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Coexpression cluster:C789: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0003075!5.02e-33!82;UBERON:0007284!5.02e-33!82;UBERON:0002346!2.30e-31!86;UBERON:0001782!8.77e-27!3;UBERON:0005424!8.77e-27!3;UBERON:0001049!7.91e-26!56;UBERON:0005068!7.91e-26!56;UBERON:0006241!7.91e-26!56;UBERON:0007135!7.91e-26!56;UBERON:0010371!1.90e-25!104;UBERON:0000966!1.73e-23!6;UBERON:0005388!1.73e-23!6;UBERON:0001802!1.73e-23!6;UBERON:0000073!1.76e-23!53;UBERON:0002616!1.76e-23!53;UBERON:0002298!7.54e-23!6;UBERON:0007023!2.05e-20!114;UBERON:0003056!2.33e-20!61;UBERON:0001781!3.00e-20!4;UBERON:0001017!1.08e-19!81;UBERON:0010314!2.03e-19!132;UBERON:0000955!1.30e-17!68;UBERON:0006238!1.30e-17!68;UBERON:0001893!1.61e-17!34;UBERON:0001016!1.64e-17!89;UBERON:0004121!7.46e-16!171;UBERON:0000924!7.46e-16!171;UBERON:0006601!7.46e-16!171;UBERON:0002780!2.16e-14!41;UBERON:0001890!2.16e-14!41;UBERON:0003080!2.16e-14!41;UBERON:0006240!2.16e-14!41;UBERON:0003076!5.80e-14!15;UBERON:0003057!5.80e-14!15;UBERON:0003528!7.98e-14!34;UBERON:0002020!7.98e-14!34;UBERON:0001896!2.03e-12!3;UBERON:0005290!2.03e-12!3;UBERON:0010096!2.03e-12!3;UBERON:0002619!3.47e-12!22;UBERON:0000988!3.57e-12!3;UBERON:0004733!1.55e-11!12;UBERON:0002028!1.55e-11!12;UBERON:0007277!1.55e-11!12;UBERON:0002791!2.89e-11!32;UBERON:0001869!2.94e-11!32;UBERON:0000956!9.90e-11!25;UBERON:0000203!9.90e-11!25;UBERON:0004732!1.16e-10!13;UBERON:0000970!3.26e-10!21;UBERON:0002104!3.26e-10!21;UBERON:0002336!6.31e-10!1;UBERON:0011215!6.31e-10!1;UBERON:0001018!6.31e-10!1;UBERON:0002473!6.31e-10!1;UBERON:0005340!6.31e-10!1;UBERON:0003544!6.31e-10!1;UBERON:0005970!6.31e-10!1;UBERON:0002316!6.31e-10!1;UBERON:0001020!6.31e-10!1;UBERON:0002437!6.31e-10!1;UBERON:0002146!8.91e-10!1;UBERON:0005623!8.91e-10!1;UBERON:0001301!1.25e-09!1;UBERON:0002038!1.36e-09!1;UBERON:0009661!1.36e-09!1;UBERON:0002950!1.36e-09!1;UBERON:0001891!1.36e-09!1;UBERON:0009616!1.36e-09!1;UBERON:0010286!1.36e-09!1;UBERON:0007190!1.48e-09!1;UBERON:0001950!1.83e-09!20;UBERON:0002902!1.91e-09!1;UBERON:0009899!1.91e-09!1;UBERON:0002022!2.67e-09!1;UBERON:0000020!6.54e-09!24;UBERON:0001032!6.54e-09!24;UBERON:0004456!6.54e-09!24;UBERON:0000025!4.04e-08!192;UBERON:0000064!5.24e-08!218;UBERON:0007625!1.09e-07!11;UBERON:0000483!1.77e-07!306;UBERON:0000119!2.26e-07!309;UBERON:0000019!3.73e-07!20;UBERON:0000047!3.73e-07!20;UBERON:0010312!3.73e-07!20;UBERON:0004088!3.73e-07!20;UBERON:0010230!3.73e-07!20;UBERON:0003072!3.73e-07!20;UBERON:0004128!3.73e-07!20;UBERON:0003071!3.73e-07!20
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|tfbs_overrepresentation_for_novel_motifs=0.280498,0.216121,0.273994,0.404877,0.237701,0.403356,0.474413,0.434224,1.36876,0.437939,0.375531,0.515448,0.107365,0.46359,0.236531,0.712999,0.68716,0.559826,0.116269,0.178097,0.274046,0.270268,0.396189,0.233338,0.314616,0.537051,0.310025,1.02097,0.240354,0.994584,0.935963,0.722879,0.958783,0.352585,0.20845,0.568934,0.20579,0.404426,0.547451,0.789486,0.597291,0.340749,1.7121,0.663127,1.25354,0.301189,0.47544,0.365597,0.827284,0.240465,0.550604,0.486559,0.468946,0.797754,0.947672,0.466348,0.244111,0.435652,0.59006,0.434711,0.762758,0.477672,0.430344,0.660336,0.494624,0.627106,1.0348,1.4,0.712787,1.2388,0.328852,0.445273,0.0579262,0.945703,1.14624,0.316793,2.71443,0.644006,1.68999,0.309107,0.11972,0.659298,0.49429,0.439665,0.89511,0.140048,0.175904,1.99753,0.575506,1.4989,1.12715,0.868602,1.75131,0.171001,0.238337,0.18161,0.368981,0.780743,0.579925,0.244963,0.187593,0.733724,0.775299,0.690713,0.616014,0.37138,0.675372,0.460348,0.31439,0.22412,2.16863,0.772599,0.269151,0.99905,1.07963,0.590599,1.19911,0.354459,0.624851,0.173291,0.937551,0.57318,0.400807,0.504966,1.18924,0.644741,0.468435,0.744085,0.979528,1.62707,0.869279,0.358161,0.993705,1.25332,1.13991,0.260985,0.9239,1.02211,1.09788,1.95265,1.55112,1.06096,0.470062,0.777301,0.617705,0.42776,0.601672,1.79367,1.60827,0.168379,1.61906,0.0287097,0.869654,0.414185,2.0853,1.26919,0.560015,0.225815,0.314669,0.28899,1.05976,0.851493,0.708865,0.793294,0.633206,0.493542,0.479645,0.473159,1.66584
}}
}}

Revision as of 14:28, 26 November 2012


Full id: C789_retina_Retinal_medulla_stomach_lung_eye_corpus



Phase1 CAGE Peaks

Hg19::chr11:109990513..109990520,-p@chr11:109990513..109990520
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Hg19::chr11:61522820..61522823,+p9@C11orf9
Hg19::chr11:61522844..61522875,+p2@C11orf9
Hg19::chr13:99135322..99135327,-p@chr13:99135322..99135327
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Hg19::chr14:87636652..87636657,-p@chr14:87636652..87636657
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Hg19::chr21:36041264..36041274,+p3@CLIC6
Hg19::chr21:36041275..36041282,+p5@CLIC6
Hg19::chr21:36041286..36041333,+p1@CLIC6
Hg19::chr5:70308745..70308754,-p@chr5:70308745..70308754
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Hg19::chr9:140088882..140088898,-p@chr9:140088882..140088898
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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:0005247voltage-gated chloride channel activity0.0445095728958841
GO:0022844voltage-gated anion channel activity0.0445095728958841
GO:0043168anion binding0.0445095728958841
GO:0031404chloride ion binding0.0445095728958841
GO:0005254chloride channel activity0.0445095728958841
GO:0006821chloride transport0.0445095728958841
GO:0005253anion channel activity0.0445095728958841



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>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
retinal pigment epithelial cell8.77e-273
visual pigment cell3.00e-204
pigment cell4.09e-1014
Uber Anatomy
Ontology termp-valuen
neural plate5.02e-3382
presumptive neural plate5.02e-3382
neurectoderm2.30e-3186
pigmented layer of retina8.77e-273
presumptive retinal pigmented epithelium8.77e-273
neural tube7.91e-2656
neural rod7.91e-2656
future spinal cord7.91e-2656
neural keel7.91e-2656
ecto-epithelium1.90e-25104
retina1.73e-236
photoreceptor array1.73e-236
posterior segment of eyeball1.73e-236
regional part of nervous system1.76e-2353
regional part of brain1.76e-2353
brainstem7.54e-236
adult organism2.05e-20114
pre-chordal neural plate2.33e-2061
layer of retina3.00e-204
central nervous system1.08e-1981
structure with developmental contribution from neural crest2.03e-19132
brain1.30e-1768
future brain1.30e-1768
telencephalon1.61e-1734
nervous system1.64e-1789
ectoderm-derived structure7.46e-16171
ectoderm7.46e-16171
presumptive ectoderm7.46e-16171
regional part of forebrain2.16e-1441
forebrain2.16e-1441
anterior neural tube2.16e-1441
future forebrain2.16e-1441
posterior neural tube5.80e-1415
chordal neural plate5.80e-1415
brain grey matter7.98e-1434
gray matter7.98e-1434
medulla oblongata2.03e-123
myelencephalon2.03e-123
future myelencephalon2.03e-123
regional part of cerebral cortex3.47e-1222
pons3.57e-123
segmental subdivision of hindbrain1.55e-1112
hindbrain1.55e-1112
presumptive hindbrain1.55e-1112
regional part of telencephalon2.89e-1132
cerebral hemisphere2.94e-1132
cerebral cortex9.90e-1125
pallium9.90e-1125
segmental subdivision of nervous system1.16e-1013
eye3.26e-1021
visual system3.26e-1021
corpus callosum6.31e-101
central nervous system cell part cluster6.31e-101
axon tract6.31e-101
intercerebral commissure6.31e-101
dorsal telencephalic commissure6.31e-101
brain white matter6.31e-101
brain commissure6.31e-101
white matter6.31e-101
nervous system commissure6.31e-101
cerebral hemisphere white matter6.31e-101
pulmonary valve8.91e-101
semi-lunar valve8.91e-101
epididymis1.25e-091
substantia nigra1.36e-091
midbrain nucleus1.36e-091
regional part of midbrain1.36e-091
midbrain1.36e-091
presumptive midbrain1.36e-091
midbrain neural tube1.36e-091
paracentral gyrus1.48e-091
neocortex1.83e-0920
occipital pole1.91e-091
pole of cerebral hemisphere1.91e-091
insula2.67e-091
sense organ6.54e-0924
sensory system6.54e-0924
entire sense organ system6.54e-0924
tube4.04e-08192
organ part5.24e-08218
pigment epithelium of eye1.09e-0711
epithelium1.77e-07306
cell layer2.26e-07309
camera-type eye3.73e-0720
simple eye3.73e-0720
immature eye3.73e-0720
ocular region3.73e-0720
eyeball of camera-type eye3.73e-0720
optic cup3.73e-0720
optic vesicle3.73e-0720
eye primordium3.73e-0720


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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