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Coexpression cluster:C1313: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;3.55314,MA0004.1;0.558729,MA0006.1;0.391183,MA0007.1;2.2901,MA0009.1;1.03681,MA0014.1;3.10532,MA0017.1;2.88372,MA0019.1;0.7124,MA0024.1;0.929647,MA0025.1;1.17262,MA0027.1;5.61447,MA0028.1;0.408079,MA0029.1;0.949428,MA0030.1;0.937696,MA0031.1;0.871496,MA0038.1;0.665566,MA0040.1;0.955415,MA0041.1;0.578072,MA0042.1;0.544748,MA0043.1;1.03713,MA0046.1;1.02569,MA0048.1;2.79473,MA0050.1;0.545671,MA0051.1;0.661179,MA0052.1;0.959373,MA0055.1;0.465994,MA0056.1;0,MA0057.1;0.450439,MA0058.1;0.458909,MA0059.1;0.457555,MA0060.1;0.267412,MA0061.1;0.23892,MA0063.1;0,MA0066.1;0.66601,MA0067.1;1.35893,MA0068.1;0.199491,MA0069.1;1.02175,MA0070.1;1.01032,MA0071.1;0.625297,MA0072.1;1.00572,MA0073.1;3.04208,MA0074.1;0.660398,MA0076.1;0.475586,MA0077.1;0.997832,MA0078.1;0.763954,MA0081.1;0.457725,MA0083.1;1.04447,MA0084.1;1.5477,MA0087.1;1.00322,MA0088.1;1.09824,MA0089.1;0,MA0090.1;0.490736,MA0091.1;1.37996,MA0092.1;0.522012,MA0093.1;0.394379,MA0095.1;0,MA0098.1;0,MA0100.1;0.679972,MA0101.1;1.81721,MA0103.1;0.381434,MA0105.1;0.419295,MA0106.1;5.46746,MA0107.1;0.857383,MA0108.2;0.868347,MA0109.1;0,MA0111.1;0.504913,MA0113.1;1.72264,MA0114.1;2.32368,MA0115.1;1.28169,MA0116.1;1.55935,MA0117.1;1.07516,MA0119.1;1.12205,MA0122.1;2.49233,MA0124.1;1.23968,MA0125.1;1.15445,MA0130.1;0,MA0131.1;0.782708,MA0132.1;0,MA0133.1;0,MA0135.1;1.06778,MA0136.1;0.672893,MA0139.1;1.19942,MA0140.1;0.622527,MA0141.1;0.455728,MA0142.1;0.838805,MA0143.1;0.725558,MA0144.1;0.299851,MA0145.1;0.107156,MA0146.1;0.441872,MA0147.1;0.327615,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;0.23336,MA0035.2;0.621793,MA0039.2;8.11431,MA0138.2;0.765223,MA0002.2;0.255126,MA0137.2;0.414885,MA0104.2;0.26661,MA0047.2;0.695777,MA0112.2;0.101413,MA0065.2;3.77022,MA0150.1;1.21643,MA0151.1;0,MA0152.1;0.629368,MA0153.1;1.13732,MA0154.1;2.59196,MA0155.1;11.6682,MA0156.1;0.417278,MA0157.1;0.810597,MA0158.1;0,MA0159.1;2.38949,MA0160.1;0.600559,MA0161.1;0,MA0162.1;4.94781,MA0163.1;4.41596,MA0164.1;0.738243,MA0080.2;0.394469,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;29.0454,MA0102.2;1.58513,MA0258.1;0.289793,MA0259.1;0.893594,MA0442.1;0
}}
}}

Revision as of 19:50, 22 January 2013


Full id: C1313_Placental_mesothelioma_amniotic_neuroectodermal_renal_chorionic_carcinosarcoma



Phase1 CAGE Peaks

Hg19::chr10:50817847..50817867,+p4@SLC18A3
Hg19::chr10:50818275..50818286,+p6@SLC18A3
Hg19::chr10:50818288..50818298,+p5@SLC18A3
Hg19::chr10:50818343..50818362,+p2@SLC18A3
Hg19::chr10:50818377..50818400,+p1@SLC18A3
Hg19::chr10:50818416..50818427,+p3@SLC18A3


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>disease_data<br>

Cell Type
Ontology termp-valuen
extraembryonic cell2.46e-1819
placental epithelial cell5.11e-153
amniotic epithelial cell1.03e-092
amnion mesenchymal stem cell3.33e-095
Uber Anatomy
Ontology termp-valuen
extraembryonic membrane1.73e-2514
membranous layer1.73e-2514
neural nucleus1.85e-229
nucleus of brain1.85e-229
brainstem3.42e-186
amnion2.30e-167
telencephalic nucleus7.79e-157
sympathetic nervous system1.63e-145
autonomic nervous system1.63e-145
ectoderm-derived structure1.86e-14171
ectoderm1.86e-14171
presumptive ectoderm1.86e-14171
somatic layer of lateral plate mesoderm2.77e-148
extraembryonic structure3.67e-1424
pons1.04e-133
posterior neural tube1.91e-1315
chordal neural plate1.91e-1315
neurectoderm1.92e-1386
nervous system1.76e-1289
basal ganglion1.72e-119
nuclear complex of neuraxis1.72e-119
aggregate regional part of brain1.72e-119
collection of basal ganglia1.72e-119
cerebral subcortex1.72e-119
placenta2.25e-114
allantois2.25e-114
chorion4.54e-117
locus ceruleus4.81e-102
brainstem nucleus4.81e-102
hindbrain nucleus4.81e-102
neural tube5.62e-1056
neural rod5.62e-1056
future spinal cord5.62e-1056
neural keel5.62e-1056
corpus striatum6.27e-104
striatum6.27e-104
ventral part of telencephalon6.27e-104
future corpus striatum6.27e-104
globus pallidus1.66e-092
pallidum1.66e-092
segmental subdivision of hindbrain5.73e-0912
hindbrain5.73e-0912
presumptive hindbrain5.73e-0912
central nervous system2.69e-0881
neural plate2.80e-0882
presumptive neural plate2.80e-0882
segmental subdivision of nervous system2.96e-0813
peripheral nervous system4.27e-088
organ part1.35e-07218
regional part of nervous system1.81e-0753
regional part of brain1.81e-0753
medulla oblongata7.17e-073
myelencephalon7.17e-073
future myelencephalon7.17e-073
spinal cord9.33e-073
dorsal region element9.33e-073
dorsum9.33e-073
Disease
Ontology termp-valuen
neuroectodermal tumor2.10e-2710
neuroendocrine tumor4.11e-126
germ cell and embryonal cancer9.43e-1222
germ cell cancer9.43e-1222


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)
MA0003.13.55314
MA0004.10.558729
MA0006.10.391183
MA0007.12.2901
MA0009.11.03681
MA0014.13.10532
MA0017.12.88372
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.15.61447
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.12.79473
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.465994
MA0056.10
MA0057.10.450439
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.13.04208
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.11.09824
MA0089.10
MA0090.10.490736
MA0091.11.37996
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.11.81721
MA0103.10.381434
MA0105.10.419295
MA0106.15.46746
MA0107.10.857383
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.11.72264
MA0114.12.32368
MA0115.11.28169
MA0116.11.55935
MA0117.11.07516
MA0119.11.12205
MA0122.12.49233
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.11.19942
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.107156
MA0146.10.441872
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.28.11431
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.101413
MA0065.23.77022
MA0150.11.21643
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.12.59196
MA0155.111.6682
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.12.38949
MA0160.10.600559
MA0161.10
MA0162.14.94781
MA0163.14.41596
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.229.0454
MA0102.21.58513
MA0258.10.289793
MA0259.10.893594
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

No analysis results for this cluster

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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C1313&oldid=2569824"