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Coexpression cluster:C2542: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;0.233555,MA0004.1;0.71247,MA0006.1;1.31813,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;1.86845,MA0017.1;0.577281,MA0019.1;0.873355,MA0024.1;1.09684,MA0025.1;1.34373,MA0027.1;2.83281,MA0028.1;0.550763,MA0029.1;1.11704,MA0030.1;1.10506,MA0031.1;1.03735,MA0038.1;0.824639,MA0040.1;1.12314,MA0041.1;0.732902,MA0042.1;0.697662,MA0043.1;1.20635,MA0046.1;1.19471,MA0048.1;0.25531,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.791759,MA0056.1;0,MA0057.1;0.248209,MA0058.1;0.605914,MA0059.1;0.604454,MA0060.1;0.393285,MA0061.1;0.360128,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;0.841508,MA0069.1;4.32878,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;2.83685,MA0074.1;0.819248,MA0076.1;0.623864,MA0077.1;2.62367,MA0078.1;0.926725,MA0081.1;0.604638,MA0083.1;1.21381,MA0084.1;1.72172,MA0087.1;1.17185,MA0088.1;0.182167,MA0089.1;0,MA0090.1;0.640115,MA0091.1;4.13319,MA0092.1;0.673508,MA0093.1;0.535768,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;0.539569,MA0103.1;0.521546,MA0105.1;0.232357,MA0106.1;0.869173,MA0107.1;0.453492,MA0108.2;1.03412,MA0109.1;0,MA0111.1;1.57689,MA0113.1;0.886811,MA0114.1;0.447443,MA0115.1;1.45393,MA0116.1;1.15856,MA0117.1;1.24497,MA0119.1;0.586221,MA0122.1;1.27173,MA0124.1;1.41151,MA0125.1;1.32534,MA0130.1;0,MA0131.1;0.94608,MA0132.1;0,MA0133.1;0,MA0135.1;1.23748,MA0136.1;0.832277,MA0139.1;0.344952,MA0140.1;0.779643,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;0.569905,MA0146.1;1.75643,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;0.483275,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;0.392359,MA0047.2;0.856092,MA0112.2;0.187982,MA0065.2;0.577908,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.229241,MA0155.1;0.533581,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;0.309472,MA0163.1;0.918944,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;2.00408,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0
}}
}}

Revision as of 20:44, 22 January 2013


Full id: C2542_cerebellum_neuroblastoma_retinoblastoma_pineal_parietal_medulloblastoma_small



Phase1 CAGE Peaks

Hg19::chr1:180897209..180897230,+p8@KIAA1614
Hg19::chr1:180897243..180897261,+p9@KIAA1614
Hg19::chr1:180897269..180897295,+p6@KIAA1614
Hg19::chr8:9764421..9764432,+p@chr8:9764421..9764432
+


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
neural cell8.13e-0925
neuronal stem cell8.33e-098
neurectodermal cell4.37e-0759
Uber Anatomy
Ontology termp-valuen
nervous system2.70e-7189
central nervous system5.62e-7081
regional part of nervous system3.35e-6553
regional part of brain3.35e-6553
brain1.40e-6368
future brain1.40e-6368
neural tube3.15e-6156
neural rod3.15e-6156
future spinal cord3.15e-6156
neural keel3.15e-6156
regional part of forebrain3.41e-5141
forebrain3.41e-5141
anterior neural tube3.41e-5141
future forebrain3.41e-5141
neurectoderm1.06e-4886
neural plate1.82e-4682
presumptive neural plate1.82e-4682
telencephalon6.75e-4634
brain grey matter9.15e-4634
gray matter9.15e-4634
cerebral hemisphere1.63e-4132
regional part of telencephalon3.20e-4132
pre-chordal neural plate5.20e-4061
ectoderm-derived structure7.43e-40171
ectoderm7.43e-40171
presumptive ectoderm7.43e-40171
regional part of cerebral cortex2.71e-3822
neocortex9.11e-3820
ecto-epithelium1.17e-36104
cerebral cortex2.72e-3325
pallium2.72e-3325
adult organism7.25e-29114
structure with developmental contribution from neural crest1.41e-26132
organ system subdivision3.49e-26223
parietal lobe1.23e-155
segmental subdivision of hindbrain1.22e-1412
hindbrain1.22e-1412
presumptive hindbrain1.22e-1412
neural nucleus9.81e-149
nucleus of brain9.81e-149
segmental subdivision of nervous system2.12e-1313
tube5.47e-13192
gyrus8.39e-136
anatomical cluster1.21e-12373
regional part of metencephalon1.60e-119
metencephalon1.60e-119
future metencephalon1.60e-119
brainstem1.74e-116
posterior neural tube2.03e-1115
chordal neural plate2.03e-1115
temporal lobe2.16e-106
basal ganglion3.79e-109
nuclear complex of neuraxis3.79e-109
aggregate regional part of brain3.79e-109
collection of basal ganglia3.79e-109
cerebral subcortex3.79e-109
occipital lobe6.50e-105
telencephalic nucleus2.57e-097
anatomical conduit3.12e-09240
organ part7.47e-09218
pons8.65e-093
pineal body1.29e-072
regional part of epithalamus1.29e-072
secretory circumventricular organ1.29e-072
circumventricular organ1.29e-072
epithalamus1.29e-072
epithelium1.54e-07306
gland of diencephalon1.79e-074
neuroendocrine gland1.79e-074
regional part of diencephalon1.83e-074
cell layer2.28e-07309
middle temporal gyrus3.77e-072
diencephalon6.76e-077
future diencephalon6.76e-077
Disease
Ontology termp-valuen
neuroectodermal tumor4.97e-0710


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)
MA0003.10.233555
MA0004.10.71247
MA0006.11.31813
MA0007.10.6918
MA0009.11.20602
MA0014.11.86845
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.791759
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.841508
MA0069.14.32878
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.12.83685
MA0074.10.819248
MA0076.10.623864
MA0077.12.62367
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.14.13319
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.11.57689
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.11.15856
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.569905
MA0146.11.75643
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.483275
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.577908
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.533581
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.309472
MA0163.10.918944
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.22.00408
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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
REST#597837.237521537096020.004104697304192610.0195811666629777



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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