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Coexpression cluster:C840: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.76751,5.64182,0.752661,0.404877,0.237701,0.403356,0.474413,0.855419,1.36876,0.712545,0.375531,0.515448,0.348369,0.46359,0.236531,0.256724,0.68716,0.191625,1.22644,1.542,0.274046,3.15036,0.396189,0.233338,0.314616,3.35747,4.25038,0.39419,0.240354,0.281506,0.355553,0.722879,0.165252,0.715457,0.600053,1.47818,0.20579,0.404426,0.547451,0.789486,0.207288,0.340749,0.031261,0.663127,0.644296,0.814459,1.19689,0.365597,0.0278865,1.94453,0.550604,0.486559,0.812657,0.797754,0.947672,0.466348,0.244111,0.435652,3.32376,0.434711,0.762758,0.477672,0.848838,0.660336,0.494624,0.627106,1.0348,1.4,0.712787,1.2388,0.876593,0.445273,0.0579262,0.945703,0.693535,0.652929,1.52025,0.644006,0.709631,0.309107,0.380738,0.659298,0.49429,0.142768,0.89511,2.26844,0.396373,0.575051,0.575506,1.4989,1.12715,0.868602,0.739223,0.171001,0.238337,0.53563,0.368981,0.780743,0.579925,0.244963,0.187593,0.733724,0.775299,1.6507,0.616014,0.970906,0.675372,0.460348,0.31439,0.637089,0.283874,0.772599,0.741574,0.384185,1.07963,0.204477,0.857495,0.354459,0.624851,0.173291,0.937551,0.57318,0.400807,0.504966,1.18924,0.644741,0.468435,0.744085,0.979528,0.182384,0.869279,0.358161,0.993705,0.50181,1.13991,0.553614,0.350108,0.394712,1.09788,1.95265,1.55112,1.06096,0.470062,0.777301,0.617705,0.42776,0.601672,1.79367,0.896414,0.503344,1.61906,0.52751,0.869654,1.92742,0.477214,1.26919,0.560015,0.225815,0.314669,0.28899,1.05976,0.851493,1.68841,1.44414,0.633206,0.493542,1.49005,0.473159,2.80954
|tfbs_overrepresentation_for_novel_motifs=0.76751,5.64182,0.752661,0.404877,0.237701,0.403356,0.474413,0.855419,1.36876,0.712545,0.375531,0.515448,0.348369,0.46359,0.236531,0.256724,0.68716,0.191625,1.22644,1.542,0.274046,3.15036,0.396189,0.233338,0.314616,3.35747,4.25038,0.39419,0.240354,0.281506,0.355553,0.722879,0.165252,0.715457,0.600053,1.47818,0.20579,0.404426,0.547451,0.789486,0.207288,0.340749,0.031261,0.663127,0.644296,0.814459,1.19689,0.365597,0.0278865,1.94453,0.550604,0.486559,0.812657,0.797754,0.947672,0.466348,0.244111,0.435652,3.32376,0.434711,0.762758,0.477672,0.848838,0.660336,0.494624,0.627106,1.0348,1.4,0.712787,1.2388,0.876593,0.445273,0.0579262,0.945703,0.693535,0.652929,1.52025,0.644006,0.709631,0.309107,0.380738,0.659298,0.49429,0.142768,0.89511,2.26844,0.396373,0.575051,0.575506,1.4989,1.12715,0.868602,0.739223,0.171001,0.238337,0.53563,0.368981,0.780743,0.579925,0.244963,0.187593,0.733724,0.775299,1.6507,0.616014,0.970906,0.675372,0.460348,0.31439,0.637089,0.283874,0.772599,0.741574,0.384185,1.07963,0.204477,0.857495,0.354459,0.624851,0.173291,0.937551,0.57318,0.400807,0.504966,1.18924,0.644741,0.468435,0.744085,0.979528,0.182384,0.869279,0.358161,0.993705,0.50181,1.13991,0.553614,0.350108,0.394712,1.09788,1.95265,1.55112,1.06096,0.470062,0.777301,0.617705,0.42776,0.601672,1.79367,0.896414,0.503344,1.61906,0.52751,0.869654,1.92742,0.477214,1.26919,0.560015,0.225815,0.314669,0.28899,1.05976,0.851493,1.68841,1.44414,0.633206,0.493542,1.49005,0.473159,2.80954
|tfbs_overrepresentation_jaspar=MA0003.1;4.81936,MA0004.1;0.380329,MA0006.1;0.665232,MA0007.1;0.363007,MA0009.1;0.828613,MA0014.1;0.686562,MA0017.1;0.744788,MA0019.1;0.520264,MA0024.1;0.725404,MA0025.1;0.960689,MA0027.1;2.43535,MA0028.1;0.25013,MA0029.1;0.744375,MA0030.1;0.733118,MA0031.1;0.669876,MA0038.1;0.477043,MA0040.1;0.750125,MA0041.1;0.397617,MA0042.1;0.367902,MA0043.1;0.828925,MA0046.1;0.817858,MA0048.1;1.25863,MA0050.1;0.368721,MA0051.1;0.473017,MA0052.1;0.753928,MA0055.1;0.344701,MA0056.1;0,MA0057.1;0.802927,MA0058.1;0.796055,MA0059.1;0.79343,MA0060.1;0.138988,MA0061.1;0.118318,MA0063.1;0,MA0066.1;0.477449,MA0067.1;1.1435,MA0068.1;0.0911063,MA0069.1;0.814052,MA0070.1;0.803003,MA0071.1;0.440254,MA0072.1;0.798564,MA0073.1;0.932483,MA0074.1;0.4723,MA0076.1;0.307383,MA0077.1;0.790956,MA0078.1;0.568317,MA0081.1;0.292043,MA0083.1;0.836033,MA0084.1;1.32998,MA0087.1;0.79615,MA0088.1;2.19929,MA0089.1;0,MA0090.1;0.320494,MA0091.1;0.382762,MA0092.1;0.347826,MA0093.1;0.671378,MA0095.1;0,MA0098.1;0,MA0100.1;3.14791,MA0101.1;0.241637,MA0103.1;0.646502,MA0105.1;0.741916,MA0106.1;0.516528,MA0107.1;0.179177,MA0108.2;0.666881,MA0109.1;0,MA0111.1;0.33284,MA0113.1;0.532314,MA0114.1;0.174997,MA0115.1;1.06753,MA0116.1;0.536665,MA0117.1;0.865782,MA0119.1;2.13645,MA0122.1;0.891407,MA0124.1;1.0263,MA0125.1;0.942948,MA0130.1;0,MA0131.1;0.585907,MA0132.1;0,MA0133.1;0,MA0135.1;0.858623,MA0136.1;0.483775,MA0139.1;0.716757,MA0140.1;0.437738,MA0141.1;1.43869,MA0142.1;0.638837,MA0143.1;0.532484,MA0144.1;0.951129,MA0145.1;1.81958,MA0146.1;5.19153,MA0147.1;0.184931,MA0148.1;0.403564,MA0149.1;1.922,MA0062.2;0.114378,MA0035.2;0.437071,MA0039.2;2.48443,MA0138.2;3.50115,MA0002.2;0.407187,MA0137.2;0.710884,MA0104.2;0.845907,MA0047.2;0.504873,MA0112.2;6.91351,MA0065.2;1.37627,MA0150.1;0.315136,MA0151.1;0,MA0152.1;0.443956,MA0153.1;0.926242,MA0154.1;2.09876,MA0155.1;0.866026,MA0156.1;0.257809,MA0157.1;0.612166,MA0158.1;0,MA0159.1;0.185458,MA0160.1;1.07255,MA0161.1;0,MA0162.1;0.403951,MA0163.1;2.94358,MA0164.1;0.544294,MA0080.2;0.238846,MA0018.2;0.517858,MA0099.2;0.444294,MA0079.2;2.02097,MA0102.2;1.36707,MA0258.1;2.82472,MA0259.1;0.191914,MA0442.1;0
}}
}}

Revision as of 19:29, 22 January 2013


Full id: C840_hippocampus_cerebellum_amygdala_corpus_occipital_thalamus_medulla



Phase1 CAGE Peaks

Hg19::chr16:70698572..70698585,-p@chr16:70698572..70698585
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Hg19::chr16:70698603..70698617,-p@chr16:70698603..70698617
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Hg19::chr16:70698854..70698876,-p@chr16:70698854..70698876
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Hg19::chr16:70711768..70711786,-p@chr16:70711768..70711786
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Hg19::chr16:70712186..70712228,-p@chr16:70712186..70712228
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Hg19::chr16:70712229..70712245,-p@chr16:70712229..70712245
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Hg19::chr16:70712299..70712316,-p@chr16:70712299..70712316
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Hg19::chr16:70713931..70713962,-p3@MTSS1L
Hg19::chr16:70714740..70714774,-p@chr16:70714740..70714774
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Hg19::chr16:70719925..70719989,-p1@MTSS1L


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><br>

Uber Anatomy
Ontology termp-valuen
neural tube3.06e-3156
neural rod3.06e-3156
future spinal cord3.06e-3156
neural keel3.06e-3156
regional part of nervous system5.11e-2953
regional part of brain5.11e-2953
central nervous system1.02e-2881
ectoderm-derived structure2.90e-28171
ectoderm2.90e-28171
presumptive ectoderm2.90e-28171
brain5.05e-2868
future brain5.05e-2868
neurectoderm2.18e-2786
neural plate7.82e-2782
presumptive neural plate7.82e-2782
nervous system2.56e-2589
ecto-epithelium4.23e-24104
organ system subdivision4.16e-23223
structure with developmental contribution from neural crest1.14e-21132
regional part of forebrain1.56e-2141
forebrain1.56e-2141
anterior neural tube1.56e-2141
future forebrain1.56e-2141
brain grey matter8.25e-2134
gray matter8.25e-2134
adult organism1.06e-20114
telencephalon1.31e-2034
regional part of telencephalon2.14e-1932
pre-chordal neural plate2.84e-1961
cerebral hemisphere3.30e-1932
organ part1.37e-17218
multi-tissue structure9.43e-15342
cerebral cortex1.07e-1425
pallium1.07e-1425
regional part of cerebral cortex3.00e-1422
neocortex8.95e-1320
multi-cellular organism9.42e-12656
anatomical cluster1.38e-11373
organ4.56e-11503
posterior neural tube6.98e-1115
chordal neural plate6.98e-1115
segmental subdivision of nervous system2.19e-0913
cell layer3.33e-09309
epithelium5.03e-09306
anatomical system9.32e-09624
segmental subdivision of hindbrain9.38e-0912
hindbrain9.38e-0912
presumptive hindbrain9.38e-0912
anatomical group1.32e-08625
basal ganglion9.09e-089
nuclear complex of neuraxis9.09e-089
aggregate regional part of brain9.09e-089
collection of basal ganglia9.09e-089
cerebral subcortex9.09e-089
neural nucleus1.17e-079
nucleus of brain1.17e-079
surface structure2.72e-0799
anatomical conduit9.48e-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)
MA0003.14.81936
MA0004.10.380329
MA0006.10.665232
MA0007.10.363007
MA0009.10.828613
MA0014.10.686562
MA0017.10.744788
MA0019.10.520264
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.10.25013
MA0029.10.744375
MA0030.10.733118
MA0031.10.669876
MA0038.10.477043
MA0040.10.750125
MA0041.10.397617
MA0042.10.367902
MA0043.10.828925
MA0046.10.817858
MA0048.11.25863
MA0050.10.368721
MA0051.10.473017
MA0052.10.753928
MA0055.10.344701
MA0056.10
MA0057.10.802927
MA0058.10.796055
MA0059.10.79343
MA0060.10.138988
MA0061.10.118318
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.10.0911063
MA0069.10.814052
MA0070.10.803003
MA0071.10.440254
MA0072.10.798564
MA0073.10.932483
MA0074.10.4723
MA0076.10.307383
MA0077.10.790956
MA0078.10.568317
MA0081.10.292043
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.12.19929
MA0089.10
MA0090.10.320494
MA0091.10.382762
MA0092.10.347826
MA0093.10.671378
MA0095.10
MA0098.10
MA0100.13.14791
MA0101.10.241637
MA0103.10.646502
MA0105.10.741916
MA0106.10.516528
MA0107.10.179177
MA0108.20.666881
MA0109.10
MA0111.10.33284
MA0113.10.532314
MA0114.10.174997
MA0115.11.06753
MA0116.10.536665
MA0117.10.865782
MA0119.12.13645
MA0122.10.891407
MA0124.11.0263
MA0125.10.942948
MA0130.10
MA0131.10.585907
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.10.483775
MA0139.10.716757
MA0140.10.437738
MA0141.11.43869
MA0142.10.638837
MA0143.10.532484
MA0144.10.951129
MA0145.11.81958
MA0146.15.19153
MA0147.10.184931
MA0148.10.403564
MA0149.11.922
MA0062.20.114378
MA0035.20.437071
MA0039.22.48443
MA0138.23.50115
MA0002.20.407187
MA0137.20.710884
MA0104.20.845907
MA0047.20.504873
MA0112.26.91351
MA0065.21.37627
MA0150.10.315136
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.12.09876
MA0155.10.866026
MA0156.10.257809
MA0157.10.612166
MA0158.10
MA0159.10.185458
MA0160.11.07255
MA0161.10
MA0162.10.403951
MA0163.12.94358
MA0164.10.544294
MA0080.20.238846
MA0018.20.517858
MA0099.20.444294
MA0079.22.02097
MA0102.21.36707
MA0258.12.82472
MA0259.10.191914
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.

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