138768,0.336276,0.468444,0.258219,0.446557,0.000201897,0.00448654,0.390974,0.149257,0.029557,0.161598,0.00310283,1.48581e-06,8.02175e-05,4.65435e-05,0.37357,0.00500957,0.138234,3.25586e-05,0.160298,0.185744,0.20342,0.200493,0.20558,0.300504,0.25656,0.425963,0.349197,0.383291,0.156104,0.141318,0.411941,0.0961477,0.055627,0.0101316,0.163828,0.230581,0.120226,0.28424,0.562405,0.314429,0.0175523,0.282286,0.000180531,0.0165273,0.408413,0.000926901,0.322213,0.656109,0.33942,0.0156581,0.387276,0.522605,0.0248202,0.00800402,0.222037,0.102227,0.00228427,0.0252635,0.382478,0.000280804,0.204817,0.122646,0.138871,0.308032,0.166905,0.19783,0.0833851,0.056391,0.48065,0.0163316,0.332919,0.373557,0.00101302,0.0980968,0.365487,0.178743,0.0889149,0.363192,0.236011,0.203486,0.273398,0.0123025,0.4466,0.351067,0.275347,0.00388821,0.305885,0.241132,0.371414,0.30666,0.303709,0.0323359,0.0135408,0.508064,0.250964,0.383276,0.00360665,0.0344603,0.00213139,0.159791,3.52795e-06,0.191517,0.463751,0.0145214,0.0529819,0.00367772,0.283463,0.0517073,0.0272975,0.0151656,0.273281,0.368095,0.0418805,0.384593,0.47795,0.359231,0.00088965,0.197805,0.0690807,0.387069,0.332774,0.52832,0.00579439,0.0814305,0.205413,0.17639,0.00311629,0.276869,0.022685,0.0337138,0.18966,0.00358475,0.188263,0.0719199,0.0386691,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.0348699,0.378361,0.255516,0.20753,0.0224033,0.179412,0.193601,0.220904,0.222977,0.341681,0.0542164,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.0172483,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.20847,0.266544,0.000263373,0.145701,8.06964e-06,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.00753169,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.0367308,0.261744,0.203781,0.0246892,0.00176424,0.141867,0.00140109,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.036274,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.0488311,0.00499908,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.2868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}}
}}

Revision as of 14:14, 5 September 2012


Full id: C4673_retina_substantia_optic_Astrocyte_melanoma_Neural_thalamus



Phase1 CAGE Peaks

Hg19::chr7:20371077..20371122,+p6@ITGB8
Hg19::chr7:20371123..20371138,+p17@ITGB8
Hg19::chr7:20371139..20371164,+p4@ITGB8


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
regional part of nervous system2.25e-3894
nervous system2.25e-3894
central nervous system4.61e-3782
neural tube1.21e-3457
neural rod1.21e-3457
future spinal cord1.21e-3457
neural keel1.21e-3457
adult organism1.16e-29115
brain3.23e-2969
future brain3.23e-2969
regional part of forebrain3.09e-2741
forebrain3.09e-2741
future forebrain3.09e-2741
regional part of brain5.76e-2759
anterior neural tube5.48e-2642
neural plate4.22e-2586
presumptive neural plate4.22e-2586
gray matter4.39e-2434
brain grey matter4.39e-2434
telencephalon4.52e-2434
neurectoderm7.96e-2490
anterior region of body1.17e-23129
craniocervical region1.17e-23129
head1.18e-23123
regional part of telencephalon2.17e-2333
ectoderm-derived structure1.33e-22169
cerebral hemisphere1.55e-2232
ectoderm5.62e-22173
presumptive ectoderm5.62e-22173
embryo9.96e-19612
pre-chordal neural plate2.33e-1861
cerebral cortex8.42e-1825
pallium8.42e-1825
multi-cellular organism2.44e-17659
embryonic structure3.11e-16605
developing anatomical structure3.11e-16605
anatomical system4.25e-16625
germ layer6.54e-16604
embryonic tissue6.54e-16604
presumptive structure6.54e-16604
epiblast (generic)6.54e-16604
anatomical group7.00e-16626
regional part of cerebral cortex1.50e-1522
anatomical conduit2.64e-15241
neocortex2.67e-1420
organ7.68e-12511
anatomical cluster8.12e-12286
tube1.42e-11194
posterior neural tube1.13e-0915
chordal neural plate1.13e-0915
multi-tissue structure2.21e-08347
segmental subdivision of nervous system2.45e-0813
nucleus of brain9.86e-089
neural nucleus9.86e-089
segmental subdivision of hindbrain1.35e-0712
hindbrain1.35e-0712
presumptive hindbrain1.35e-0712
basal ganglion1.70e-079
nuclear complex of neuraxis1.70e-079
aggregate regional part of brain1.70e-079
collection of basal ganglia1.70e-079
cerebral subcortex1.70e-079
organism subdivision4.48e-07365


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#186934.907389214879320.008460985347239390.032764436361896
SMARCB1#6598318.25271578115740.000164397760679890.00204010666915958



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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