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Coexpression cluster:C1711: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!9.30e-45!82;UBERON:0001049!4.59e-44!57;UBERON:0005068!4.59e-44!57;UBERON:0006241!4.59e-44!57;UBERON:0007135!4.59e-44!57;UBERON:0005743!6.17e-43!86;UBERON:0002616!2.44e-39!59;UBERON:0000073!3.94e-39!94;UBERON:0001016!3.94e-39!94;UBERON:0000955!2.59e-36!69;UBERON:0006238!2.59e-36!69;UBERON:0003075!2.46e-35!86;UBERON:0007284!2.46e-35!86;UBERON:0002346!8.04e-34!90;UBERON:0002780!6.37e-33!41;UBERON:0001890!6.37e-33!41;UBERON:0006240!6.37e-33!41;UBERON:0003080!8.80e-32!42;UBERON:0002020!2.54e-29!34;UBERON:0003528!2.54e-29!34;UBERON:0001893!2.80e-29!34;UBERON:0002791!2.45e-28!33;UBERON:0007023!9.89e-28!115;UBERON:0001869!3.19e-27!32;UBERON:0000153!4.33e-27!129;UBERON:0007811!4.33e-27!129;UBERON:0003056!4.62e-27!61;UBERON:0000033!1.32e-25!123;UBERON:0004121!1.09e-22!169;UBERON:0000924!3.34e-22!173;UBERON:0006601!3.34e-22!173;UBERON:0000956!3.80e-21!25;UBERON:0000203!3.80e-21!25;UBERON:0002619!9.04e-18!22;UBERON:0001950!4.64e-16!20;UBERON:0003076!4.15e-13!15;UBERON:0003057!4.15e-13!15;UBERON:0000064!2.88e-12!219;UBERON:0000025!1.51e-11!194;UBERON:0004732!3.40e-11!13;UBERON:0004733!3.28e-10!12;UBERON:0002028!3.28e-10!12;UBERON:0007277!3.28e-10!12;UBERON:0000477!1.27e-09!286;UBERON:0002308!1.29e-09!9;UBERON:0000125!1.29e-09!9;UBERON:0004111!1.80e-09!241;UBERON:0002420!3.30e-09!9;UBERON:0007245!3.30e-09!9;UBERON:0010009!3.30e-09!9;UBERON:0010011!3.30e-09!9;UBERON:0000454!3.30e-09!9;UBERON:0000475!4.43e-09!365;UBERON:0000119!1.43e-08!312;UBERON:0000483!1.70e-08!309;UBERON:0000062!3.45e-08!511;UBERON:0000922!1.16e-07!612;UBERON:0009663!1.28e-07!7;UBERON:0002298!2.61e-07!8;UBERON:0002680!2.87e-07!9;UBERON:0001895!2.87e-07!9;UBERON:0010092!2.87e-07!9;UBERON:0000481!3.62e-07!347
|ontology_enrichment_uberon=UBERON:0001017!9.30e-45!82;UBERON:0001049!4.59e-44!57;UBERON:0005068!4.59e-44!57;UBERON:0006241!4.59e-44!57;UBERON:0007135!4.59e-44!57;UBERON:0005743!6.17e-43!86;UBERON:0002616!2.44e-39!59;UBERON:0000073!3.94e-39!94;UBERON:0001016!3.94e-39!94;UBERON:0000955!2.59e-36!69;UBERON:0006238!2.59e-36!69;UBERON:0003075!2.46e-35!86;UBERON:0007284!2.46e-35!86;UBERON:0002346!8.04e-34!90;UBERON:0002780!6.37e-33!41;UBERON:0001890!6.37e-33!41;UBERON:0006240!6.37e-33!41;UBERON:0003080!8.80e-32!42;UBERON:0002020!2.54e-29!34;UBERON:0003528!2.54e-29!34;UBERON:0001893!2.80e-29!34;UBERON:0002791!2.45e-28!33;UBERON:0007023!9.89e-28!115;UBERON:0001869!3.19e-27!32;UBERON:0000153!4.33e-27!129;UBERON:0007811!4.33e-27!129;UBERON:0003056!4.62e-27!61;UBERON:0000033!1.32e-25!123;UBERON:0004121!1.09e-22!169;UBERON:0000924!3.34e-22!173;UBERON:0006601!3.34e-22!173;UBERON:0000956!3.80e-21!25;UBERON:0000203!3.80e-21!25;UBERON:0002619!9.04e-18!22;UBERON:0001950!4.64e-16!20;UBERON:0003076!4.15e-13!15;UBERON:0003057!4.15e-13!15;UBERON:0000064!2.88e-12!219;UBERON:0000025!1.51e-11!194;UBERON:0004732!3.40e-11!13;UBERON:0004733!3.28e-10!12;UBERON:0002028!3.28e-10!12;UBERON:0007277!3.28e-10!12;UBERON:0000477!1.27e-09!286;UBERON:0002308!1.29e-09!9;UBERON:0000125!1.29e-09!9;UBERON:0004111!1.80e-09!241;UBERON:0002420!3.30e-09!9;UBERON:0007245!3.30e-09!9;UBERON:0010009!3.30e-09!9;UBERON:0010011!3.30e-09!9;UBERON:0000454!3.30e-09!9;UBERON:0000475!4.43e-09!365;UBERON:0000119!1.43e-08!312;UBERON:0000483!1.70e-08!309;UBERON:0000062!3.45e-08!511;UBERON:0000922!1.16e-07!612;UBERON:0009663!1.28e-07!7;UBERON:0002298!2.61e-07!8;UBERON:0002680!2.87e-07!9;UBERON:0001895!2.87e-07!9;UBERON:0010092!2.87e-07!9;UBERON:0000481!3.62e-07!347
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}}
}}

Revision as of 12:00, 5 September 2012


Full id: C1711_astrocytoma_Astrocyte_Neural_Wilms_acute_Ciliary_Lens



Phase1 CAGE Peaks

Hg19::chr13:99349888..99349893,+p@chr13:99349888..99349893
+
Hg19::chr6:151042225..151042241,+p5@PLEKHG1
Hg19::chr6:151042248..151042293,+p2@PLEKHG1
Hg19::chr6:151042296..151042316,+p8@PLEKHG1
Hg19::chr6:151042333..151042356,+p9@PLEKHG1


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

Cell Type
Ontology termp-valuen
oligodendrocyte5.21e-097
macroglial cell5.21e-097
astrocyte5.21e-097
oligodendrocyte precursor cell5.21e-097
Uber Anatomy
Ontology termp-valuen
central nervous system9.30e-4582
neural tube4.59e-4457
neural rod4.59e-4457
future spinal cord4.59e-4457
neural keel4.59e-4457
regional part of brain2.44e-3959
regional part of nervous system3.94e-3994
nervous system3.94e-3994
brain2.59e-3669
future brain2.59e-3669
neural plate2.46e-3586
presumptive neural plate2.46e-3586
neurectoderm8.04e-3490
regional part of forebrain6.37e-3341
forebrain6.37e-3341
future forebrain6.37e-3341
anterior neural tube8.80e-3242
gray matter2.54e-2934
brain grey matter2.54e-2934
telencephalon2.80e-2934
regional part of telencephalon2.45e-2833
adult organism9.89e-28115
cerebral hemisphere3.19e-2732
anterior region of body4.33e-27129
craniocervical region4.33e-27129
pre-chordal neural plate4.62e-2761
head1.32e-25123
ectoderm-derived structure1.09e-22169
ectoderm3.34e-22173
presumptive ectoderm3.34e-22173
cerebral cortex3.80e-2125
pallium3.80e-2125
regional part of cerebral cortex9.04e-1822
neocortex4.64e-1620
posterior neural tube4.15e-1315
chordal neural plate4.15e-1315
organ part2.88e-12219
tube1.51e-11194
segmental subdivision of nervous system3.40e-1113
segmental subdivision of hindbrain3.28e-1012
hindbrain3.28e-1012
presumptive hindbrain3.28e-1012
anatomical cluster1.27e-09286
nucleus of brain1.29e-099
neural nucleus1.29e-099
anatomical conduit1.80e-09241
basal ganglion3.30e-099
nuclear complex of neuraxis3.30e-099
aggregate regional part of brain3.30e-099
collection of basal ganglia3.30e-099
cerebral subcortex3.30e-099
organism subdivision4.43e-09365
cell layer1.43e-08312
epithelium1.70e-08309
organ3.45e-08511
embryo1.16e-07612
telencephalic nucleus1.28e-077
brainstem2.61e-078
regional part of metencephalon2.87e-079
metencephalon2.87e-079
future metencephalon2.87e-079
multi-tissue structure3.62e-07347


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
BATF#10538419.48624143384291.37275300118359e-050.000332026286916658
BCL11A#53335422.69556408288567.49488101632307e-060.000214278094296131
BCLAF1#9774417.32211808809752.18923511079637e-050.000481451938800721
CTCF#1066444.288205098460020.005152015588243280.0239291717522254
E2F1#186943.925911371903460.007214984547106360.0298733654898209
EBF1#187947.12517347725520.0007230531046774210.00576978477990565
EP300#203345.419153380978560.00209386927943890.0121146536854091
ESR1#2099424.61488263692365.42856809638808e-060.000165582425063865
IRF4#3662417.53161014939532.08739444052064e-050.000460801919200031
JUN#3725410.01026335386910.0001908531347801070.00230486939677377
JUND#372745.595731153496820.001849593301755460.0109320698835336
MAFF#23764445.05228519195614.89188569148035e-072.30033160617972e-05
MAFK#7975421.68058651026398.98818656648185e-060.000242062201345229
MEF2A#4205414.99458472771523.876195075647e-050.000727973273701666
MEF2C#4208433.04908359409921.68127439756556e-066.36197886983151e-05
NFKB1#479044.390450739355070.004707732692524960.0221993360427404
NR3C1#2908411.97841866493849.4122920812787e-050.00136529218427315
PAX5#507945.335652424942260.002223389586187790.0127769662700488
POU2F2#545247.284899246194020.0006631223288743860.00542374758440849
SP1#666744.558705102512720.00407573565781680.0194803787637512
SPI1#668846.563458806818180.0009957429636454020.00714149151079262
TRIM28#10155414.872420036214.00368496902357e-050.000734611480112179



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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