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{{Coexpression_clusters
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|full_id=C4835_rhabdomyosarcoma_rectum_colon_stomach_duodenum_small_testis
|id=C4835
|ontology_enrichment_celltype=
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}}

Latest revision as of 14:20, 17 September 2013


Full id: C4835_rhabdomyosarcoma_rectum_colon_stomach_duodenum_small_testis



Phase1 CAGE Peaks

Hg19::chr9:98279050..98279078,-p4@PTCH1
Hg19::chr9:98279086..98279094,-p15@PTCH1
Hg19::chr9:98279099..98279113,-p11@PTCH1


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>

Cell Type
Ontology termp-valuen
embryonic stem cell6.50e-095
Uber Anatomy
Ontology termp-valuen
neural tube1.87e-2056
neural rod1.87e-2056
future spinal cord1.87e-2056
neural keel1.87e-2056
regional part of nervous system1.42e-1853
regional part of brain1.42e-1853
adult organism1.54e-15114
nervous system1.59e-1589
brain8.63e-1568
future brain8.63e-1568
central nervous system1.70e-1481
brain grey matter6.10e-1434
gray matter6.10e-1434
neurectoderm9.90e-1486
telencephalon1.06e-1334
neural plate1.23e-1382
presumptive neural plate1.23e-1382
cerebral hemisphere2.77e-1332
regional part of cerebral cortex1.68e-1222
gastrointestinal system2.23e-1225
intestine2.45e-1217
neocortex4.37e-1220
regional part of forebrain7.82e-1241
forebrain7.82e-1241
anterior neural tube7.82e-1241
future forebrain7.82e-1241
regional part of telencephalon8.09e-1232
organ system subdivision1.63e-11223
posterior neural tube8.71e-1115
chordal neural plate8.71e-1115
cerebral cortex1.19e-1025
pallium1.19e-1025
brainstem2.64e-106
ecto-epithelium8.04e-10104
large intestine4.46e-0911
segmental subdivision of hindbrain8.11e-0912
hindbrain8.11e-0912
presumptive hindbrain8.11e-0912
segmental subdivision of nervous system5.06e-0813
lower digestive tract2.41e-075
pre-chordal neural plate2.42e-0761
small intestine6.23e-074
temporal lobe8.54e-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)
MA0003.13.8806
MA0004.13.20493
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.758317
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.12.74347
MA0031.12.60497
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.14.13609
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.12.0778
MA0072.11.29561
MA0073.10.668628
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.11.31954
MA0089.10
MA0090.11.77664
MA0091.10.829044
MA0092.10.785956
MA0093.13.82193
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.11.5295
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.12.26598
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.13.29283
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.432958
MA0138.21.04628
MA0002.20.476938
MA0137.21.60005
MA0104.20.491226
MA0047.23.66129
MA0112.20.731309
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.12.47657
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.8915
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.21.54885
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
ATF3#467322.46317452600878.81932387510763e-050.00130114615933376
CCNT2#90536.336201576962630.003930750035764890.0191430917689554
CHD2#1106310.34402283411690.0009033701102746880.00663248301911973
E2F6#187635.017155731697390.00791769806886330.0324803200681101
ELF1#199734.258097958807540.01295179875054610.0465427832539064
FOXA1#3169311.08141974938550.000734755275698670.00584975653595772
FOXA2#3170324.63046375266526.68983856509345e-050.00107787727537765
MAX#414936.452555509007120.003721913834265510.0187629945907639
TAL1#6886329.86861667744023.75103522793067e-050.000723595064960936
USF1#739136.361499277207960.00388404057290560.0191396297722793
USF2#7392312.99219738506960.0004558979393427810.00423494840229661



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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