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Coexpression cluster:C472: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!2.42e-28!82;UBERON:0000073!1.40e-27!94;UBERON:0001016!1.40e-27!94;UBERON:0001049!1.70e-27!57;UBERON:0005068!1.70e-27!57;UBERON:0006241!1.70e-27!57;UBERON:0007135!1.70e-27!57;UBERON:0005743!1.22e-26!86;UBERON:0002780!8.06e-25!41;UBERON:0001890!8.06e-25!41;UBERON:0006240!8.06e-25!41;UBERON:0000955!1.01e-23!69;UBERON:0006238!1.01e-23!69;UBERON:0003080!1.15e-23!42;UBERON:0002616!1.57e-23!59;UBERON:0007023!1.15e-21!115;UBERON:0001893!5.87e-21!34;UBERON:0002020!6.41e-21!34;UBERON:0003528!6.41e-21!34;UBERON:0002346!1.09e-20!90;UBERON:0002791!3.31e-20!33;UBERON:0001869!6.58e-20!32;UBERON:0003075!4.05e-19!86;UBERON:0007284!4.05e-19!86;UBERON:0003056!1.77e-16!61;UBERON:0002619!3.86e-16!22;UBERON:0000956!3.96e-15!25;UBERON:0000203!3.96e-15!25;UBERON:0001950!1.23e-14!20;UBERON:0000924!2.12e-12!173;UBERON:0006601!2.12e-12!173;UBERON:0000153!1.99e-11!129;UBERON:0007811!1.99e-11!129;UBERON:0004121!2.83e-11!169;UBERON:0000033!3.38e-10!123;UBERON:0002420!1.32e-07!9;UBERON:0007245!1.32e-07!9;UBERON:0010009!1.32e-07!9;UBERON:0010011!1.32e-07!9;UBERON:0000454!1.32e-07!9;UBERON:0002308!2.74e-07!9;UBERON:0000125!2.74e-07!9
|ontology_enrichment_uberon=UBERON:0001017!2.42e-28!82;UBERON:0000073!1.40e-27!94;UBERON:0001016!1.40e-27!94;UBERON:0001049!1.70e-27!57;UBERON:0005068!1.70e-27!57;UBERON:0006241!1.70e-27!57;UBERON:0007135!1.70e-27!57;UBERON:0005743!1.22e-26!86;UBERON:0002780!8.06e-25!41;UBERON:0001890!8.06e-25!41;UBERON:0006240!8.06e-25!41;UBERON:0000955!1.01e-23!69;UBERON:0006238!1.01e-23!69;UBERON:0003080!1.15e-23!42;UBERON:0002616!1.57e-23!59;UBERON:0007023!1.15e-21!115;UBERON:0001893!5.87e-21!34;UBERON:0002020!6.41e-21!34;UBERON:0003528!6.41e-21!34;UBERON:0002346!1.09e-20!90;UBERON:0002791!3.31e-20!33;UBERON:0001869!6.58e-20!32;UBERON:0003075!4.05e-19!86;UBERON:0007284!4.05e-19!86;UBERON:0003056!1.77e-16!61;UBERON:0002619!3.86e-16!22;UBERON:0000956!3.96e-15!25;UBERON:0000203!3.96e-15!25;UBERON:0001950!1.23e-14!20;UBERON:0000924!2.12e-12!173;UBERON:0006601!2.12e-12!173;UBERON:0000153!1.99e-11!129;UBERON:0007811!1.99e-11!129;UBERON:0004121!2.83e-11!169;UBERON:0000033!3.38e-10!123;UBERON:0002420!1.32e-07!9;UBERON:0007245!1.32e-07!9;UBERON:0010009!1.32e-07!9;UBERON:0010011!1.32e-07!9;UBERON:0000454!1.32e-07!9;UBERON:0002308!2.74e-07!9;UBERON:0000125!2.74e-07!9
|tfbs_overrepresentation=0.023025,0.331733,0.335859,0.278153,0.43736,0.660465,0.254025,0.691783,0.19891,0.159377,0.632492,0.507512,0.752092,0.592479,0.0942279,0.34688,0.269061,0.152023,0.303714,0.533434,0.164953,0.245191,0.434598,0.485582,0.246535,0.221301,0.791196,0.469547,0.0867736,0.479763,0.451842,0.193823,0.114237,0.0729541,0.0780189,0.118085,0.786664,0.253822,0.211057,0.368856,0.491545,0.153064,0.634243,0.392802,0.576487,0.218154,0.227704,0.046699,0.544567,0.0116337,0.30663,0.0540392,0.384296,0.478328,0.771797,0.22984,0.531331,0.473253,0.419427,0.524699,0.18057,0.0953692,0.53533,0.409379,0.312089,0.292053,0.552946,0.33805,0.451202,0.124565,0.61492,0.0804197,0.462958,0.571536,0.0487968,0.108728,0.147672,0.257589,0.223589,0.0473677,0.145482,0.820171,0.251385,0.556604,0.402831,0.305522,0.358125,0.790561,0.435149,0.350799,0.449938,0.287563,0.14486,0.276425,0.44846,0.196487,0.695965,0.6711,0.477371,0.360051,0.326114,0.365232,0.271608,0.0268517,0.807685,0.243156,0.370137,0.518761,0.0214239,0.348185,0.739244,0.205935,0.293622,0.112155,0.50907,0.204593,0.12802,0.322144,0.631348,0.0215411,0.343085,0.478722,0.634483,0.450042,0.513233,0.726908,0.133144,0.0945827,0.117819,0.619518,0.336022,0.404618,0.324829,0.14244,0.226146,0.533585,0.360515,0.3158,0.200674,0.0260747,0.142381,0.597514,0.19629,0.677182,0.721782,0.380542,0.153614,0.443775,0.00254063,0.0562042,0.439834,0.644436,0.14957,0.164404,0.0349538,0.565554,0.404295,0.250308,0.298044,0.204443,0.248784,0.487038,0.0513582,0.288554,0.881153,0.554721,0.238428,0.596783,0.240129,0.241141,0.147629,0.627634,0.596604,0.0539596,0.107441,0.467044,0.63508,0.151678,0.37686,0.0249403,0.320391,0.216921,0.16911,0.559029,0.39984,0.0538785,0.389977,0.239186,0.438254,0.362821,0.530244,0.051782,0.582927,0.0317036,0.549288,0.274901,0.419128,0.33935,0.373106,0.53904,0.464002,0.339875,0.188427,0.340837,0.25616,0.594552,0.628254,0.666457,0.785688,0.376601,0.268759,0.520377,0.577248,0.550063,0.10865,0.128108,0.697535,0.508055,0.351944,0.515476,0.271768,0.600181,0.312363,0.114181,0.400424,0.0135824,0.262988,0.450805,0.340133,0.33752,0.491906,0.406052,0.24794,0.411739,0.489443,0.479092,0.275683,0.603448,0.695841,0.800539,0.0475209,0.545092,0.498702,0.114816,0.56138,0.257258,0.0199655,0.187347,0.955398,0.563838,0.68489,0.744652,0.159266,0.497328,0.497555,0.686441,0.530583,0.0660363,0.0844435,0.832149,0.346979,0.139057,0.118181,0.599018,0.208759,0.430855,0.431251,0.136553,0.567285,0.407538,0.370518,0.353312,0.583181,0.20655,0.123156,0.0281929,0.0678434,0.836035,0.452982,0.439987,0.510104,0.0547964,0.606343,0.76595,0.140688,0.0737252,0.867526,0.5549,0.205166,0.235256,0.659,0.133666,0.124401,0.132008,0.252696,0.453911,0.624477,0.201369,0.456872,0.251268,0.523436,0.0882309,0.162222,0.353753,0.0468735,0.501122,0.540124,0.28123,0.0847283,0.508511,0.610396,0.126593,0.0952039,0.385751,0.867002,0.199824,0.480882,0.81693,0.580209,0.635755,0.220207,0.932742,0.0447871,0.814818,0.190532,0.419745,0.383882,0.11148,0.127709,0.403786,0.0489338,0.677236,0.483725,0.0305136,0.929123,0.193415,0.0399984,0.35292,0.292373,0.388089,0.0394199,0.264682,0.69731,0.170351,0.108499,0.397485,0.0681367,0.579167,0.352277,0.482225,0.684275,0.525248,0.370377,0.297833,0.37853,0.139785,0.117954,0.370414,0.0920342,0.395012,0.721972,0.619684,0.363619,0.688245,0.214395,0.432474,0.0930771,0.559043,0.228243,0.242625,0.535824,0.0386654,0.0956996,0.82339,0.271199,0.382942,0.842574,0.411247,0.065427,0.434397,0.663527,0.0521194,0.643753,0.886044,0.657737,0.0846504,0.514777,0.757261,0.769591,0.106346,0.0584193,0.495017,0.447633,0.300979,0.117611,0.974837,0.290507,0.647558,0.282098,0.629716,0.385457,0.362026,0.0247231,0.306479,0.302626,0.272351,0.0772057,0.86473,0.619095,0.499393,0.0426041,0.40875,0.187114,0.309827,0.440852,0.100063,0.27446,0.190275,0.126505,0.386127,0.148379,0.796261,0.245446,0.861123,0.155595,0.187051,0.0617933,0.587979,0.455366,0.233224,0.274555,0.533024,0.618067,0.146578,0.0939693,0.00751801,0.271277,0.054235,0.866669,0.322621,0.111487,0.815915,0.259213,0.753604,0.46336,0.335949,0.232412,0.637375,0.776346,0.4135,0.163491,0.0707822,0.671026,0.248501,0.494323,0.920637,0.382542,0.317477,0.759679,0.418059,0.326504,0.646217,0.502224,0.448234,0.351611,0.744735,0.758153,0.546778,0.663824,0.256782,0.223302,0.594032,0.619281,0.529349,0.627664,0.351009,0.620478,0.113509,0.434324,0.642526,0.640499,0.271901,0.710329,0.19528,0.521098,0.466555,0.123412,0.323237,0.530123,0.258466,0.025653,0.220024,0.602257,0.792909,0.42023,0.774778,0.289501,0.43836,0.368815,0.0472749,0.544548,0.491428,0.285437,0.178951,0.244128,0.406117,0.280495,0.187992,0.674067,0.597981,0.369213,0.394134,0.35036,0.457458,0.14448,0.0726865,0.499649,0.175053,0.170162,0.0316538,0.363243,0.637294,0.470194,0.18416,0.609493,0.26187,0.301312,0.206848,0.101302,0.425556,0.495066,0.687621,0.584798,0.46926,0.318066,0.381127,0.863187,0.626498,0.0933967,0.364302,0.47061,0.00718809,0.0190767,0.408703,0.115492,0.418932,0.31371,0.417948,0.319884,0.247538,0.208915,0.232279,0.58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}}
}}

Revision as of 20:17, 8 August 2012


Full id: C472_amygdala_medial_hippocampus_insula_frontal_temporal_paracentral



Phase1 CAGE Peaks

Hg19::chr10:103946143..103946171,+p@chr10:103946143..103946171
+
Hg19::chr10:117026289..117026299,+p@chr10:117026289..117026299
+
Hg19::chr11:64059464..64059475,+p5@KCNK4
Hg19::chr11:99941186..99941205,+p5@CNTN5
Hg19::chr14:76241802..76241811,+p@chr14:76241802..76241811
+
Hg19::chr17:74864215..74864221,+p9@MGAT5B
Hg19::chr19:54409564..54409575,+p@chr19:54409564..54409575
+
Hg19::chr19:55690675..55690695,-p5@SYT5
Hg19::chr19:7982540..7982547,+p@chr19:7982540..7982547
+
Hg19::chr20:54579338..54579354,-p3@CBLN4
Hg19::chr21:22881212..22881223,+p@chr21:22881212..22881223
+
Hg19::chr2:242815160..242815176,+p@chr2:242815160..242815176
+
Hg19::chr2:80816155..80816168,+p9@CTNNA2
Hg19::chr5:146257643..146257659,-p19@PPP2R2B
Hg19::chr5:72509751..72509785,+p1@ENST00000513379
p1@ENST00000515556
Hg19::chr6:130742231..130742252,+p15@TMEM200A
Hg19::chr7:130151475..130151483,+p@chr7:130151475..130151483
+
Hg19::chr8:117658838..117658848,-p@chr8:117658838..117658848
-
Hg19::chr9:88058857..88058883,-p@chr9:88058857..88058883
-
Hg19::chrX:12083655..12083665,+p@chrX:12083655..12083665
+


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:0030054cell junction0.00734677943850633
GO:0030144alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase activity0.022457689244041
GO:0055038recycling endosome membrane0.0448995149596783
GO:0055037recycling endosome0.0458063293216049
GO:0045296cadherin binding0.0458063293216049
GO:0050839cell adhesion molecule binding0.0458063293216049
GO:0016020membrane0.0458063293216049



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
central nervous system2.42e-2882
regional part of nervous system1.40e-2794
nervous system1.40e-2794
neural tube1.70e-2757
neural rod1.70e-2757
future spinal cord1.70e-2757
neural keel1.70e-2757
regional part of forebrain8.06e-2541
forebrain8.06e-2541
future forebrain8.06e-2541
brain1.01e-2369
future brain1.01e-2369
anterior neural tube1.15e-2342
regional part of brain1.57e-2359
adult organism1.15e-21115
telencephalon5.87e-2134
gray matter6.41e-2134
brain grey matter6.41e-2134
neurectoderm1.09e-2090
regional part of telencephalon3.31e-2033
cerebral hemisphere6.58e-2032
neural plate4.05e-1986
presumptive neural plate4.05e-1986
pre-chordal neural plate1.77e-1661
regional part of cerebral cortex3.86e-1622
cerebral cortex3.96e-1525
pallium3.96e-1525
neocortex1.23e-1420
ectoderm2.12e-12173
presumptive ectoderm2.12e-12173
anterior region of body1.99e-11129
craniocervical region1.99e-11129
ectoderm-derived structure2.83e-11169
head3.38e-10123
basal ganglion1.32e-079
nuclear complex of neuraxis1.32e-079
aggregate regional part of brain1.32e-079
collection of basal ganglia1.32e-079
cerebral subcortex1.32e-079
nucleus of brain2.74e-079
neural nucleus2.74e-079


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)

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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


No analysis results for this cluster

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.