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Coexpression cluster:C3112: Difference between revisions

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{{Coexpression_clusters
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|full_id=C3112_rhabdomyosarcoma_retina_occipital_Fibroblast_skeletal_Melanocyte_insula
|id=C3112
}}

Latest revision as of 12:19, 17 September 2013


Full id: C3112_rhabdomyosarcoma_retina_occipital_Fibroblast_skeletal_Melanocyte_insula



Phase1 CAGE Peaks

Hg19::chr11:125034586..125034604,+p3@PKNOX2
Hg19::chr11:125034605..125034636,+p2@PKNOX2
Hg19::chr11:125034640..125034655,+p1@PKNOX2


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>

Uber Anatomy
Ontology termp-valuen
central nervous system1.21e-4081
nervous system1.31e-3989
adult organism3.41e-37114
brain9.82e-3668
future brain9.82e-3668
neural tube1.53e-3456
neural rod1.53e-3456
future spinal cord1.53e-3456
neural keel1.53e-3456
regional part of nervous system8.10e-3353
regional part of brain8.10e-3353
neurectoderm3.32e-3186
neural plate4.25e-3182
presumptive neural plate4.25e-3182
structure with developmental contribution from neural crest1.64e-26132
anatomical cluster2.73e-26373
regional part of forebrain3.26e-2541
forebrain3.26e-2541
anterior neural tube3.26e-2541
future forebrain3.26e-2541
ectoderm-derived structure4.64e-24171
ectoderm4.64e-24171
presumptive ectoderm4.64e-24171
telencephalon2.73e-2334
brain grey matter4.08e-2334
gray matter4.08e-2334
ecto-epithelium8.52e-23104
cerebral hemisphere1.16e-2232
multi-tissue structure3.13e-22342
organ system subdivision4.02e-22223
regional part of telencephalon4.39e-2232
cell layer3.54e-21309
pre-chordal neural plate4.72e-2161
epithelium1.11e-20306
tube2.18e-19192
cerebral cortex7.81e-1925
pallium7.81e-1925
regional part of cerebral cortex7.51e-1822
neocortex9.13e-1720
anatomical conduit5.57e-16240
germ layer4.45e-14560
germ layer / neural crest4.45e-14560
embryonic tissue4.45e-14560
presumptive structure4.45e-14560
germ layer / neural crest derived structure4.45e-14560
epiblast (generic)4.45e-14560
embryonic structure6.84e-14564
embryo7.16e-14592
developing anatomical structure5.99e-13581
muscle tissue8.10e-1364
musculature8.10e-1364
musculature of body8.10e-1364
skeletal muscle tissue2.19e-1262
striated muscle tissue2.19e-1262
myotome2.19e-1262
multi-cellular organism4.60e-12656
posterior neural tube2.39e-1015
chordal neural plate2.39e-1015
anatomical system1.81e-09624
paraxial mesoderm1.83e-0972
presumptive paraxial mesoderm1.83e-0972
anatomical group2.55e-09625
dense mesenchyme tissue4.30e-0973
somite5.33e-0971
presomitic mesoderm5.33e-0971
presumptive segmental plate5.33e-0971
dermomyotome5.33e-0971
trunk paraxial mesoderm5.33e-0971
primary circulatory organ7.19e-0927
segmental subdivision of nervous system7.61e-0913
organ part7.77e-09218
segmental subdivision of hindbrain9.22e-0912
hindbrain9.22e-0912
presumptive hindbrain9.22e-0912
heart2.06e-0824
primitive heart tube2.06e-0824
primary heart field2.06e-0824
anterior lateral plate mesoderm2.06e-0824
heart tube2.06e-0824
heart primordium2.06e-0824
cardiac mesoderm2.06e-0824
cardiogenic plate2.06e-0824
heart rudiment2.06e-0824
epithelial vesicle1.47e-0778
splanchnic layer of lateral plate mesoderm2.04e-0783
organ4.06e-07503
regional part of metencephalon4.85e-079
metencephalon4.85e-079
future metencephalon4.85e-079
multilaminar epithelium6.15e-0783


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)
MA0003.10.401049
MA0004.10.826076
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
MA0030.11.22561
MA0031.11.15713
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
MA0055.11.06172
MA0056.10
MA0057.12.4146
MA0058.10.716037
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
MA0071.10.897953
MA0072.11.29561
MA0073.125.9278
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
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
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
MA0139.11.96087
MA0140.10.894983
MA0141.10.712476
MA0142.12.53618
MA0143.11.00455
MA0144.11.31729
MA0145.10.273764
MA0146.10.707589
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.23.37171
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.13.71118
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.8915
MA0163.112.6211
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.29.48295
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
CTBP2#1488362.71700033932814.049570681927e-060.00012906106574604
CTCF#1066435.360256373075030.0064925092527670.0278320064790762
CTCFL#140690319.74647435897440.0001298372005551160.00171126544532759
PBX3#5090321.91451268674419.49854535978121e-050.00136023389391223
RAD21#5885310.35503389545630.0009004912073565420.00661879099198465
ZBTB7A#5134137.35190930787590.002516255860282270.0139606484164906



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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