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Coexpression cluster:C3681: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;0.708947,MA0004.1;0.826076,MA0006.1;1.5435,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;0.377374,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;1.21731,MA0025.1;1.46617,MA0027.1;2.95767,MA0028.1;0.658629,MA0029.1;1.23771,MA0030.1;1.22561,MA0031.1;1.15713,MA0038.1;0.94098,MA0040.1;1.24388,MA0041.1;0.847069,MA0042.1;0.810843,MA0043.1;1.32783,MA0046.1;1.31611,MA0048.1;5.4446,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;3.15032,MA0056.1;0,MA0057.1;0.886807,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;0.492218,MA0061.1;0.456531,MA0063.1;0,MA0066.1;0.941452,MA0067.1;1.65513,MA0068.1;0.405474,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;0.668628,MA0074.1;0.935474,MA0076.1;0.734647,MA0077.1;1.28751,MA0078.1;1.04495,MA0081.1;0.714712,MA0083.1;1.33535,MA0084.1;1.84562,MA0087.1;1.29304,MA0088.1;0.715722,MA0089.1;0,MA0090.1;0.751469,MA0091.1;0.829044,MA0092.1;0.785956,MA0093.1;0.642957,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;0.646932,MA0103.1;0.628063,MA0105.1;0.31555,MA0106.1;0.986396,MA0107.1;0.556367,MA0108.2;1.15387,MA0109.1;0,MA0111.1;0.767139,MA0113.1;1.00436,MA0114.1;1.35563,MA0115.1;1.57693,MA0116.1;0.560723,MA0117.1;1.36676,MA0119.1;0.695578,MA0122.1;1.39371,MA0124.1;1.53432,MA0125.1;1.44766,MA0130.1;0,MA0131.1;1.06461,MA0132.1;0,MA0133.1;0,MA0135.1;1.35921,MA0136.1;0.948776,MA0139.1;0.440097,MA0140.1;0.894983,MA0141.1;1.6959,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;4.49708,MA0145.1;0.273764,MA0146.1;0.107247,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;2.07011,MA0039.2;0.195278,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;1.60005,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;0.264678,MA0065.2;1.39232,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.312019,MA0155.1;0.256269,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.149099,MA0163.1;1.84145,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.69213,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0
}}
}}

Revision as of 21:32, 22 January 2013


Full id: C3681_neuroblastoma_optic_teratocarcinoma_substantia_diencephalon_corpus_globus



Phase1 CAGE Peaks

Hg19::chr17:74540323..74540336,+p6@PRCD
Hg19::chr17:74540344..74540355,+p8@PRCD
Hg19::chr17:74540357..74540388,+p1@PRCD


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 tube3.05e-7256
neural rod3.05e-7256
future spinal cord3.05e-7256
neural keel3.05e-7256
neurectoderm3.24e-6586
regional part of nervous system1.56e-6353
regional part of brain1.56e-6353
nervous system2.15e-6289
neural plate3.96e-6282
presumptive neural plate3.96e-6282
brain4.97e-5768
future brain4.97e-5768
central nervous system6.43e-5681
regional part of forebrain2.02e-5041
forebrain2.02e-5041
anterior neural tube2.02e-5041
future forebrain2.02e-5041
ecto-epithelium1.27e-49104
brain grey matter4.00e-4734
gray matter4.00e-4734
telencephalon4.00e-4734
pre-chordal neural plate9.44e-4761
regional part of telencephalon1.83e-4132
cerebral hemisphere3.52e-4132
ectoderm-derived structure1.77e-38171
ectoderm1.77e-38171
presumptive ectoderm1.77e-38171
adult organism3.12e-38114
structure with developmental contribution from neural crest3.41e-37132
regional part of cerebral cortex1.86e-3022
neocortex4.01e-2920
cerebral cortex1.61e-2625
pallium1.61e-2625
neural nucleus3.23e-249
nucleus of brain3.23e-249
posterior neural tube4.34e-2215
chordal neural plate4.34e-2215
organ system subdivision1.13e-21223
brainstem2.11e-216
basal ganglion2.46e-189
nuclear complex of neuraxis2.46e-189
aggregate regional part of brain2.46e-189
collection of basal ganglia2.46e-189
cerebral subcortex2.46e-189
telencephalic nucleus6.36e-187
tube3.19e-17192
segmental subdivision of nervous system1.09e-1613
cell layer2.09e-14309
gyrus2.40e-146
segmental subdivision of hindbrain8.31e-1412
hindbrain8.31e-1412
presumptive hindbrain8.31e-1412
epithelium9.30e-14306
anatomical conduit5.38e-12240
anatomical cluster7.98e-12373
medulla oblongata1.24e-113
myelencephalon1.24e-113
future myelencephalon1.24e-113
pons1.65e-113
spinal cord1.71e-113
dorsal region element1.71e-113
dorsum1.71e-113
occipital lobe1.79e-115
organ part6.01e-11218
multi-tissue structure1.21e-09342
retina2.31e-096
photoreceptor array2.31e-096
posterior segment of eyeball2.31e-096
multi cell component structure9.24e-092
neuron projection bundle9.24e-092
dorsal plus ventral thalamus9.95e-092
thalamic complex9.95e-092
globus pallidus1.44e-082
pallidum1.44e-082
corpus striatum3.50e-084
striatum3.50e-084
ventral part of telencephalon3.50e-084
future corpus striatum3.50e-084
locus ceruleus4.12e-082
brainstem nucleus4.12e-082
hindbrain nucleus4.12e-082
temporal lobe4.67e-086
middle temporal gyrus5.29e-082
sympathetic nervous system1.24e-075
autonomic nervous system1.24e-075
germ layer1.52e-07560
germ layer / neural crest1.52e-07560
embryonic tissue1.52e-07560
presumptive structure1.52e-07560
germ layer / neural crest derived structure1.52e-07560
epiblast (generic)1.52e-07560
embryonic structure2.08e-07564
peripheral nervous system3.98e-078
developing anatomical structure7.63e-07581
parietal lobe9.70e-075
Disease
Ontology termp-valuen
neuroectodermal tumor4.85e-0910


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)
MA0003.10.708947
MA0004.10.826076
MA0006.11.5435
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
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
MA0048.15.4446
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.13.15032
MA0056.10
MA0057.10.886807
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
MA0073.10.668628
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
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
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.11.35563
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
MA0141.11.6959
MA0142.11.12317
MA0143.11.00455
MA0144.14.49708
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.22.07011
MA0039.20.195278
MA0138.21.04628
MA0002.20.476938
MA0137.21.60005
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.21.39232
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.11.84145
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.69213
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
EP300#203336.77394172622320.003216880500103790.0167356305130929
GATA2#2624312.7449317335540.0004829527704283790.00436777835043034
RAD21#5885310.35503389545630.0009004912073565420.00663513483879708
YY1#752834.911170749853860.008441455341808260.0329010730871441



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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