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{{Coexpression_clusters
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|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:37, 17 September 2013


Full id: C1098_acute_teratocarcinoma_myelodysplastic_colon_adult_Mast_merkel



Phase1 CAGE Peaks

Hg19::chrX:80370321..80370336,-p@chrX:80370321..80370336
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Hg19::chrX:80370650..80370666,-p@chrX:80370650..80370666
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Hg19::chrX:80371754..80371768,-p@chrX:80371754..80371768
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Hg19::chrX:80373952..80373966,-p@chrX:80373952..80373966
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Hg19::chrX:80373978..80373996,-p@chrX:80373978..80373996
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Hg19::chrX:80377100..80377111,-p5@HMGN5
Hg19::chrX:80377118..80377149,-p1@HMGN5
Hg19::chrX:80377162..80377180,-p2@HMGN5


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><br>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
neural tube9.45e-1356
neural rod9.45e-1356
future spinal cord9.45e-1356
neural keel9.45e-1356
regional part of forebrain3.64e-1241
forebrain3.64e-1241
anterior neural tube3.64e-1241
future forebrain3.64e-1241
regional part of nervous system1.91e-1153
regional part of brain1.91e-1153
central nervous system6.53e-1181
nervous system8.60e-1189
brain grey matter8.30e-1034
gray matter8.30e-1034
neurectoderm1.02e-0986
pre-chordal neural plate7.50e-0961
regional part of telencephalon8.19e-0932
neural plate1.09e-0882
presumptive neural plate1.09e-0882
adult organism1.46e-08114
telencephalon2.05e-0834
brain2.06e-0868
future brain2.06e-0868
organ system subdivision6.76e-08223
ecto-epithelium7.31e-08104
cerebral hemisphere9.33e-0832
larynx1.45e-079
ectoderm-derived structure7.09e-07171
ectoderm7.09e-07171
presumptive ectoderm7.09e-07171
Disease
Ontology termp-valuen
hematologic cancer1.95e-1851
immune system cancer1.95e-1851
cancer2.79e-17235
disease of cellular proliferation7.13e-17239
leukemia9.48e-1639
myeloid leukemia5.93e-1231
organ system cancer2.60e-10137


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)
MA0003.10.0264723
MA0004.10.455723
MA0006.10.300178
MA0007.12.90631
MA0009.12.12026
MA0014.10.00962431
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.315574
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.10.0955945
MA0050.10.443405
MA0051.11.36251
MA0052.10.842664
MA0055.10.118169
MA0056.10
MA0057.10.0912556
MA0058.10.362328
MA0059.10.361075
MA0060.10.556724
MA0061.10.165998
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.133123
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.19.20286e-05
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.054222
MA0089.10
MA0090.10.391903
MA0091.11.16006
MA0092.10.421159
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.30624
MA0103.10.291333
MA0105.10.0818021
MA0106.10.59853
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.11.49247
MA0114.10.231781
MA0115.11.1606
MA0116.10.239768
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.155155
MA0140.10.516266
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.10.218541
MA0145.10.0613434
MA0146.10.00761723
MA0147.10.243042
MA0148.11.20731
MA0149.10.506665
MA0062.20.161302
MA0035.20.515566
MA0039.20.0325944
MA0138.20.653421
MA0002.20.179788
MA0137.20.321796
MA0104.20.189646
MA0047.20.586412
MA0112.20.0572179
MA0065.20.0631316
MA0150.10.386144
MA0151.10
MA0152.14.44584
MA0153.12.32222
MA0154.10.0799828
MA0155.10.0535085
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.10.243637
MA0160.10.495355
MA0161.10
MA0162.10.0163939
MA0163.10.0104024
MA0164.10.627336
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.21.41562e-07
MA0102.21.46209
MA0258.10.209744
MA0259.10.25092
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
IRF3#3661317.61823207930860.0004979994386673570.00440096153113726
MAFF#23764321.11825868372940.0002930101691141860.00310803260736507
MAFK#7975310.16277492668620.002445573107139520.0137689061852585
NFYA#480036.909592762436450.007279727237130680.0301235164990171
NFYB#480136.284922470076170.009473769012482620.0356976210230066
PBX3#509038.217942257529050.004473206582808440.0211679756366983
SP2#666839.807573935191740.002707184665085610.014887876322304



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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