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Coexpression cluster:C1143: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0007023!3.63e-67!114;UBERON:0001049!2.06e-60!56;UBERON:0005068!2.06e-60!56;UBERON:0006241!2.06e-60!56;UBERON:0007135!2.06e-60!56;UBERON:0000073!1.39e-54!53;UBERON:0002616!1.39e-54!53;UBERON:0001017!4.47e-48!81;UBERON:0000955!1.77e-46!68;UBERON:0006238!1.77e-46!68;UBERON:0001016!2.68e-44!89;UBERON:0002780!3.25e-44!41;UBERON:0001890!3.25e-44!41;UBERON:0003080!3.25e-44!41;UBERON:0006240!3.25e-44!41;UBERON:0003528!1.28e-43!34;UBERON:0002020!1.28e-43!34;UBERON:0001893!1.47e-43!34;UBERON:0003075!1.07e-41!82;UBERON:0007284!1.07e-41!82;UBERON:0002791!1.80e-39!32;UBERON:0001869!2.43e-39!32;UBERON:0002346!3.69e-39!86;UBERON:0010371!3.88e-35!104;UBERON:0003056!5.31e-31!61;UBERON:0011216!5.86e-31!223;UBERON:0002619!2.04e-30!22;UBERON:0010314!1.05e-28!132;UBERON:0004121!3.18e-28!171;UBERON:0000924!3.18e-28!171;UBERON:0006601!3.18e-28!171;UBERON:0001950!1.39e-26!20;UBERON:0000956!3.00e-26!25;UBERON:0000203!3.00e-26!25;UBERON:0000477!1.12e-20!373;UBERON:0000125!5.66e-20!9;UBERON:0002308!5.66e-20!9;UBERON:0004111!2.97e-18!240;UBERON:0000025!4.93e-18!192;UBERON:0003076!1.12e-16!15;UBERON:0003057!1.12e-16!15;UBERON:0009663!1.16e-15!7;UBERON:0002420!2.58e-15!9;UBERON:0007245!2.58e-15!9;UBERON:0010009!2.58e-15!9;UBERON:0010011!2.58e-15!9;UBERON:0000454!2.58e-15!9;UBERON:0002298!1.55e-14!6;UBERON:0000481!1.59e-14!342;UBERON:0004732!3.18e-13!13;UBERON:0000062!1.98e-12!503;UBERON:0000483!2.16e-11!306;UBERON:0004733!2.70e-11!12;UBERON:0002028!2.70e-11!12;UBERON:0007277!2.70e-11!12;UBERON:0000119!3.91e-11!309;UBERON:0002021!4.25e-11!5;UBERON:0000064!3.60e-10!218;UBERON:0000200!2.20e-09!6;UBERON:0000369!3.17e-09!4;UBERON:0002435!3.17e-09!4;UBERON:0000204!3.17e-09!4;UBERON:0010082!3.17e-09!4;UBERON:0000467!4.15e-09!624;UBERON:0005423!4.36e-09!581;UBERON:0000922!4.38e-09!592;UBERON:0000923!4.63e-09!560;UBERON:0010316!4.63e-09!560;UBERON:0005291!4.63e-09!560;UBERON:0006598!4.63e-09!560;UBERON:0010317!4.63e-09!560;UBERON:0002532!4.63e-09!560;UBERON:0000480!4.65e-09!625;UBERON:0002050!7.49e-09!564;UBERON:0000988!3.50e-08!3;UBERON:0000468!3.57e-08!656;UBERON:0001896!4.94e-08!3;UBERON:0005290!4.94e-08!3;UBERON:0010096!4.94e-08!3;UBERON:0002240!1.14e-07!3;UBERON:0005174!1.14e-07!3;UBERON:0001137!1.14e-07!3;UBERON:0001871!1.19e-07!6;UBERON:0001872!1.39e-07!5;UBERON:0000349!1.74e-07!5;UBERON:0005383!2.93e-07!3;UBERON:0005382!2.93e-07!3
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|tfbs_overrepresentation_for_novel_motifs=0.392069,1.1011,0.384703,0.529489,1.62733,0.52784,0.604235,0.226729,0.224331,0.773341,0.497563,0.647852,0.184039,0.592674,0.341795,0.365029,0.827563,0.786991,1.08139,0.66776,0.384762,0.23059,0.520063,0.338096,0.430372,0.670692,2.1826,0.517892,1.63811,0.150685,0.475674,0.864517,0.257226,0.186138,0.309012,0.232776,0.825031,0.529001,0.282922,0.207499,0.307642,0.459366,0.254304,0.340293,0.109128,0.415364,0.60533,0.486696,0.237549,0.346342,0.684981,0.617179,0.373994,0.941629,1.09491,0.595623,0.924875,0.562713,0.459282,0.561701,0.905643,0.60771,0.224801,0.799729,0.625758,0.76514,1.18348,1.55228,0.854088,1.38987,0.4462,0.232216,0.369103,1.0929,0.179863,0.168304,0.473656,0.782748,0.850825,0.424224,0.580264,0.798651,0.625403,0.229431,1.04131,0.0324537,0.097572,0.146388,0.711163,1.65172,1.27705,1.01423,0.881388,0.26423,0.343884,0.277058,0.194299,0.924148,0.715799,0.132387,2.17049,0.875714,0.918549,0.831244,0.753567,0.493026,0.815341,0.589207,1.92716,0.327379,1.81048,0.915771,0.379203,0.507004,1.22894,1.48924,0.155979,0.474472,0.762789,0.26701,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,0.597853,0.886402,1.12733,0.27799,3.79029,0.47854,1.14174,2.59532,1.28996,0.854586,0.469685,1.28879,4.50163,2.10682,1.70417,1.21002,0.59959,0.920609,1.78463,0.554217,0.738579,1.94751,2.99223,0.722945,0.345641,0.0685123,1.0153,0.619774,0.607223,1.42052,0.694887,0.329354,0.430431,0.401655,1.2088,0.996724,0.850033,0.404861,1.81801,0.624608,0.24928,0.602897,0.00626991
}}
}}

Revision as of 14:42, 26 November 2012


Full id: C1143_parotid_salivary_corpus_optic_temporal_thalamus_globus



Phase1 CAGE Peaks

Hg19::chr11:49230087..49230098,-p7@FOLH1B
p7@FOLH1
Hg19::chr11:49230144..49230164,-p1@FOLH1B
p1@FOLH1
Hg19::chr11:49230172..49230183,-p6@FOLH1B
p6@FOLH1
Hg19::chr11:49230184..49230198,-p5@FOLH1B
p5@FOLH1
Hg19::chr13:88323717..88323728,+p@chr13:88323717..88323728
+
Hg19::chr15:101402041..101402067,+p1@ENST00000558475
p1@ENST00000558641
p1@ENST00000559673
Hg19::chr3:138022481..138022501,-p@chr3:138022481..138022501
-


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
adult organism3.63e-67114
neural tube2.06e-6056
neural rod2.06e-6056
future spinal cord2.06e-6056
neural keel2.06e-6056
regional part of nervous system1.39e-5453
regional part of brain1.39e-5453
central nervous system4.47e-4881
brain1.77e-4668
future brain1.77e-4668
nervous system2.68e-4489
regional part of forebrain3.25e-4441
forebrain3.25e-4441
anterior neural tube3.25e-4441
future forebrain3.25e-4441
brain grey matter1.28e-4334
gray matter1.28e-4334
telencephalon1.47e-4334
neural plate1.07e-4182
presumptive neural plate1.07e-4182
regional part of telencephalon1.80e-3932
cerebral hemisphere2.43e-3932
neurectoderm3.69e-3986
ecto-epithelium3.88e-35104
pre-chordal neural plate5.31e-3161
organ system subdivision5.86e-31223
regional part of cerebral cortex2.04e-3022
structure with developmental contribution from neural crest1.05e-28132
ectoderm-derived structure3.18e-28171
ectoderm3.18e-28171
presumptive ectoderm3.18e-28171
neocortex1.39e-2620
cerebral cortex3.00e-2625
pallium3.00e-2625
anatomical cluster1.12e-20373
neural nucleus5.66e-209
nucleus of brain5.66e-209
anatomical conduit2.97e-18240
tube4.93e-18192
posterior neural tube1.12e-1615
chordal neural plate1.12e-1615
telencephalic nucleus1.16e-157
basal ganglion2.58e-159
nuclear complex of neuraxis2.58e-159
aggregate regional part of brain2.58e-159
collection of basal ganglia2.58e-159
cerebral subcortex2.58e-159
brainstem1.55e-146
multi-tissue structure1.59e-14342
segmental subdivision of nervous system3.18e-1313
organ1.98e-12503
epithelium2.16e-11306
segmental subdivision of hindbrain2.70e-1112
hindbrain2.70e-1112
presumptive hindbrain2.70e-1112
cell layer3.91e-11309
occipital lobe4.25e-115
organ part3.60e-10218
gyrus2.20e-096
corpus striatum3.17e-094
striatum3.17e-094
ventral part of telencephalon3.17e-094
future corpus striatum3.17e-094
anatomical system4.15e-09624
developing anatomical structure4.36e-09581
embryo4.38e-09592
germ layer4.63e-09560
germ layer / neural crest4.63e-09560
embryonic tissue4.63e-09560
presumptive structure4.63e-09560
germ layer / neural crest derived structure4.63e-09560
epiblast (generic)4.63e-09560
anatomical group4.65e-09625
embryonic structure7.49e-09564
pons3.50e-083
multi-cellular organism3.57e-08656
medulla oblongata4.94e-083
myelencephalon4.94e-083
future myelencephalon4.94e-083
spinal cord1.14e-073
dorsal region element1.14e-073
dorsum1.14e-073
temporal lobe1.19e-076
parietal lobe1.39e-075
limbic system1.74e-075
caudate-putamen2.93e-073
dorsal striatum2.93e-073


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

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.

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