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Coexpression cluster:C2273: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;0.443649,MA0004.1;0.71247,MA0006.1;0.532262,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;0.244769,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;1.66514,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;4.01633,MA0056.1;0,MA0057.1;3.6449,MA0058.1;0.605914,MA0059.1;1.47051,MA0060.1;0.393285,MA0061.1;3.49299,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;0.841508,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;0.866596,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;1.62583,MA0089.1;0,MA0090.1;1.54523,MA0091.1;0.715356,MA0092.1;0.673508,MA0093.1;0.535768,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;2.29123,MA0103.1;1.29536,MA0105.1;1.90157,MA0106.1;0.869173,MA0107.1;2.98058,MA0108.2;1.03412,MA0109.1;0,MA0111.1;0.655276,MA0113.1;0.886811,MA0114.1;0.447443,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;0.061409,MA0147.1;2.03364,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;0.777367,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;1.79838,MA0047.2;0.856092,MA0112.2;1.65877,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;1.02191,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;1.06783,MA0163.1;2.49771,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;9.35212,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;1.1888,MA0442.1;0
}}
}}

Revision as of 20:32, 22 January 2013


Full id: C2273_Neural_Astrocyte_small_teratocarcinoma_testicular_brain_Neurons



Phase1 CAGE Peaks

Hg19::chr13:95364761..95364780,-p2@SOX21
Hg19::chr13:95364784..95364806,-p1@SOX21
Hg19::chr13:95364963..95364978,+p1@SOX21-AS1
Hg19::chr13:95365715..95365734,-p@chr13:95365715..95365734
-


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
neural cell1.61e-1125
neuronal stem cell1.27e-098
embryonic stem cell4.54e-095
oligodendrocyte1.78e-087
macroglial cell1.78e-087
astrocyte1.78e-087
oligodendrocyte precursor cell1.78e-087
Uber Anatomy
Ontology termp-valuen
central nervous system1.16e-6681
neural tube3.59e-6256
neural rod3.59e-6256
future spinal cord3.59e-6256
neural keel3.59e-6256
nervous system5.74e-5889
regional part of nervous system1.53e-5753
regional part of brain1.53e-5753
brain2.87e-5168
future brain2.87e-5168
regional part of forebrain7.20e-4541
forebrain7.20e-4541
anterior neural tube7.20e-4541
future forebrain7.20e-4541
telencephalon5.16e-4434
brain grey matter1.14e-4334
gray matter1.14e-4334
cerebral hemisphere4.55e-4132
regional part of telencephalon4.68e-4132
neural plate1.40e-4082
presumptive neural plate1.40e-4082
neurectoderm6.89e-3886
organ system subdivision2.68e-32223
cerebral cortex2.55e-3125
pallium2.55e-3125
ecto-epithelium3.78e-31104
ectoderm-derived structure5.81e-31171
ectoderm5.81e-31171
presumptive ectoderm5.81e-31171
pre-chordal neural plate1.60e-2961
adult organism2.16e-28114
regional part of cerebral cortex1.73e-2622
structure with developmental contribution from neural crest9.24e-24132
neocortex9.44e-2420
posterior neural tube9.72e-1815
chordal neural plate9.72e-1815
tube5.39e-14192
basal ganglion7.19e-149
nuclear complex of neuraxis7.19e-149
aggregate regional part of brain7.19e-149
collection of basal ganglia7.19e-149
cerebral subcortex7.19e-149
neural nucleus1.16e-139
nucleus of brain1.16e-139
anatomical conduit2.00e-13240
segmental subdivision of hindbrain2.01e-1312
hindbrain2.01e-1312
presumptive hindbrain2.01e-1312
anatomical cluster3.22e-13373
segmental subdivision of nervous system3.62e-1213
telencephalic nucleus3.70e-117
organ part8.61e-11218
gyrus1.14e-096
brainstem1.61e-096
regional part of metencephalon2.17e-099
metencephalon2.17e-099
future metencephalon2.17e-099
limbic system1.50e-085
occipital lobe2.74e-085
temporal lobe2.89e-086
embryo5.39e-08592
corpus striatum6.11e-074
striatum6.11e-074
ventral part of telencephalon6.11e-074
future corpus striatum6.11e-074
embryonic structure7.10e-07564
multi-tissue structure8.33e-07342
multi-cellular organism8.77e-07656
germ layer9.68e-07560
germ layer / neural crest9.68e-07560
embryonic tissue9.68e-07560
presumptive structure9.68e-07560
germ layer / neural crest derived structure9.68e-07560
epiblast (generic)9.68e-07560


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)
MA0003.10.443649
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.244769
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
MA0042.11.66514
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.14.01633
MA0056.10
MA0057.13.6449
MA0058.10.605914
MA0059.11.47051
MA0060.10.393285
MA0061.13.49299
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.841508
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.866596
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.62583
MA0089.10
MA0090.11.54523
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.12.29123
MA0103.11.29536
MA0105.11.90157
MA0106.10.869173
MA0107.12.98058
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
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
MA0146.10.061409
MA0147.12.03364
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.777367
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.21.79838
MA0047.20.856092
MA0112.21.65877
MA0065.20.577908
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.11.02191
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.11.06783
MA0163.12.49771
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.29.35212
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
ZNF263#1012736.166381227758010.006539814347975980.0279647752492738



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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