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Coexpression cluster:C3268: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!3.64e-35!115;UBERON:0005743!4.91e-32!86;UBERON:0001017!7.61e-32!82;UBERON:0000073!1.15e-30!94;UBERON:0001016!1.15e-30!94;UBERON:0001049!8.71e-30!57;UBERON:0005068!8.71e-30!57;UBERON:0006241!8.71e-30!57;UBERON:0007135!8.71e-30!57;UBERON:0002616!5.43e-28!59;UBERON:0000955!5.21e-27!69;UBERON:0006238!5.21e-27!69;UBERON:0002346!4.92e-24!90;UBERON:0003080!5.03e-24!42;UBERON:0003075!8.33e-24!86;UBERON:0007284!8.33e-24!86;UBERON:0002780!2.27e-23!41;UBERON:0001890!2.27e-23!41;UBERON:0006240!2.27e-23!41;UBERON:0002020!3.89e-20!34;UBERON:0003528!3.89e-20!34;UBERON:0001893!6.23e-20!34;UBERON:0003056!7.34e-20!61;UBERON:0000033!1.04e-19!123;UBERON:0000153!1.56e-19!129;UBERON:0007811!1.56e-19!129;UBERON:0002791!2.10e-19!33;UBERON:0000924!3.58e-19!173;UBERON:0006601!3.58e-19!173;UBERON:0001869!5.36e-19!32;UBERON:0004121!9.91e-19!169;UBERON:0000956!1.52e-15!25;UBERON:0000203!1.52e-15!25;UBERON:0002619!7.57e-14!22;UBERON:0001950!1.51e-12!20;UBERON:0000922!8.33e-12!612;UBERON:0000481!1.13e-11!347;UBERON:0000477!1.44e-11!286;UBERON:0002050!2.71e-10!605;UBERON:0005423!2.71e-10!605;UBERON:0000923!6.18e-10!604;UBERON:0005291!6.18e-10!604;UBERON:0006598!6.18e-10!604;UBERON:0002532!6.18e-10!604;UBERON:0004111!3.67e-09!241;UBERON:0000468!2.31e-08!659;UBERON:0000483!3.22e-08!309;UBERON:0000119!6.12e-08!312;UBERON:0000025!9.27e-08!194;UBERON:0000475!1.63e-07!365;UBERON:0003076!4.99e-07!15;UBERON:0003057!4.99e-07!15;UBERON:0000062!6.68e-07!511
|ontology_enrichment_uberon=UBERON:0001017!2.88e-36!81;UBERON:0007023!2.05e-35!114;UBERON:0001049!9.28e-35!56;UBERON:0005068!9.28e-35!56;UBERON:0006241!9.28e-35!56;UBERON:0007135!9.28e-35!56;UBERON:0001016!2.67e-34!89;UBERON:0000073!2.35e-32!53;UBERON:0002616!2.35e-32!53;UBERON:0000955!3.05e-31!68;UBERON:0006238!3.05e-31!68;UBERON:0003075!1.30e-28!82;UBERON:0007284!1.30e-28!82;UBERON:0002346!6.54e-28!86;UBERON:0002780!6.74e-27!41;UBERON:0001890!6.74e-27!41;UBERON:0003080!6.74e-27!41;UBERON:0006240!6.74e-27!41;UBERON:0003528!7.71e-25!34;UBERON:0002020!7.71e-25!34;UBERON:0001893!3.93e-24!34;UBERON:0011216!2.61e-23!223;UBERON:0002791!3.50e-23!32;UBERON:0001869!5.92e-23!32;UBERON:0003056!1.62e-21!61;UBERON:0004121!6.90e-21!171;UBERON:0000924!6.90e-21!171;UBERON:0006601!6.90e-21!171;UBERON:0010371!4.69e-20!104;UBERON:0000956!1.04e-18!25;UBERON:0000203!1.04e-18!25;UBERON:0010314!1.21e-17!132;UBERON:0002619!1.16e-16!22;UBERON:0000477!2.00e-16!373;UBERON:0001950!4.85e-15!20;UBERON:0000481!2.19e-11!342;UBERON:0000922!3.79e-10!592;UBERON:0000923!1.07e-09!560;UBERON:0010316!1.07e-09!560;UBERON:0005291!1.07e-09!560;UBERON:0006598!1.07e-09!560;UBERON:0010317!1.07e-09!560;UBERON:0002532!1.07e-09!560;UBERON:0002050!1.14e-09!564;UBERON:0003076!5.99e-09!15;UBERON:0003057!5.99e-09!15;UBERON:0005423!6.42e-09!581;UBERON:0004111!7.49e-09!240;UBERON:0000483!5.04e-08!306;UBERON:0000025!1.20e-07!192;UBERON:0000119!1.28e-07!309;UBERON:0000125!1.45e-07!9;UBERON:0002308!1.45e-07!9;UBERON:0000468!1.59e-07!656;UBERON:0002420!4.68e-07!9;UBERON:0007245!4.68e-07!9;UBERON:0010009!4.68e-07!9;UBERON:0010011!4.68e-07!9;UBERON:0000454!4.68e-07!9;UBERON:0004733!9.35e-07!12;UBERON:0002028!9.35e-07!12;UBERON:0007277!9.35e-07!12
|tf_chipseq_enrich=CTBP2#1488;2:41.8113335595521:0.000754340825991485:0.00593331838573013!SUZ12#23512;2:33.4105206073753:0.0011782676453603:0.00799591258049278
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0952322,0.0112557,0.222432,0.107043,0.0043762,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.0135691,0.123526,0.0906475,0.0558058,0.28262,0.000112257,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.000803238,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.00340073,0.170307,0.201033,0.0488949,0.174921,0.00132287,0.0330727,0.348757,0.219556,0.0394698,0.0596469,0.0178982,0.122476,0.108872,0.11002,0.26144,0.0286025,0.001389,0.0109933,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.019326,0.131088,0.0144628,0.0027004,0.286988,0.0761239,0.000982125,0.0818785,0.182701,0.000835367,0.011488,0.000527702,0.167267,0.140622,0.0889592,0.0538132,0.28711,0.0473033,0.094881,0.118532,0.00924871,0.0774373,0.109194,0.128564,0.131452,2.96714e-05,0.448776,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.047822,1.60279e-05,0.000123443,2.91589e-05,0.119215,0.192475,0.177967,0.547859,0.057571,0.047591,0.392974,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.291114,0.0355833,0.125606,1.64175e-09,0.00352878,0.00217769,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,1.57209e-05,0.0539144,0.000271748,0.0929549,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.0457643,0.152372,0.194941,0.218271,0.101607,2.14872e-07,0.172982,0.340936,0.151597,0.0626744,0.0195983,0.148574,0.000797393,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.0119616,0.0973823,0.15503,1.61793e-06,0.193653,0.00987736,3.35636e-07,0.251466,0.0050797,0.11903,0.0838874,0.331451,0.113145,0.000260208,0.186638,0.174776,0.0948451,0.264079,0.0339656,0.140533,0.0997756,0.257598,0.103667,0.00664782,0.025556,0.16791,0.09066,0.0597157,0.166967,0.188651,0.00340589,0.00122372,0.000720136,0.311847,0.0062542,0.0590944,0.0334734,0.178389,0.218229,0.231073,0.0020598,0.00318326,0.0360851,0.412187,1.45218e-05,0.0434602,0.133616,0.418146,0.36927,0.00328135,0.407369,0.00249898,0.000168888,0.43956,0.37006,0.42622,0.448797,0.197484,0.00182638,0.36145,0.406019,0.0129,0.580441,0.276075,0.11074,0.000369536,0.390366,0.48809,0.153829,0.0217093,0.522904,0.0608227,0.00516504,0.00235168,0.166658,6.55614e-05,0.0135352,0.284625,0.156746,0.0091887,0.000415039,0.28907,0.164197,0.462688,0.287881,0.0556235,0.478174,0.336276,0.468444,0.258219,0.119142,0.243383,0.0186777,0.390974,7.41696e-05,0.00120937,0.161598,0.013901,0.021206,0.150692,0.21803,0.37357,0.0203982,0.477353,0.199161,0.0132585,3.61308e-06,0.20342,0.200493,0.20558,0.300504,0.0361545,0.425963,0.349197,0.383291,0.156104,0.141318,0.00217346,0.0961477,0.314438,0.0101316,0.163828,0.230581,0.120226,0.28424,0.20075,0.00677385,0.181415,0.282286,0.0674279,0.24884,0.408413,0.165147,0.322213,0.656109,4.95344e-06,0.0700181,0.387276,0.522605,0.802166,0.537348,0.0267088,0.416621,0.416292,0.462712,7.37404e-05,0.215157,0.204817,0.452428,0.138871,2.27405e-05,0.166905,0.19783,0.0833851,0.00691922,0.00457272,0.175199,0.332919,0.0805711,0.0393909,0.0980968,0.0111982,0.534741,0.39088,0.363192,0.000176604,0.0222706,0.0413386,0.0123025,0.4466,0.351067,0.275347,0.00388821,0.000553931,0.241132,0.371414,0.30666,0.303709,0.495883,0.386538,0.508064,0.250964,0.383276,0.457886,0.504711,0.220231,0.0355483,0.00149391,0.191517,0.000467747,0.0663581,0.307334,0.459728,0.0048173,0.563586,0.472935,0.0932845,0.00427533,0.000116083,0.0418805,0.000150309,0.00444763,0.359231,0.0656472,0.197805,0.00278185,0.387069,0.0627969,0.52832,0.299887,0.0193657,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.255516,0.20753,0.447185,0.179412,0.193601,0.220904,0.222977,0.341681,0.00651011,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.00455899,0.00376943,0.131118,0.00178627,0.247588,0.00219731,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,9.99207e-07,0.201602,0.00972162,0.154941,0.000318033,0.0986735,0.108462,0.0595618,5.79916e-06,0.158479,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.0254879,0.123917,0.0181384,0.0183464,0.0723291,0.258496,0.00371613,0.203781,0.21382,0.207559,0.010576,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.00282612,0.0129343,0.13108,0.256963,0.222798,0.0157468,0.176789,0.0969345,0.202137,0.310405,0.00467879,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.000648679,0.078016,0.0407233,0.0537355,0.0577193,0.000277451,0.00186843,0.187731,0.0297055,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.00168003,0.295769,0.286691,0.0687209,0.141729,0.0037817,0.255956,0.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}}
}}

Revision as of 14:56, 19 October 2012


Full id: C3268_parietal_temporal_pineal_occipital_gastrointestinal_mature_extraskeletal



Phase1 CAGE Peaks

Hg19::chr12:24715342..24715354,-p4@SOX5
Hg19::chr12:24715376..24715432,-p1@SOX5
Hg19::chr12:24715495..24715532,-p2@ENST00000540811


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
central nervous system2.88e-3681
adult organism2.05e-35114
neural tube9.28e-3556
neural rod9.28e-3556
future spinal cord9.28e-3556
neural keel9.28e-3556
nervous system2.67e-3489
regional part of nervous system2.35e-3253
regional part of brain2.35e-3253
brain3.05e-3168
future brain3.05e-3168
neural plate1.30e-2882
presumptive neural plate1.30e-2882
neurectoderm6.54e-2886
regional part of forebrain6.74e-2741
forebrain6.74e-2741
anterior neural tube6.74e-2741
future forebrain6.74e-2741
brain grey matter7.71e-2534
gray matter7.71e-2534
telencephalon3.93e-2434
organ system subdivision2.61e-23223
regional part of telencephalon3.50e-2332
cerebral hemisphere5.92e-2332
pre-chordal neural plate1.62e-2161
ectoderm-derived structure6.90e-21171
ectoderm6.90e-21171
presumptive ectoderm6.90e-21171
ecto-epithelium4.69e-20104
cerebral cortex1.04e-1825
pallium1.04e-1825
structure with developmental contribution from neural crest1.21e-17132
regional part of cerebral cortex1.16e-1622
anatomical cluster2.00e-16373
neocortex4.85e-1520
multi-tissue structure2.19e-11342
embryo3.79e-10592
germ layer1.07e-09560
germ layer / neural crest1.07e-09560
embryonic tissue1.07e-09560
presumptive structure1.07e-09560
germ layer / neural crest derived structure1.07e-09560
epiblast (generic)1.07e-09560
embryonic structure1.14e-09564
posterior neural tube5.99e-0915
chordal neural plate5.99e-0915
developing anatomical structure6.42e-09581
anatomical conduit7.49e-09240
epithelium5.04e-08306
tube1.20e-07192
cell layer1.28e-07309
neural nucleus1.45e-079
nucleus of brain1.45e-079
multi-cellular organism1.59e-07656
basal ganglion4.68e-079
nuclear complex of neuraxis4.68e-079
aggregate regional part of brain4.68e-079
collection of basal ganglia4.68e-079
cerebral subcortex4.68e-079
segmental subdivision of hindbrain9.35e-0712
hindbrain9.35e-0712
presumptive hindbrain9.35e-0712


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
CTBP2#1488241.81133355955210.0007543408259914850.00593331838573013
SUZ12#23512233.41052060737530.00117826764536030.00799591258049278



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.