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Coexpression cluster:C1884: Difference between revisions

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{{Coexpression_clusters
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DNA binding!0.0329591072552472!1745;1746$GO:0003727!single-stranded RNA binding!0.0329591072552472!1746$GO:0003700!transcription factor activity!0.0363204124571804!1745;1746$GO:0007275!multicellular organismal development!0.0380691710092592!1745;1746$GO:0003682!chromatin binding!0.0380691710092592!1746$GO:0007420!brain development!0.0380691710092592!1746$GO:0045944!positive regulation of transcription from RNA polymerase II promoter!0.0380691710092592!1746$GO:0032502!developmental process!0.0380691710092592!1745;1746$GO:0006355!regulation of transcription, DNA-dependent!0.0380691710092592!1745;1746$GO:0006351!transcription, DNA-dependent!0.0380691710092592!1745;1746$GO:0032774!RNA biosynthetic process!0.0380691710092592!1745;1746$GO:0003677!DNA binding!0.0380691710092592!1745;1746$GO:0045449!regulation of transcription!0.0380691710092592!1745;1746$GO:0019219!regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0380691710092592!1745;1746$GO:0006350!transcription!0.0380691710092592!1745;1746$GO:0032501!multicellular organismal process!0.0380691710092592!1745;1746$GO:0010468!regulation of gene expression!0.0380691710092592!1745;1746$GO:0045893!positive regulation of transcription, DNA-dependent!0.0380691710092592!1746$GO:0031323!regulation of cellular metabolic process!0.0380691710092592!1745;1746$GO:0007417!central nervous system development!0.0380691710092592!1746$GO:0019222!regulation of metabolic process!0.0380691710092592!1745;1746$GO:0016070!RNA metabolic process!0.0380691710092592!1745;1746$GO:0045941!positive regulation of transcription!0.0395310782558458!1746$GO:0045935!positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0395310782558458!1746$GO:0031325!positive regulation of cellular metabolic process!0.0478758800868458!1746$GO:0009893!positive regulation of metabolic 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|full_id=C1884_small_parietal_temporal_duodenum_occipital_rhabdomyosarcoma_acute
|id=C1884
}}

Latest revision as of 11:54, 17 September 2013


Full id: C1884_small_parietal_temporal_duodenum_occipital_rhabdomyosarcoma_acute



Phase1 CAGE Peaks

Hg19::chr2:172949484..172949522,+p1@DLX1
Hg19::chr2:172949532..172949541,+p6@DLX1
Hg19::chr2:172950053..172950081,-p@chr2:172950053..172950081
-
Hg19::chr2:172950227..172950249,+p2@DLX1
Hg19::chr2:172967621..172967637,-p1@DLX2


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:0043565sequence-specific DNA binding0.0329591072552472
GO:0003727single-stranded RNA binding0.0329591072552472
GO:0003700transcription factor activity0.0363204124571804
GO:0007275multicellular organismal development0.0380691710092592
GO:0003682chromatin binding0.0380691710092592
GO:0007420brain development0.0380691710092592
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.0380691710092592
GO:0032502developmental process0.0380691710092592
GO:0006355regulation of transcription, DNA-dependent0.0380691710092592
GO:0006351transcription, DNA-dependent0.0380691710092592
GO:0032774RNA biosynthetic process0.0380691710092592
GO:0003677DNA binding0.0380691710092592
GO:0045449regulation of transcription0.0380691710092592
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0380691710092592
GO:0006350transcription0.0380691710092592
GO:0032501multicellular organismal process0.0380691710092592
GO:0010468regulation of gene expression0.0380691710092592
GO:0045893positive regulation of transcription, DNA-dependent0.0380691710092592
GO:0031323regulation of cellular metabolic process0.0380691710092592
GO:0007417central nervous system development0.0380691710092592
GO:0019222regulation of metabolic process0.0380691710092592
GO:0016070RNA metabolic process0.0380691710092592
GO:0045941positive regulation of transcription0.0395310782558458
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0395310782558458
GO:0031325positive regulation of cellular metabolic process0.0478758800868458
GO:0009893positive regulation of metabolic process0.0492946969816967



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>

Cell Type
Ontology termp-valuen
neural cell6.13e-0825
skin fibroblast1.11e-0723
Uber Anatomy
Ontology termp-valuen
cerebral hemisphere7.35e-1632
regional part of telencephalon1.83e-1432
telencephalon2.81e-1434
cerebral cortex1.21e-1325
pallium1.21e-1325
regional part of cerebral cortex1.88e-1322
nervous system4.39e-1389
brain grey matter5.35e-1334
gray matter5.35e-1334
neocortex2.05e-1220
regional part of forebrain1.47e-1141
forebrain1.47e-1141
anterior neural tube1.47e-1141
future forebrain1.47e-1141
ectoderm-derived structure2.34e-11171
ectoderm2.34e-11171
presumptive ectoderm2.34e-11171
central nervous system3.53e-1181
brain2.16e-1068
future brain2.16e-1068
skin of body3.03e-0841
regional part of nervous system3.29e-0853
regional part of brain3.29e-0853
organ system subdivision3.58e-08223
neural tube3.16e-0756
neural rod3.16e-0756
future spinal cord3.16e-0756
neural keel3.16e-0756
Disease
Ontology termp-valuen
disease of cellular proliferation5.29e-20239
cancer8.74e-20235
cell type cancer6.71e-17143
carcinoma1.80e-08106
sarcoma2.01e-0720
disease of anatomical entity7.19e-0739


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)
MA0003.12.24383
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.660087
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.569896
MA0050.12.53085
MA0051.10.731787
MA0052.11.03442
MA0055.10.288856
MA0056.10
MA0057.11.05691
MA0058.10.523638
MA0059.10.522232
MA0060.13.25531
MA0061.10.791444
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.11.05325
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.412364
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.11.15584
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.11.16366
MA0103.11.12656
MA0105.10.520776
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.994489
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.759606
MA0140.10.692258
MA0141.11.29278
MA0142.10.912455
MA0143.10.797437
MA0144.11.67417
MA0145.10.868598
MA0146.10.946108
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.15493
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.839774
MA0065.20.880827
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.11.57192
MA0155.10.813062
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.0592265
MA0163.12.54221
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.21.81596
MA0102.21.66336
MA0258.10.914277
MA0259.10.395396
MA0442.10



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
CHD2#1106510.34402283411698.43981772346334e-060.000230262832607311
CTBP2#1488225.08680013573130.002461438599678380.0138515106369853
E2F1#186954.907389214879320.0003512818099256460.00353138135978675
E2F4#187437.600836189170660.004354147360375710.0206504153385531
E2F6#187655.017155731697390.0003144978599297790.00322999724586549
ETS1#211359.728760922202341.14685159850452e-050.000292279243768212
FOS#235335.398773185336640.01153895317278740.0421944865520377
HEY1#2346254.040111043105710.0009288852205177990.00674677262296811
HMGN3#932458.178547723350592.73180911341838e-050.000582378877314354
MAFK#7975210.8402932551320.01263683277337880.045689198158932
NFYA#4800311.05534841989830.001470892907644430.00941290345474732
NFYB#4801310.05587595212190.001938165606725460.0113885494430517
REST#597847.720022972902420.0005286363773650570.00457379294305602
SUZ12#23512220.04631236442520.003824075654154750.0188744157487839
TAL1#6886211.94744667097610.0104757781809920.0388081653463614
TBP#690853.706770687096390.001428755106721120.00919677994396594
TFAP2C#702236.485537165916130.006858951517940.0290628869515635
THAP1#55145318.82148676171080.0003085221948150010.00317549517140868
ZBTB33#10009212.66589001199250.009357016059651590.035341846597011
ZBTB7A#5134145.881527446300720.001524947561042230.0097159589023725



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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