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Coexpression cluster:C990: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005743!4.33e-36!86;UBERON:0000073!4.92e-35!94;UBERON:0001016!4.92e-35!94;UBERON:0001017!5.38e-35!82;UBERON:0007023!7.56e-33!115;UBERON:0003075!1.56e-32!86;UBERON:0007284!1.56e-32!86;UBERON:0002346!1.82e-32!90;UBERON:0001049!1.29e-31!57;UBERON:0005068!1.29e-31!57;UBERON:0006241!1.29e-31!57;UBERON:0007135!1.29e-31!57;UBERON:0000924!1.06e-28!173;UBERON:0006601!1.06e-28!173;UBERON:0000955!1.99e-28!69;UBERON:0006238!1.99e-28!69;UBERON:0004121!2.38e-28!169;UBERON:0003056!2.00e-27!61;UBERON:0002616!3.24e-27!59;UBERON:0000153!2.17e-26!129;UBERON:0007811!2.17e-26!129;UBERON:0003080!1.39e-25!42;UBERON:0002780!1.52e-25!41;UBERON:0001890!1.52e-25!41;UBERON:0006240!1.52e-25!41;UBERON:0000033!9.43e-25!123;UBERON:0001893!1.50e-21!34;UBERON:0002020!1.88e-21!34;UBERON:0003528!1.88e-21!34;UBERON:0002791!7.68e-21!33;UBERON:0001869!8.90e-21!32;UBERON:0000956!8.09e-17!25;UBERON:0000203!8.09e-17!25;UBERON:0002619!4.87e-16!22;UBERON:0001950!5.21e-15!20;UBERON:0000475!6.39e-08!365;UBERON:0003076!2.69e-07!15;UBERON:0003057!2.69e-07!15;UBERON:0000468!3.62e-07!659;UBERON:0000922!6.05e-07!612;UBERON:0000064!6.10e-07!219
|ontology_enrichment_uberon=UBERON:0001049!4.19e-55!56;UBERON:0005068!4.19e-55!56;UBERON:0006241!4.19e-55!56;UBERON:0007135!4.19e-55!56;UBERON:0000073!2.00e-50!53;UBERON:0002616!2.00e-50!53;UBERON:0001017!2.87e-50!81;UBERON:0002780!1.73e-49!41;UBERON:0001890!1.73e-49!41;UBERON:0003080!1.73e-49!41;UBERON:0006240!1.73e-49!41;UBERON:0001016!5.51e-48!89;UBERON:0003075!7.75e-48!82;UBERON:0007284!7.75e-48!82;UBERON:0000955!1.38e-47!68;UBERON:0006238!1.38e-47!68;UBERON:0002346!4.05e-47!86;UBERON:0003056!1.41e-45!61;UBERON:0007023!6.01e-43!114;UBERON:0001893!9.26e-41!34;UBERON:0003528!2.89e-40!34;UBERON:0002020!2.89e-40!34;UBERON:0001950!4.25e-38!20;UBERON:0010371!4.94e-38!104;UBERON:0001869!8.49e-38!32;UBERON:0002619!1.07e-37!22;UBERON:0002791!2.27e-37!32;UBERON:0000956!1.55e-32!25;UBERON:0000203!1.55e-32!25;UBERON:0004121!1.21e-31!171;UBERON:0000924!1.21e-31!171;UBERON:0006601!1.21e-31!171;UBERON:0010314!1.75e-29!132;UBERON:0011216!2.30e-17!223;UBERON:0000200!1.85e-13!6;UBERON:0002021!1.24e-11!5;UBERON:0000477!1.24e-11!373;UBERON:0000025!1.47e-11!192;UBERON:0001872!2.04e-11!5;UBERON:0001871!8.89e-11!6;UBERON:0004111!8.95e-11!240;UBERON:0000483!3.27e-10!306;UBERON:0001894!5.82e-10!7;UBERON:0006222!5.82e-10!7;UBERON:0000119!5.85e-10!309;UBERON:0002420!1.36e-09!9;UBERON:0007245!1.36e-09!9;UBERON:0010009!1.36e-09!9;UBERON:0010011!1.36e-09!9;UBERON:0000454!1.36e-09!9;UBERON:0000125!3.13e-09!9;UBERON:0002308!3.13e-09!9;UBERON:0002784!1.09e-08!4;UBERON:0000922!1.09e-08!592;UBERON:0000481!2.11e-08!342;UBERON:0003076!3.98e-08!15;UBERON:0003057!3.98e-08!15;UBERON:0000468!4.99e-08!656;UBERON:0000064!5.42e-08!218;UBERON:0002050!9.65e-08!564;UBERON:0001870!1.64e-07!3;UBERON:0000923!1.93e-07!560;UBERON:0010316!1.93e-07!560;UBERON:0005291!1.93e-07!560;UBERON:0006598!1.93e-07!560;UBERON:0010317!1.93e-07!560;UBERON:0002532!1.93e-07!560;UBERON:0005423!2.63e-07!581;UBERON:0000062!2.71e-07!503;UBERON:0002298!3.08e-07!6;UBERON:0000349!9.97e-07!5
|tf_chipseq_enrich=ZNF263#10127;5:5.13865102313167:0.00108253124903356:0.00764063533944823
|tf_chipseq_enrich=ZNF263#10127;5:5.13865102313167:0.00108253124903356:0.00764063533944823
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89558,0.375413,0.435903,0.139793,0.19465,0.142897,0.10753,0.0894806,0.100334,0.185405,0.0895574,0.450361,0.125132,0.401145,0.127941,0.0857811,0.316921,0.48369,0.101821,0.151258,0.765247,0.294186,0.0385906,0.267153,0.0486002,0.0744668,0.626906,0.340579,0.10027,0.216542,0.140095,0.339551,0.541739,0.479289,0.429978,0.312506,0.737097,0.514064,0.228257,0.190339,0.39643,0.203718,0.416086,0.0972082,0.346997,0.33418,0.386217,0.332439,0.219989,0.627646,0.228423,0.121222,0.233436,0.792498,0.316293,0.0200406,0.265337,0.307168,0.313275,0.815358,0.795728,0.132332,0.243599,0.127929,0.1565,0.188908,0.230656,0.00874691,0.0881682,0.18579,0.214833,0.972382,0.000734514,0.139727,0.597758,0.28717,0.434522,0.0971332,0.879571,0.146252,0.12193,0.384175,0.154198,0.0944863,0.614575,0.0170855,0.491271,0.600481,0.0043775,0.300879,0.0942623,0.064638,0.93441,0.460251,0.48128,0.00378916,0.169668,0.264355,0.126386,0.235621,0.45894,0.0191203,0.117159,0.0395039,0.1766,0.495277,0.0738066,0.0973803,0.315733,0.115553,0.13739,0.276387,0.229078,0.0916273,0.255961,0.144828,0.0111046,0.509288,0.190011,0.0631125,0.0728245,0.439115,0.481419,0.000221206,0.000787213,0.397384,0.305299,0.0721342,0.158525,0.43239,0.348785,0.120717,0.36346,0.180408,0.226687,0.152678,0.340038,0.35297,0.239072,0.361869,0.39215,0.0206227,0.0598402,0.152528,0.538083,0.595929,0.28677,0.208355,0.0943487,0.273994,0.272914,0.106007,0.00191142,0.233355,0.197579,0.534095,0.332254,0.24444,0.189162,0.253118,0.273827,0.0667061,0.387479,0.223866,0.0895238,0.385626,0.427353,0.202588,0.420356,0.07633,0.263009,0.29963,0.149927,0.176074,0.097558,0.481345,0.156045,0.406358,0.924193,0.0933565,0.413996,0.0549043,0.111737,0.317827,0.058823,0.34783,0.471691,0.752206,0.504402,0.349984,0.45682,0.127603,0.186488,0.21365,0.443827,0.154289,0.119679,0.750697,0.0410648,0.408236,0.760703,0.0189799,0.0236074,0.147454,0.832307,0.552306,0.206715,0.138114,0.11122,0.0520571,0.151285,0.309631,0.117701,0.728237,0.225029,0.846474,0.361393,0.676036,0.597402,0.380163,0.493115,0.595604,0.664388,0.0318567,0.0981855,0.502142,0.549112,0.210866,0.524662,0.0514771,0.148073,0.282108,0.0906584,0.375011,0.314583,0.299144,0.545241,0.0696488,0.712705,0.121362,0.516094,0.387693,0.305935,0.753324,0.454729,0.44937,0.126438,0.0718717,0.187826,0.0631773,0.317577,0.369258,0.364029,0.0632446,0.170336,0.236293,0.0815395,0.689159,0.379433,0.155452,0.289349,0.590067,0.889628,0.0815334,0.413633,0.221848,0.0534081,0.723803,0.753368,0.306531,0.0213495,0.31842,0.66902,0.715376,0.729164,0.0501415,0.433594,0.0052382,0.488054,0.0157692,0.000719674,0.809211,0.0681697,0.00956399,0.457276,0.799317,0.328805,0.349364,0.385504,0.117909,0.207197,0.0829992,0.521252,0.0943672,0.000879905,0.130904,0.138834,0.408815,0.342088,0.604827,0.733391,0.00783545,0.512211,0.124111,0.573299,0.133035,0.467867,0.684354,0.576345,0.752343,0.622298,0.520881,0.0371672,0.0760525,0.619131,0.839028,0.728293,0.563902,0.180674,0.140337,0.00663828,0.846436,0.484879,0.124815,2.0257e-07,0.0199737,0.810194,0.233058,0.076519,0.227503,0.00222274,0.380263,0.509178,0.0127429,0.573115,0.0358923,0.212149,0.37126,0.251595,0.694833,0.303513,0.44442,0.242122,0.375068,0.00502065,0.0530037,0.246113,0.502199,0.45836,0.00198243,0.194485,0.578712,0.458152,0.0873966,0.42925,0.55014,0.0190106,0.180477,0.198633,0.376936,0.431837,0.377907,0.142234,0.463074,0.222529,0.234528,0.00156273,0.182225,0.718529,0.544718,0.462199,0.794152,0.409798,0.436622,0.486064,0.489702,0.672033,0.629206,0.140585,0.445913,0.0185884,0.296003,0.447485,0.0845698,0.229886,0.0494598,0.410714,0.49649,0.581581,0.212206,0.31257,0.463718,0.0416546,0.145642,0.000931797,0.129677,0.56248,0.041492,0.342908,0.500922,0.376098,0.500105,0.389123,0.0993883,0.1667,0.133211,0.116907,0.565967,0.122032,0.683557,0.361689,0.289284,0.241971,0.0383137,0.151053,0.477267,0.368791,0.485034,0.43963,0.297904,0.551399,0.625257,0.412086,0.371597,0.0464517,0.353179,0.00451284,0.297272,0.0178829,0.42109,0.18144,0.54956,0.194533,0.455388,0.473509,0.0251749,0.335015,0.0204322,0.53418,0.28015,0.492484,0.529209,0.397471,0.120747,0.330704,0.443138,0.519779,0.0765161,0.312488,0.547073,0.48939,0.0913415,0.404755,0.238065,0.0233313,0.260955,0.585012,0.14076,0.204547,0.452254,0.259924,0.136638,0.137048,0.353983,0.194753,0.104944,0.136955,0.0207614,0.554772,0.0265104,0.425619,0.50814,0.109065,0.202353,0.240717,0.162041,0.0478574,0.161384,0.255196,0.167238,0.190639,0.0530548,0.265287,0.113346,0.168727,0.221472,0.095012,0.0580072,0.456504,0.0152622,0.0135037,0.679098,0.334729,0.557075,0.545435,0.448658,0.151747,0.243993,0.183915,0.0968284,0.589165,0.559083,0.055434,0.373141,0.459861,0.447066,0.228122,0.162595,0.649607,0.0434152,0.140634,0.0312514,0.0430331,0.021033,0.110579,0.586217,0.223113,0.179394,0.381036,0.491941,0.230489,0.285747,0.149677,0.462673,0.23568,0.213047,0.638022,0.394858,0.00130817,0.207064,0.178571,0.568909,0.0334453,0.48895,0.015631,0.366377,0.476867,0.540268,0.459344,0.119665
}}
}}

Revision as of 16:57, 19 October 2012


Full id: C990_pineal_occipital_merkel_Lens_medial_parietal_middle



Phase1 CAGE Peaks

Hg19::chr11:124589340..124589351,+p@chr11:124589340..124589351
+
Hg19::chr12:57735480..57735493,-p9@R3HDM2
Hg19::chr9:77112225..77112238,+p2@RORB
Hg19::chr9:77112244..77112262,+p1@RORB
Hg19::chr9:77114317..77114328,-p3@ENST00000417576
Hg19::chr9:77114341..77114368,-p1@ENST00000417576
Hg19::chr9:77114385..77114400,-p2@ENST00000417576
Hg19::chr9:77302053..77302065,+p@chr9:77302053..77302065
+


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


GO IDGO nameFDR corrected p-value
GO:0042462eye photoreceptor cell development0.00918254698947879
GO:0001754eye photoreceptor cell differentiation0.00918254698947879
GO:0042461photoreceptor cell development0.00918254698947879
GO:0043193positive regulation of gene-specific transcription0.00918254698947879
GO:0046530photoreceptor cell differentiation0.00918254698947879
GO:0032583regulation of gene-specific transcription0.00918254698947879
GO:0048592eye morphogenesis0.0170497870118158
GO:0001654eye development0.0269598341411594
GO:0007423sensory organ development0.0438243772124945



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
neural tube4.19e-5556
neural rod4.19e-5556
future spinal cord4.19e-5556
neural keel4.19e-5556
regional part of nervous system2.00e-5053
regional part of brain2.00e-5053
central nervous system2.87e-5081
regional part of forebrain1.73e-4941
forebrain1.73e-4941
anterior neural tube1.73e-4941
future forebrain1.73e-4941
nervous system5.51e-4889
neural plate7.75e-4882
presumptive neural plate7.75e-4882
brain1.38e-4768
future brain1.38e-4768
neurectoderm4.05e-4786
pre-chordal neural plate1.41e-4561
adult organism6.01e-43114
telencephalon9.26e-4134
brain grey matter2.89e-4034
gray matter2.89e-4034
neocortex4.25e-3820
ecto-epithelium4.94e-38104
cerebral hemisphere8.49e-3832
regional part of cerebral cortex1.07e-3722
regional part of telencephalon2.27e-3732
cerebral cortex1.55e-3225
pallium1.55e-3225
ectoderm-derived structure1.21e-31171
ectoderm1.21e-31171
presumptive ectoderm1.21e-31171
structure with developmental contribution from neural crest1.75e-29132
organ system subdivision2.30e-17223
gyrus1.85e-136
occipital lobe1.24e-115
anatomical cluster1.24e-11373
tube1.47e-11192
parietal lobe2.04e-115
temporal lobe8.89e-116
anatomical conduit8.95e-11240
epithelium3.27e-10306
diencephalon5.82e-107
future diencephalon5.82e-107
cell layer5.85e-10309
basal ganglion1.36e-099
nuclear complex of neuraxis1.36e-099
aggregate regional part of brain1.36e-099
collection of basal ganglia1.36e-099
cerebral subcortex1.36e-099
neural nucleus3.13e-099
nucleus of brain3.13e-099
regional part of diencephalon1.09e-084
embryo1.09e-08592
multi-tissue structure2.11e-08342
posterior neural tube3.98e-0815
chordal neural plate3.98e-0815
multi-cellular organism4.99e-08656
organ part5.42e-08218
embryonic structure9.65e-08564
frontal cortex1.64e-073
germ layer1.93e-07560
germ layer / neural crest1.93e-07560
embryonic tissue1.93e-07560
presumptive structure1.93e-07560
germ layer / neural crest derived structure1.93e-07560
epiblast (generic)1.93e-07560
developing anatomical structure2.63e-07581
organ2.71e-07503
brainstem3.08e-076
limbic system9.97e-075


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
ZNF263#1012755.138651023131670.001082531249033560.00764063533944823



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.