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Coexpression cluster:C647: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.82e-48!115;UBERON:0001049!5.43e-31!57;UBERON:0005068!5.43e-31!57;UBERON:0006241!5.43e-31!57;UBERON:0007135!5.43e-31!57;UBERON:0000073!9.36e-30!94;UBERON:0001016!9.36e-30!94;UBERON:0001017!1.02e-29!82;UBERON:0005743!5.01e-29!86;UBERON:0002616!2.37e-26!59;UBERON:0003080!1.43e-25!42;UBERON:0002780!3.30e-25!41;UBERON:0001890!3.30e-25!41;UBERON:0006240!3.30e-25!41;UBERON:0000955!3.79e-25!69;UBERON:0006238!3.79e-25!69;UBERON:0002346!2.47e-23!90;UBERON:0003075!2.04e-22!86;UBERON:0007284!2.04e-22!86;UBERON:0002020!9.64e-21!34;UBERON:0003528!9.64e-21!34;UBERON:0001893!1.19e-20!34;UBERON:0002791!4.76e-20!33;UBERON:0001869!2.10e-19!32;UBERON:0003056!3.83e-16!61;UBERON:0000924!8.21e-16!173;UBERON:0006601!8.21e-16!173;UBERON:0000956!5.10e-15!25;UBERON:0000203!5.10e-15!25;UBERON:0004121!5.61e-15!169;UBERON:0000153!2.18e-14!129;UBERON:0007811!2.18e-14!129;UBERON:0002619!3.25e-14!22;UBERON:0000033!1.25e-13!123;UBERON:0001950!5.85e-13!20;UBERON:0002308!3.21e-07!9;UBERON:0000125!3.21e-07!9;UBERON:0002420!3.23e-07!9;UBERON:0007245!3.23e-07!9;UBERON:0010009!3.23e-07!9;UBERON:0010011!3.23e-07!9;UBERON:0000454!3.23e-07!9;UBERON:0003076!8.76e-07!15;UBERON:0003057!8.76e-07!15
|ontology_enrichment_uberon=UBERON:0007023!1.82e-48!115;UBERON:0001049!5.43e-31!57;UBERON:0005068!5.43e-31!57;UBERON:0006241!5.43e-31!57;UBERON:0007135!5.43e-31!57;UBERON:0000073!9.36e-30!94;UBERON:0001016!9.36e-30!94;UBERON:0001017!1.02e-29!82;UBERON:0005743!5.01e-29!86;UBERON:0002616!2.37e-26!59;UBERON:0003080!1.43e-25!42;UBERON:0002780!3.30e-25!41;UBERON:0001890!3.30e-25!41;UBERON:0006240!3.30e-25!41;UBERON:0000955!3.79e-25!69;UBERON:0006238!3.79e-25!69;UBERON:0002346!2.47e-23!90;UBERON:0003075!2.04e-22!86;UBERON:0007284!2.04e-22!86;UBERON:0002020!9.64e-21!34;UBERON:0003528!9.64e-21!34;UBERON:0001893!1.19e-20!34;UBERON:0002791!4.76e-20!33;UBERON:0001869!2.10e-19!32;UBERON:0003056!3.83e-16!61;UBERON:0000924!8.21e-16!173;UBERON:0006601!8.21e-16!173;UBERON:0000956!5.10e-15!25;UBERON:0000203!5.10e-15!25;UBERON:0004121!5.61e-15!169;UBERON:0000153!2.18e-14!129;UBERON:0007811!2.18e-14!129;UBERON:0002619!3.25e-14!22;UBERON:0000033!1.25e-13!123;UBERON:0001950!5.85e-13!20;UBERON:0002308!3.21e-07!9;UBERON:0000125!3.21e-07!9;UBERON:0002420!3.23e-07!9;UBERON:0007245!3.23e-07!9;UBERON:0010009!3.23e-07!9;UBERON:0010011!3.23e-07!9;UBERON:0000454!3.23e-07!9;UBERON:0003076!8.76e-07!15;UBERON:0003057!8.76e-07!15
|tf_chipseq_enrich=USF2#7392;4:3.99759919540603:0.0142546073921536:0.0499945241933349
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586,0.0422281,0.472782,0.0617442,0.255074,0.643368,0.293515,0.303732,0.289321,0.534587,0.605588,0.217057,0.296563,0.221643,0.168782,0.141293,0.157864,0.0405174,0.194458,0.254145,0.195258,0.203187,0.143789,0.135616,0.285075,0.65843,0.160125,0.233943,0.0105464,0.432296,0.393162,0.396542,0.145945,0.118166,0.670558,0.491678,0.157767,0.327371,0.217504,0.146856,0.135586,0.0917421,0.0650781,0.0240028,0.174966,0.690478,0.0170111,0.290434,0.198578,0.309388,0.582826,0.527646,0.153213,0.483637,0.547598,0.481442,0.332173,0.0239787,0.769273,0.189406,0.350781,0.723904,0.460907,0.294795,0.394111,0.00328595,0.0241864,0.137392,0.016572,0.205993,0.011118,0.199435,0.241617,0.288395,0.00939975,0.490408,0.0101842,0.283944,0.410253,0.0728818,0.316875,0.286862,0.435422,0.423098,0.0148026,0.0547589,0.263208,0.226588,0.190466,0.636352,0.238251,0.203945,0.458534,0.274311,0.0992298,0.188879,0.1453,0.441018,0.565736,0.0682337,0.150612,0.632877,0.0233488,0.391404,0.260762,0.392794,0.0208503,0.0716327,0.0799552,0.288625,0.183307,0.0920381,0.270765,0.305028,0.514206,0.153367,0.460189,0.180891,0.2135,0.098091,0.344773,0.559616,0.0843341,0.295773,0.225154,0.0301456,0.00518859,0.182425,0.0361619,0.0695405,0.655985,0.371428,0.0956697,0.560898,0.539159,0.0061126,0.244574,0.234943,0.00566835,0.192118,0.0384114,0.00442784,0.0663709,0.236025,0.490999,0.507107,0.35852,0.166287,0.554684,0.606515,0.472484,0.674421,0.132676,0.0173119,0.105465,0.0561853,0.0325493,0.0964279,0.0956818,0.225753,0.20291,0.0702798,0.383325,0.0374473,0.481208,0.0770174,0.0421775,0.377651,0.405448,0.106119,0.549109,0.337559,0.733733,0.00134813,0.595828,0.307795,0.587773,0.521111,0.481364,0.20314,0.0292721,0.348615,0.573204,0.00479091,0.67974,0.0798818,0.131599,0.147225,0.899992,0.456059,0.0163203,0.462872,0.416294,0.14236,0.260314,0.661496,0.107921,0.662221,0.00433831,0.0166564,0.693124,0.0476638,0.247085,0.179064,0.13287,0.392599,0.34469,0.179116,0.823334,0.702572,0.650177,0.362384,0.554413,0.35471,0.46571,0.0450353,0.0428669,0.0681105,0.0269633,0.0159513,0.128953,0.164599,0.059697,0.0129076,0.458812,0.0301275,0.062967,0.540325,0.0560721,0.0620815,0.0821769,0.0667351,0.263011,0.515744,0.141594,0.117477,0.0345161,0.20954,0.17069,0.128271,0.235092,0.178253,0.0858418,0.167002,0.0808629,0.0514138,0.14774,0.137005,0.770902,0.0747952,0.14813,0.197414,0.626754,0.620775,0.631122,0.787478,0.0415833,0.692703,0.0410111,0.876874,0.168227,0.483258,0.0300128,0.0101239,0.805223,0.850248,0.539445,0.678851,0.42596,0.059419,0.153321,0.0838314,0.215628,0.420975,0.21575,0.783315,0.0808289,0.386144,0.814617,0.185362,0.268511,0.00929967,0.0643959,0.959405,0.553476,0.0536584,0.663109,0.20787,0.412658,0.932252,0.0676343,0.0865831,0.261712,0.00545068,0.137906,0.216273,0.546744,0.0722514,0.314286,0.00158049,0.539816,0.203717,0.0092368,0.055093,0.10694,0.0288105,0.315536,0.240276,0.0225257,0.581837,0.325248,0.0777222,0.0519337,0.334728,0.117524,0.558771,0.165441,0.0783075,0.0763765,0.335813,0.326542,0.213292,0.464871,0.179406,0.355072,0.0915719,0.132024,0.34887,0.494844,0.362772,0.292889,0.595126,0.613492,0.601978,0.506461,0.369401,0.0776096,0.13236,0.177334,0.154926,0.524614,0.647973,0.402376,0.320366,0.165069,0.0206042,0.0665702,0.304034,0.036319,0.61522,0.224349,0.0213448,0.826813,0.0481264,0.457085,0.273333,0.630785,0.568687,0.296329,0.754563,0.262678,0.138097,0.598001,0.000400086,0.0634914,0.0422827,0.0117872,0.53643,0.600958,0.537603,0.291253,0.268133,0.335704,0.352283,0.544901,0.13361,0.0582337,0.365581,0.26716,0.0467545,0.575502,0.606405,0.00507243,0.298493,0.272493,0.800547,0.288366,0.616898,0.226076,0.434669,0.073813,0.133755,0.345889,0.436693,0.576571,0.672083,0.413616,0.0582564,0.456129,0.0826205,0.708497,0.000140567,0.260709,0.269053,0.152968,0.00201804,0.149707,0.105568,0.535416,0.00599689,0.0475515,0.156425,0.256463,0.2073,0.182928,0.392982,0.62305,0.0416651,0.517856,0.425875,0.010891,0.391951,0.0297099,0.651499,0.0401993,0.659873,0.242598,0.437148,0.143495,0.0234054,0.0117163,0.00745722,0.724446,0.507366,0.653769,0.436325,0.586389,0.0609344,0.0427309,0.141965,0.731529,0.259636,0.0882769,0.0194885,0.484689,0.238279,0.711029,0.413837,0.667833,0.706001,0.561,0.0747411,0.479249,0.613776,0.696372,0.521613,0.456024,0.0418131,0.298129,0.197903,0.206748,0.35714,0.0177008,0.219355,0.173602,0.288674,0.310557,0.256206,0.0135769,0.212386,0.212993,0.508361,0.29671,0.164865,0.212856,0.235064,0.378446,0.642555,0.593838,0.684324,0.0646415,0.307463,0.360772,0.249696,0.430714,0.24874,0.380462,0.257244,0.290861,0.0228373,0.394043,0.177566,0.2594,0.334235,0.149754,0.4665,0.628727,0.00473729,0.0612029,0.0116535,0.484329,0.381419,0.366492,0.0744261,0.0271283,0.45399,0.135344,0.0545125,0.764381,0.73571,0.0243428,0.531832,0.632445,0.618193,0.182466,0.113885,0.243869,0.413389,0.0232949,0.0991821,0.411844,0.0695785,0.234272,0.174758,0.176969,0.35406,0.541376,0.667256,0.34672,0.0309068,0.304171,0.267686,0.0100433,0.322489,0.229974,0.557903,0.527439,0.398227,0.273599,0.158664,0.369652,0.664067,0.567651,0.523596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}}
}}

Revision as of 12:45, 5 September 2012


Full id: C647_pineal_cerebellum_pituitary_occipital_parietal_medial_hippocampus



Phase1 CAGE Peaks

Hg19::chr10:133879140..133879164,+p@chr10:133879140..133879164
+
Hg19::chr10:22609986..22610045,+p1@BMI1
Hg19::chr12:1192383..1192475,+p5@ERC1
Hg19::chr16:24621546..24621640,+p@chr16:24621546..24621640
+
Hg19::chr16:24661163..24661168,+p@chr16:24661163..24661168
+
Hg19::chr1:72749352..72749438,-p@chr1:72749352..72749438
-
Hg19::chr1:78444841..78444869,+p6@DNAJB4
Hg19::chr21:17443633..17443652,+p23@LINC00478
Hg19::chr2:73298446..73298468,-p5@SFXN5
Hg19::chr3:47422286..47422316,-p1@BC036224
Hg19::chr5:146762442..146762468,+p2@STK32A
Hg19::chr7:50850523..50850543,-p5@GRB10
Hg19::chrX:49012602..49012631,-p@chrX:49012602..49012631
-


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:0043522leucine zipper domain binding0.0312564375468493
GO:0030275LRR domain binding0.0312564375468493
GO:0007252I-kappaB phosphorylation0.0312564375468493
GO:0008385IkappaB kinase complex0.0338362305696425
GO:0007379segment specification0.0338362305696425
GO:0045768positive regulation of anti-apoptosis0.0338362305696425
GO:0048146positive regulation of fibroblast proliferation0.0338362305696425
GO:0048145regulation of fibroblast proliferation0.0338362305696425
GO:0048144fibroblast proliferation0.0338362305696425
GO:0045767regulation of anti-apoptosis0.0338362305696425
GO:0042734presynaptic membrane0.0338362305696425
GO:0009408response to heat0.0338362305696425



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
adult organism1.82e-48115
neural tube5.43e-3157
neural rod5.43e-3157
future spinal cord5.43e-3157
neural keel5.43e-3157
regional part of nervous system9.36e-3094
nervous system9.36e-3094
central nervous system1.02e-2982
regional part of brain2.37e-2659
anterior neural tube1.43e-2542
regional part of forebrain3.30e-2541
forebrain3.30e-2541
future forebrain3.30e-2541
brain3.79e-2569
future brain3.79e-2569
neurectoderm2.47e-2390
neural plate2.04e-2286
presumptive neural plate2.04e-2286
gray matter9.64e-2134
brain grey matter9.64e-2134
telencephalon1.19e-2034
regional part of telencephalon4.76e-2033
cerebral hemisphere2.10e-1932
pre-chordal neural plate3.83e-1661
ectoderm8.21e-16173
presumptive ectoderm8.21e-16173
cerebral cortex5.10e-1525
pallium5.10e-1525
ectoderm-derived structure5.61e-15169
anterior region of body2.18e-14129
craniocervical region2.18e-14129
regional part of cerebral cortex3.25e-1422
head1.25e-13123
neocortex5.85e-1320
nucleus of brain3.21e-079
neural nucleus3.21e-079
basal ganglion3.23e-079
nuclear complex of neuraxis3.23e-079
aggregate regional part of brain3.23e-079
collection of basal ganglia3.23e-079
cerebral subcortex3.23e-079
posterior neural tube8.76e-0715
chordal neural plate8.76e-0715


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
USF2#739243.997599195406030.01425460739215360.0499945241933349



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.