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Coexpression cluster:C2673: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;0.0938548,MA0004.1;0.71247,MA0006.1;0.532262,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;0.709734,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.791759,MA0056.1;0,MA0057.1;0.69331,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;2.31526,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;2.36824,MA0074.1;0.819248,MA0076.1;0.623864,MA0077.1;1.16637,MA0078.1;0.926725,MA0081.1;0.604638,MA0083.1;1.21381,MA0084.1;1.72172,MA0087.1;1.17185,MA0088.1;0.536981,MA0089.1;0,MA0090.1;0.640115,MA0091.1;0.715356,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;0.656404,MA0106.1;0.869173,MA0107.1;0.453492,MA0108.2;1.03412,MA0109.1;0,MA0111.1;0.655276,MA0113.1;0.886811,MA0114.1;1.13665,MA0115.1;1.45393,MA0116.1;0.457606,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;1.08195,MA0146.1;0.481,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;2.01147,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;1.01696,MA0047.2;0.856092,MA0112.2;0.551048,MA0065.2;1.7213,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.229241,MA0155.1;1.61785,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;1.57817,MA0163.1;0.539587,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;5.41326,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;1.1888,MA0442.1;0
}}
}}

Revision as of 20:49, 22 January 2013


Full id: C2673_cerebellum_small_pineal_retinoblastoma_retina_eye_neuroblastoma



Phase1 CAGE Peaks

Hg19::chr2:182521855..182521867,-p4@CERKL
Hg19::chr5:139422833..139422898,-p1@NRG2
Hg19::chr8:9764145..9764235,-p@chr8:9764145..9764235
-
Hg19::chr8:9764250..9764261,-p@chr8:9764250..9764261
-


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
neuronal stem cell4.87e-128
neuron1.46e-096
neuroblast1.46e-096
electrically signaling cell1.46e-096
embryonic stem cell2.72e-085
Uber Anatomy
Ontology termp-valuen
nervous system2.59e-6989
central nervous system2.08e-6481
neural tube4.98e-5656
neural rod4.98e-5656
future spinal cord4.98e-5656
neural keel4.98e-5656
regional part of nervous system8.17e-5253
regional part of brain8.17e-5253
brain3.50e-4768
future brain3.50e-4768
neural plate1.41e-4282
presumptive neural plate1.41e-4282
regional part of forebrain8.62e-4241
forebrain8.62e-4241
anterior neural tube8.62e-4241
future forebrain8.62e-4241
neurectoderm8.33e-4086
brain grey matter5.08e-3534
gray matter5.08e-3534
telencephalon7.09e-3534
pre-chordal neural plate1.57e-3361
cerebral hemisphere1.52e-3232
regional part of telencephalon3.63e-3232
adult organism8.75e-32114
ectoderm-derived structure9.50e-31171
ectoderm9.50e-31171
presumptive ectoderm9.50e-31171
ecto-epithelium5.19e-30104
neocortex5.26e-3020
regional part of cerebral cortex8.38e-3022
organ system subdivision4.01e-28223
cerebral cortex1.61e-2525
pallium1.61e-2525
structure with developmental contribution from neural crest2.54e-24132
posterior neural tube7.72e-1515
chordal neural plate7.72e-1515
anatomical cluster4.99e-13373
segmental subdivision of nervous system3.43e-1213
tube2.12e-11192
segmental subdivision of hindbrain5.74e-1112
hindbrain5.74e-1112
presumptive hindbrain5.74e-1112
neural nucleus7.14e-119
nucleus of brain7.14e-119
basal ganglion1.12e-109
nuclear complex of neuraxis1.12e-109
aggregate regional part of brain1.12e-109
collection of basal ganglia1.12e-109
cerebral subcortex1.12e-109
gyrus1.33e-106
brainstem2.57e-106
occipital lobe1.69e-095
parietal lobe2.76e-095
temporal lobe1.64e-086
diencephalon3.27e-087
future diencephalon3.27e-087
telencephalic nucleus4.43e-087
regional part of diencephalon1.40e-074
regional part of metencephalon4.74e-079
metencephalon4.74e-079
future metencephalon4.74e-079
anatomical conduit9.15e-07240


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)
MA0003.10.0938548
MA0004.10.71247
MA0006.10.532262
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
MA0048.10.709734
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.791759
MA0056.10
MA0057.10.69331
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.12.31526
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.12.36824
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.656404
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.11.13665
MA0115.11.45393
MA0116.10.457606
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
MA0145.11.08195
MA0146.10.481
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.22.01147
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.21.01696
MA0047.20.856092
MA0112.20.551048
MA0065.21.7213
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.11.61785
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.11.57817
MA0163.10.539587
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.25.41326
MA0102.21.75932
MA0258.10.418966
MA0259.11.1888
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
GATA2#262439.55869880016550.001818151618357440.010903585235121



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:C2673&oldid=2571184"