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Coexpression cluster:C2872: Difference between revisions

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|full_id=C2872_neuroepithelioma_neuroblastoma_Astrocyte_Neurons_carcinoid_astrocytoma_Neural
|full_id=C2872_neuroepithelioma_neuroblastoma_Astrocyte_Neurons_carcinoid_astrocytoma_Neural
|id=C2872
|id=C2872
|ontology_enrichment_celltype=CL:0002319!3.47e-12!25;CL:0000133!2.34e-09!59;CL:0000128!8.49e-09!7;CL:0000126!8.49e-09!7;CL:0000127!8.49e-09!7;CL:0002453!8.49e-09!7;CL:0000333!1.91e-08!41;CL:0000095!4.01e-08!17;CL:0000123!4.01e-08!17
|ontology_enrichment_celltype=CL:0002319!1.54e-13!25;CL:0000133!4.69e-10!59;CL:0000333!2.51e-09!41;CL:0000128!2.56e-09!7;CL:0000126!2.56e-09!7;CL:0000127!2.56e-09!7;CL:0002453!2.56e-09!7;CL:0000095!6.53e-09!17;CL:0000123!6.53e-09!17;CL:0000221!3.55e-07!72;CL:0002605!7.55e-07!3
|ontology_enrichment_disease=DOID:171!3.91e-07!10
|ontology_enrichment_disease=DOID:171!5.41e-08!10;DOID:3095!8.14e-08!22;DOID:2994!8.14e-08!22
|ontology_enrichment_uberon=UBERON:0001017!1.39e-56!82;UBERON:0000073!4.70e-56!94;UBERON:0001016!4.70e-56!94;UBERON:0005743!2.40e-54!86;UBERON:0001049!1.61e-51!57;UBERON:0005068!1.61e-51!57;UBERON:0006241!1.61e-51!57;UBERON:0007135!1.61e-51!57;UBERON:0000955!4.75e-47!69;UBERON:0006238!4.75e-47!69;UBERON:0002616!1.73e-42!59;UBERON:0002780!7.65e-38!41;UBERON:0001890!7.65e-38!41;UBERON:0006240!7.65e-38!41;UBERON:0003080!1.37e-36!42;UBERON:0002346!4.42e-36!90;UBERON:0002020!9.91e-36!34;UBERON:0003528!9.91e-36!34;UBERON:0001893!1.07e-35!34;UBERON:0002791!1.18e-34!33;UBERON:0001869!2.06e-33!32;UBERON:0003075!1.89e-32!86;UBERON:0007284!1.89e-32!86;UBERON:0000924!5.62e-30!173;UBERON:0006601!5.62e-30!173;UBERON:0004121!4.64e-27!169;UBERON:0000956!2.39e-26!25;UBERON:0000203!2.39e-26!25;UBERON:0003056!2.77e-23!61;UBERON:0002619!9.84e-23!22;UBERON:0000033!3.01e-21!123;UBERON:0001950!1.39e-20!20;UBERON:0000153!5.49e-20!129;UBERON:0007811!5.49e-20!129;UBERON:0007023!4.37e-16!115;UBERON:0003076!1.28e-15!15;UBERON:0003057!1.28e-15!15;UBERON:0004732!1.17e-13!13;UBERON:0004733!1.50e-12!12;UBERON:0002028!1.50e-12!12;UBERON:0007277!1.50e-12!12;UBERON:0002308!9.83e-11!9;UBERON:0000125!9.83e-11!9;UBERON:0002420!1.77e-10!9;UBERON:0007245!1.77e-10!9;UBERON:0010009!1.77e-10!9;UBERON:0010011!1.77e-10!9;UBERON:0000454!1.77e-10!9;UBERON:0002680!1.17e-09!9;UBERON:0001895!1.17e-09!9;UBERON:0010092!1.17e-09!9;UBERON:0009663!1.37e-08!7;UBERON:0000200!1.68e-07!6;UBERON:0002298!2.17e-07!8;UBERON:0001871!2.45e-07!7;UBERON:0000064!2.69e-07!219;UBERON:0002021!5.84e-07!5;UBERON:0001872!8.77e-07!5;UBERON:0000025!8.82e-07!194
|ontology_enrichment_uberon=UBERON:0001016!2.24e-75!89;UBERON:0001017!2.64e-74!81;UBERON:0001049!4.01e-68!56;UBERON:0005068!4.01e-68!56;UBERON:0006241!4.01e-68!56;UBERON:0007135!4.01e-68!56;UBERON:0000073!1.78e-63!53;UBERON:0002616!1.78e-63!53;UBERON:0000955!5.73e-62!68;UBERON:0006238!5.73e-62!68;UBERON:0002346!1.50e-52!86;UBERON:0002780!3.88e-52!41;UBERON:0001890!3.88e-52!41;UBERON:0003080!3.88e-52!41;UBERON:0006240!3.88e-52!41;UBERON:0003528!1.76e-51!34;UBERON:0002020!1.76e-51!34;UBERON:0001893!2.50e-51!34;UBERON:0002791!2.87e-48!32;UBERON:0001869!4.20e-48!32;UBERON:0003075!2.84e-47!82;UBERON:0007284!2.84e-47!82;UBERON:0004121!2.72e-44!171;UBERON:0000924!2.72e-44!171;UBERON:0006601!2.72e-44!171;UBERON:0010371!1.39e-40!104;UBERON:0000956!6.58e-38!25;UBERON:0000203!6.58e-38!25;UBERON:0003056!6.00e-37!61;UBERON:0002619!1.13e-32!22;UBERON:0001950!1.71e-29!20;UBERON:0010314!1.24e-27!132;UBERON:0011216!4.24e-25!223;UBERON:0007023!5.73e-21!114;UBERON:0003076!1.94e-16!15;UBERON:0003057!1.94e-16!15;UBERON:0000125!9.27e-15!9;UBERON:0002308!9.27e-15!9;UBERON:0002420!2.46e-14!9;UBERON:0007245!2.46e-14!9;UBERON:0010009!2.46e-14!9;UBERON:0010011!2.46e-14!9;UBERON:0000454!2.46e-14!9;UBERON:0004732!1.03e-13!13;UBERON:0004733!3.08e-12!12;UBERON:0002028!3.08e-12!12;UBERON:0007277!3.08e-12!12;UBERON:0000025!8.58e-12!192;UBERON:0009663!1.12e-11!7;UBERON:0002680!1.13e-10!9;UBERON:0001895!1.13e-10!9;UBERON:0010092!1.13e-10!9;UBERON:0000477!2.57e-10!373;UBERON:0000200!4.09e-10!6;UBERON:0002021!1.61e-09!5;UBERON:0000064!2.12e-09!218;UBERON:0001872!3.95e-09!5;UBERON:0000349!7.62e-09!5;UBERON:0001871!1.43e-08!6;UBERON:0000483!1.72e-07!306;UBERON:0002298!2.07e-07!6;UBERON:0000119!2.86e-07!309;UBERON:0004111!3.56e-07!240;UBERON:0000369!3.89e-07!4;UBERON:0002435!3.89e-07!4;UBERON:0000204!3.89e-07!4;UBERON:0010082!3.89e-07!4
|tf_chipseq_enrich=CCNT2#905;3:4.75215118272197:0.0138620699668949:0.0487454789654051!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00999193845285128!EGR1#1958;4:4.98817909481014:0.00161501150007605:0.0101651410869911!GATA2#2624;3:9.5586988001655:0.00181815161835744:0.0109079697190736!HMGN3#9324;3:6.13391079251294:0.00664069668332472:0.0283138485776587!NFYA#4800;4:18.4255806998305:8.67100748407158e-06:0.000235157452773034!NFYB#4801;4:16.7597932535365:1.26678572070404e-05:0.000312032627086343!REST#5978;3:7.23752153709602:0.00410469730419261:0.0195954875783961!RFX5#5993;4:12.0479108271951:4.74457429336527e-05:0.000828487869294057!SRF#6722;4:13.7971782621678:2.75840773062708e-05:0.000585539319062929!TAL1#6886;2:14.9343083387201:0.00642807757788807:0.0279539471251271!TFAP2C#7022;4:10.8092286098602:7.32289634782688e-05:0.00114868725093225!TRIM28#10155;3:13.9428937839469:0.000597285818425842:0.00499839211462952!USF1#7391;4:6.36149927720796:0.000610501139914083:0.0050898162809521!ZBTB7A#51341;3:5.51393198090692:0.00903835282108109:0.0342596642935756!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00249916961903211
|tf_chipseq_enrich=CCNT2#905;3:4.75215118272197:0.0138620699668949:0.0487454789654051!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00999193845285128!EGR1#1958;4:4.98817909481014:0.00161501150007605:0.0101651410869911!GATA2#2624;3:9.5586988001655:0.00181815161835744:0.0109079697190736!HMGN3#9324;3:6.13391079251294:0.00664069668332472:0.0283138485776587!NFYA#4800;4:18.4255806998305:8.67100748407158e-06:0.000235157452773034!NFYB#4801;4:16.7597932535365:1.26678572070404e-05:0.000312032627086343!REST#5978;3:7.23752153709602:0.00410469730419261:0.0195954875783961!RFX5#5993;4:12.0479108271951:4.74457429336527e-05:0.000828487869294057!SRF#6722;4:13.7971782621678:2.75840773062708e-05:0.000585539319062929!TAL1#6886;2:14.9343083387201:0.00642807757788807:0.0279539471251271!TFAP2C#7022;4:10.8092286098602:7.32289634782688e-05:0.00114868725093225!TRIM28#10155;3:13.9428937839469:0.000597285818425842:0.00499839211462952!USF1#7391;4:6.36149927720796:0.000610501139914083:0.0050898162809521!ZBTB7A#51341;3:5.51393198090692:0.00903835282108109:0.0342596642935756!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00249916961903211
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}}
}}

Revision as of 14:31, 19 October 2012


Full id: C2872_neuroepithelioma_neuroblastoma_Astrocyte_Neurons_carcinoid_astrocytoma_Neural



Phase1 CAGE Peaks

Hg19::chr6:99282438..99282457,+p2@POU3F2
Hg19::chr6:99282461..99282472,+p7@POU3F2
Hg19::chr6:99282475..99282501,+p1@POU3F2
Hg19::chr6:99282722..99282737,+p6@POU3F2


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
nervous system2.24e-7589
central nervous system2.64e-7481
neural tube4.01e-6856
neural rod4.01e-6856
future spinal cord4.01e-6856
neural keel4.01e-6856
regional part of nervous system1.78e-6353
regional part of brain1.78e-6353
brain5.73e-6268
future brain5.73e-6268
neurectoderm1.50e-5286
regional part of forebrain3.88e-5241
forebrain3.88e-5241
anterior neural tube3.88e-5241
future forebrain3.88e-5241
brain grey matter1.76e-5134
gray matter1.76e-5134
telencephalon2.50e-5134
regional part of telencephalon2.87e-4832
cerebral hemisphere4.20e-4832
neural plate2.84e-4782
presumptive neural plate2.84e-4782
ectoderm-derived structure2.72e-44171
ectoderm2.72e-44171
presumptive ectoderm2.72e-44171
ecto-epithelium1.39e-40104
cerebral cortex6.58e-3825
pallium6.58e-3825
pre-chordal neural plate6.00e-3761
regional part of cerebral cortex1.13e-3222
neocortex1.71e-2920
structure with developmental contribution from neural crest1.24e-27132
organ system subdivision4.24e-25223
adult organism5.73e-21114
posterior neural tube1.94e-1615
chordal neural plate1.94e-1615
neural nucleus9.27e-159
nucleus of brain9.27e-159
basal ganglion2.46e-149
nuclear complex of neuraxis2.46e-149
aggregate regional part of brain2.46e-149
collection of basal ganglia2.46e-149
cerebral subcortex2.46e-149
segmental subdivision of nervous system1.03e-1313
segmental subdivision of hindbrain3.08e-1212
hindbrain3.08e-1212
presumptive hindbrain3.08e-1212
tube8.58e-12192
telencephalic nucleus1.12e-117
regional part of metencephalon1.13e-109
metencephalon1.13e-109
future metencephalon1.13e-109
anatomical cluster2.57e-10373
gyrus4.09e-106
occipital lobe1.61e-095
organ part2.12e-09218
parietal lobe3.95e-095
limbic system7.62e-095
temporal lobe1.43e-086
epithelium1.72e-07306
brainstem2.07e-076
cell layer2.86e-07309
anatomical conduit3.56e-07240
corpus striatum3.89e-074
striatum3.89e-074
ventral part of telencephalon3.89e-074
future corpus striatum3.89e-074
Disease
Ontology termp-valuen
neuroectodermal tumor5.41e-0810
germ cell and embryonal cancer8.14e-0822
germ cell cancer8.14e-0822


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
CCNT2#90534.752151182721970.01386206996689490.0487454789654051
E2F6#187645.017155731697390.00157802193473060.00999193845285128
EGR1#195844.988179094810140.001615011500076050.0101651410869911
GATA2#262439.55869880016550.001818151618357440.0109079697190736
HMGN3#932436.133910792512940.006640696683324720.0283138485776587
NFYA#4800418.42558069983058.67100748407158e-060.000235157452773034
NFYB#4801416.75979325353651.26678572070404e-050.000312032627086343
REST#597837.237521537096020.004104697304192610.0195954875783961
RFX5#5993412.04791082719514.74457429336527e-050.000828487869294057
SRF#6722413.79717826216782.75840773062708e-050.000585539319062929
TAL1#6886214.93430833872010.006428077577888070.0279539471251271
TFAP2C#7022410.80922860986027.32289634782688e-050.00114868725093225
TRIM28#10155313.94289378394690.0005972858184258420.00499839211462952
USF1#739146.361499277207960.0006105011399140830.0050898162809521
ZBTB7A#5134135.513931980906920.009038352821081090.0342596642935756
ZNF263#1012748.221841637010680.0002187871180958320.00249916961903211



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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