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Coexpression cluster:C1711: Difference between revisions

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|full_id=C1711_astrocytoma_Astrocyte_Neural_Wilms_acute_Ciliary_Lens
|full_id=C1711_astrocytoma_Astrocyte_Neural_Wilms_acute_Ciliary_Lens
|id=C1711
|id=C1711
|ontology_enrichment_celltype=CL:0000128!5.21e-09!7;CL:0000126!5.21e-09!7;CL:0000127!5.21e-09!7;CL:0002453!5.21e-09!7
|ontology_enrichment_celltype=CL:0000128!5.88e-12!7;CL:0000126!5.88e-12!7;CL:0000127!5.88e-12!7;CL:0002453!5.88e-12!7;CL:0002319!2.87e-08!25;CL:0002605!2.94e-08!3;CL:0000064!5.18e-08!3;CL:0000067!5.18e-08!3;CL:0005012!5.18e-08!3;CL:0002304!5.18e-08!3;CL:0000047!2.41e-07!8
|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!2.41e-45!81;UBERON:0001049!1.58e-44!56;UBERON:0005068!1.58e-44!56;UBERON:0006241!1.58e-44!56;UBERON:0007135!1.58e-44!56;UBERON:0000073!1.77e-42!53;UBERON:0002616!1.77e-42!53;UBERON:0001016!1.69e-39!89;UBERON:0003075!1.99e-38!82;UBERON:0007284!1.99e-38!82;UBERON:0000955!2.87e-36!68;UBERON:0006238!2.87e-36!68;UBERON:0002346!4.84e-36!86;UBERON:0002780!3.96e-33!41;UBERON:0001890!3.96e-33!41;UBERON:0003080!3.96e-33!41;UBERON:0006240!3.96e-33!41;UBERON:0003056!3.61e-31!61;UBERON:0003528!4.87e-30!34;UBERON:0002020!4.87e-30!34;UBERON:0001893!6.98e-30!34;UBERON:0010371!1.36e-27!104;UBERON:0001869!8.48e-27!32;UBERON:0002791!9.31e-27!32;UBERON:0010314!9.42e-24!132;UBERON:0004121!1.36e-22!171;UBERON:0000924!1.36e-22!171;UBERON:0006601!1.36e-22!171;UBERON:0007023!2.06e-21!114;UBERON:0011216!8.69e-20!223;UBERON:0000956!1.10e-18!25;UBERON:0000203!1.10e-18!25;UBERON:0002619!1.42e-13!22;UBERON:0000125!1.68e-13!9;UBERON:0002308!1.68e-13!9;UBERON:0001950!7.73e-13!20;UBERON:0002298!1.18e-12!6;UBERON:0003076!3.15e-12!15;UBERON:0003057!3.15e-12!15;UBERON:0000477!4.36e-11!373;UBERON:0004733!2.37e-10!12;UBERON:0002028!2.37e-10!12;UBERON:0007277!2.37e-10!12;UBERON:0002420!5.03e-10!9;UBERON:0007245!5.03e-10!9;UBERON:0010009!5.03e-10!9;UBERON:0010011!5.03e-10!9;UBERON:0000454!5.03e-10!9;UBERON:0009663!5.61e-10!7;UBERON:0004732!1.97e-09!13;UBERON:0000025!3.00e-09!192;UBERON:0000064!7.58e-09!218;UBERON:0000369!1.04e-08!4;UBERON:0002435!1.04e-08!4;UBERON:0000204!1.04e-08!4;UBERON:0010082!1.04e-08!4;UBERON:0001778!5.18e-08!3;UBERON:0001775!5.18e-08!3;UBERON:0000200!7.28e-08!6;UBERON:0004111!2.46e-07!240;UBERON:0001896!2.56e-07!3;UBERON:0005290!2.56e-07!3;UBERON:0010096!2.56e-07!3;UBERON:0005383!3.52e-07!3;UBERON:0005382!3.52e-07!3;UBERON:0000481!3.86e-07!342;UBERON:0000988!5.45e-07!3
|tf_chipseq_enrich=BATF#10538;4:19.4862414338429:1.37275300118359e-05:0.000332026286916658!BCL11A#53335;4:22.6955640828856:7.49488101632307e-06:0.000214278094296131!BCLAF1#9774;4:17.3221180880975:2.18923511079637e-05:0.000481451938800721!CTCF#10664;4:4.28820509846002:0.00515201558824328:0.0239291717522254!E2F1#1869;4:3.92591137190346:0.00721498454710636:0.0298733654898209!EBF1#1879;4:7.1251734772552:0.000723053104677421:0.00576978477990565!EP300#2033;4:5.41915338097856:0.0020938692794389:0.0121146536854091!ESR1#2099;4:24.6148826369236:5.42856809638808e-06:0.000165582425063865!IRF4#3662;4:17.5316101493953:2.08739444052064e-05:0.000460801919200031!JUN#3725;4:10.0102633538691:0.000190853134780107:0.00230486939677377!JUND#3727;4:5.59573115349682:0.00184959330175546:0.0109320698835336!MAFF#23764;4:45.0522851919561:4.89188569148035e-07:2.30033160617972e-05!MAFK#7975;4:21.6805865102639:8.98818656648185e-06:0.000242062201345229!MEF2A#4205;4:14.9945847277152:3.876195075647e-05:0.000727973273701666!MEF2C#4208;4:33.0490835940992:1.68127439756556e-06:6.36197886983151e-05!NFKB1#4790;4:4.39045073935507:0.00470773269252496:0.0221993360427404!NR3C1#2908;4:11.9784186649384:9.4122920812787e-05:0.00136529218427315!PAX5#5079;4:5.33565242494226:0.00222338958618779:0.0127769662700488!POU2F2#5452;4:7.28489924619402:0.000663122328874386:0.00542374758440849!SP1#6667;4:4.55870510251272:0.0040757356578168:0.0194803787637512!SPI1#6688;4:6.56345880681818:0.000995742963645402:0.00714149151079262!TRIM28#10155;4:14.87242003621:4.00368496902357e-05:0.000734611480112179
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}}
}}

Revision as of 11:36, 19 October 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>


Uber Anatomy
Ontology termp-valuen
central nervous system2.41e-4581
neural tube1.58e-4456
neural rod1.58e-4456
future spinal cord1.58e-4456
neural keel1.58e-4456
regional part of nervous system1.77e-4253
regional part of brain1.77e-4253
nervous system1.69e-3989
neural plate1.99e-3882
presumptive neural plate1.99e-3882
brain2.87e-3668
future brain2.87e-3668
neurectoderm4.84e-3686
regional part of forebrain3.96e-3341
forebrain3.96e-3341
anterior neural tube3.96e-3341
future forebrain3.96e-3341
pre-chordal neural plate3.61e-3161
brain grey matter4.87e-3034
gray matter4.87e-3034
telencephalon6.98e-3034
ecto-epithelium1.36e-27104
cerebral hemisphere8.48e-2732
regional part of telencephalon9.31e-2732
structure with developmental contribution from neural crest9.42e-24132
ectoderm-derived structure1.36e-22171
ectoderm1.36e-22171
presumptive ectoderm1.36e-22171
adult organism2.06e-21114
organ system subdivision8.69e-20223
cerebral cortex1.10e-1825
pallium1.10e-1825
regional part of cerebral cortex1.42e-1322
neural nucleus1.68e-139
nucleus of brain1.68e-139
neocortex7.73e-1320
brainstem1.18e-126
posterior neural tube3.15e-1215
chordal neural plate3.15e-1215
anatomical cluster4.36e-11373
segmental subdivision of hindbrain2.37e-1012
hindbrain2.37e-1012
presumptive hindbrain2.37e-1012
basal ganglion5.03e-109
nuclear complex of neuraxis5.03e-109
aggregate regional part of brain5.03e-109
collection of basal ganglia5.03e-109
cerebral subcortex5.03e-109
telencephalic nucleus5.61e-107
segmental subdivision of nervous system1.97e-0913
tube3.00e-09192
organ part7.58e-09218
corpus striatum1.04e-084
striatum1.04e-084
ventral part of telencephalon1.04e-084
future corpus striatum1.04e-084
ciliary epithelium5.18e-083
ciliary body5.18e-083
gyrus7.28e-086
anatomical conduit2.46e-07240
medulla oblongata2.56e-073
myelencephalon2.56e-073
future myelencephalon2.56e-073
caudate-putamen3.52e-073
dorsal striatum3.52e-073
multi-tissue structure3.86e-07342
pons5.45e-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


(#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.