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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 11:29, 17 September 2013


Full id: C740_gastrointestinal_smallcell_small_nonsmall_neuroblastoma_temporal_somatostatinoma



Phase1 CAGE Peaks

Hg19::chr11:60466937..60466947,+p6@MS4A8B
Hg19::chr12:103351444..103351461,+p1@ASCL1
Hg19::chr12:103351694..103351704,+p6@ASCL1
Hg19::chr12:103352731..103352740,+p@chr12:103352731..103352740
+
Hg19::chr12:103353138..103353168,+p@chr12:103353138..103353168
+
Hg19::chr12:103353295..103353316,-p@chr12:103353295..103353316
-
Hg19::chr12:103353566..103353596,+p@chr12:103353566..103353596
+
Hg19::chr16:67219381..67219395,-p@chr16:67219381..67219395
-
Hg19::chr17:17421463..17421482,-p5@PEMT
Hg19::chr19:13743837..13743844,-p@chr19:13743837..13743844
-
Hg19::chr1:246383189..246383211,-p@chr1:246383189..246383211
-


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:0060163subpallium neuron fate commitment0.00152646717464803
GO:0014017neuroblast fate commitment0.00152646717464803
GO:0014016neuroblast differentiation0.00152646717464803
GO:0007400neuroblast fate determination0.00152646717464803
GO:0060165regulation of timing of subpallium neuron differentiation0.00152646717464803
GO:0060164regulation of timing of neuron differentiation0.00152646717464803
GO:0004608phosphatidylethanolamine N-methyltransferase activity0.00152646717464803
GO:0021544subpallium development0.00400674043006203
GO:0048505regulation of timing of cell differentiation0.00427373064729577
GO:0040034regulation of development, heterochronic0.00427373064729577
GO:0006656phosphatidylcholine biosynthetic process0.00485636913446346
GO:0046470phosphatidylcholine metabolic process0.00623197345720764
GO:0021537telencephalon development0.0090387212307888
GO:0048663neuron fate commitment0.0106811816718229
GO:0008283cell proliferation0.0113477532025367
GO:0007405neuroblast proliferation0.0113477532025367
GO:0045664regulation of neuron differentiation0.0162956577304724
GO:0010001glial cell differentiation0.0162956577304724
GO:0001709cell fate determination0.0162956577304724
GO:0042063gliogenesis0.0182987399358394
GO:0001764neuron migration0.0182987399358394
GO:0030900forebrain development0.0213397299517958
GO:0046474glycerophospholipid biosynthetic process0.0213397299517958
GO:0008170N-methyltransferase activity0.0213397299517958
GO:0007219Notch signaling pathway0.0213397299517958
GO:0045165cell fate commitment0.0291189221451797
GO:0008757S-adenosylmethionine-dependent methyltransferase activity0.0339494755587485
GO:0008654phospholipid biosynthetic process0.0350147803328724
GO:0006650glycerophospholipid metabolic process0.0371047763843612
GO:0046467membrane lipid biosynthetic process0.0401153013644764
GO:0007389pattern specification process0.0425865120099492
GO:0007420brain development0.0462258483643068
GO:0045595regulation of cell differentiation0.0464306336375757
GO:0048666neuron development0.0481803368997648



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
circulating cell2.77e-076
Uber Anatomy
Ontology termp-valuen
neural tube1.07e-3056
neural rod1.07e-3056
future spinal cord1.07e-3056
neural keel1.07e-3056
central nervous system1.19e-2381
regional part of nervous system1.51e-2353
regional part of brain1.51e-2353
nervous system6.35e-2389
neural plate1.77e-2182
presumptive neural plate1.77e-2182
neurectoderm3.06e-2086
brain3.46e-1968
future brain3.46e-1968
regional part of forebrain4.04e-1941
forebrain4.04e-1941
anterior neural tube4.04e-1941
future forebrain4.04e-1941
ecto-epithelium1.49e-17104
telencephalon1.21e-1434
spinal cord3.45e-143
dorsal region element3.45e-143
dorsum3.45e-143
pre-chordal neural plate1.11e-1361
posterior neural tube3.04e-1315
chordal neural plate3.04e-1315
regional part of cerebral cortex3.10e-1322
regional part of telencephalon3.84e-1332
cerebral hemisphere3.84e-1332
adult organism1.26e-12114
brain grey matter2.88e-1234
gray matter2.88e-1234
neocortex1.49e-1120
cerebral cortex1.58e-1125
pallium1.58e-1125
ectoderm-derived structure1.64e-11171
ectoderm1.64e-11171
presumptive ectoderm1.64e-11171
structure with developmental contribution from neural crest2.13e-11132
organ system subdivision5.90e-11223
pituitary gland4.34e-102
tube5.52e-08192
brainstem7.58e-076
gyrus7.73e-076


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)
MA0003.10.0148593
MA0004.10.349539
MA0006.11.78527
MA0007.10.332734
MA0009.10.79061
MA0014.10.21986
MA0017.10.682686
MA0019.10.486183
MA0024.10.688373
MA0025.10.921763
MA0027.12.39404
MA0028.10.224112
MA0029.10.707146
MA0030.10.696006
MA0031.10.633489
MA0038.10.443833
MA0040.10.712837
MA0041.10.366339
MA0042.10.337481
MA0043.10.790919
MA0046.10.779945
MA0048.10.185335
MA0050.10.897608
MA0051.10.439895
MA0052.10.716602
MA0055.10.736537
MA0056.10
MA0057.10.703296
MA0058.10.265212
MA0059.10.2641
MA0060.10.119532
MA0061.10.100525
MA0063.10
MA0066.11.12972
MA0067.11.1037
MA0068.10.262497
MA0069.10.776171
MA0070.10.765217
MA0071.10.40788
MA0072.10.760818
MA0073.10.0865376
MA0074.10.439193
MA0076.10.278993
MA0077.10.753278
MA0078.10.533387
MA0081.10.26424
MA0083.10.79797
MA0084.11.28962
MA0087.10.758426
MA0088.10.10094
MA0089.10
MA0090.10.291627
MA0091.10.351901
MA0092.10.318032
MA0093.10.213288
MA0095.10
MA0098.10
MA0100.10.456802
MA0101.10.216017
MA0103.10.203171
MA0105.10.0403209
MA0106.10.482519
MA0107.10.156959
MA0108.20.630531
MA0109.10
MA0111.10.819774
MA0113.11.2452
MA0114.10.465415
MA0115.11.02805
MA0116.10.935607
MA0117.10.827487
MA0119.10.698186
MA0122.10.852927
MA0124.10.98702
MA0125.10.904129
MA0130.10
MA0131.10.550695
MA0132.10
MA0133.10
MA0135.10.820382
MA0136.10.450422
MA0139.10.307853
MA0140.10.405425
MA0141.10.2626
MA0142.10.602852
MA0143.10.498176
MA0144.10.438224
MA0145.10.277793
MA0146.10.0381286
MA0147.10.162359
MA0148.11.72853
MA0149.11.02604
MA0062.20.0969238
MA0035.20.404774
MA0039.20.0468759
MA0138.20.534556
MA0002.20.111226
MA0137.20.229531
MA0104.20.378829
MA0047.21.18756
MA0112.20.260758
MA0065.20.11899
MA0150.10.286461
MA0151.10
MA0152.10.411494
MA0153.10.887528
MA0154.10.0391503
MA0155.10.099499
MA0156.10.231442
MA0157.10.576556
MA0158.10
MA0159.10.162854
MA0160.10.386031
MA0161.10
MA0162.10.0266618
MA0163.10.232847
MA0164.10.509774
MA0080.20.21336
MA0018.20.483823
MA0099.21.05945
MA0079.20.492463
MA0102.21.32663
MA0258.10.420151
MA0259.10.504687
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
CTBP2#1488211.40309097078690.01270370609783190.0458357756218981
SPI1#668853.729237958419420.006571397692282440.0280848796326998
SUZ12#23512418.22392033129564.66826240794143e-050.000816664418128969



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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