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Coexpression cluster:C2650: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.590005,0.0888524,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,0.151681,0.706765,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,1.18986,0.581762,0.505745,0.731221,0.528529,0.632849,0.892087,0.316693,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,0.344471,0.49475,0.598278,0.491074,0.740899,0.463978,0.371755,0.493145,0.66492,0.183156,0.53106,0.0946706,0.61613,0.822818,0.694903,0.173425,0.538016,0.90714,0.83543,0.699149,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,1.03936,0.248021,1.32819,0.336329,0.321165,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,1.96757,1.03184,1.27559,0.353274,0.221873,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,1.12407,0.535192,0.456994,0.354969,1.15558,0.939507,0.272395,1.17564,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.12452,0.681522,0.988625,0.444962,1.31973,2.14757,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,1.23342,0.175846,1.24902,0.383416,0.824835,1.65997,2.11789,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.0401987
|tfbs_overrepresentation_jaspar=MA0003.1;0.0214529,MA0004.1;0.71247,MA0006.1;0.532262,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;0.0695829,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;0.125954,MA0056.1;0,MA0057.1;0.69331,MA0058.1;0.605914,MA0059.1;0.604454,MA0060.1;0.393285,MA0061.1;0.946082,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;0.313194,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;0.00636811,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;1.02755,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;1.22348,MA0106.1;0.869173,MA0107.1;1.1497,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;2.05538,MA0144.1;0.430413,MA0145.1;0.195821,MA0146.1;0.061409,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;0.0247757,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;0.199162,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.229241,MA0155.1;0.180766,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;0.0928415,MA0163.1;0.0725493,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;0.0626799,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0
}}
}}

Revision as of 20:48, 22 January 2013


Full id: C2650_Neural_hippocampus_amygdala_parietal_middle_medial_caudate



Phase1 CAGE Peaks

Hg19::chr22:50523729..50523747,-p3@MLC1
Hg19::chr4:114214125..114214151,+p11@ANK2
Hg19::chr5:16741975..16741994,-p8@MYO10
Hg19::chr5:36606700..36606729,+p1@SLC1A3


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

GO IDGO nameFDR corrected p-value
GO:0015629actin cytoskeleton0.0178981509968156
GO:0005313L-glutamate transmembrane transporter activity0.0178981509968156
GO:0001504neurotransmitter uptake0.0178981509968156
GO:0000299integral to membrane of membrane fraction0.0178981509968156
GO:0015172acidic amino acid transmembrane transporter activity0.0178981509968156
GO:0015813L-glutamate transport0.0178981509968156
GO:0015800acidic amino acid transport0.0178981509968156
GO:0017153sodium:dicarboxylate symporter activity0.0178981509968156
GO:0005310dicarboxylic acid transmembrane transporter activity0.0178981509968156
GO:0006835dicarboxylic acid transport0.0178981509968156
GO:0005624membrane fraction0.0178981509968156
GO:0043232intracellular non-membrane-bound organelle0.0178981509968156
GO:0043228non-membrane-bound organelle0.0178981509968156
GO:0015179L-amino acid transmembrane transporter activity0.0263385807155217
GO:0000267cell fraction0.0264272426077618
GO:0005343organic acid:sodium symporter activity0.0264272426077618
GO:0015296anion:cation symporter activity0.0264272426077618
GO:0015171amino acid transmembrane transporter activity0.0366909263885831
GO:0006865amino acid transport0.0366909263885831
GO:0015075ion transmembrane transporter activity0.0366909263885831
GO:0006836neurotransmitter transport0.0366909263885831
GO:0001505regulation of neurotransmitter levels0.0366909263885831
GO:0015837amine transport0.0366909263885831
GO:0005856cytoskeleton0.0366909263885831
GO:0005200structural constituent of cytoskeleton0.0366909263885831
GO:0015370solute:sodium symporter activity0.0366909263885831
GO:0022891substrate-specific transmembrane transporter activity0.0366909263885831
GO:0046943carboxylic acid transmembrane transporter activity0.0366909263885831
GO:0046942carboxylic acid transport0.0366909263885831
GO:0015849organic acid transport0.0366909263885831
GO:0005342organic acid transmembrane transporter activity0.0366909263885831
GO:0016459myosin complex0.0384030294254836
GO:0022857transmembrane transporter activity0.0384966829879713
GO:0015294solute:cation symporter activity0.0384966829879713
GO:0022892substrate-specific transporter activity0.0418601036548849
GO:0007154cell communication0.0418601036548849



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 cell9.51e-108
neural cell2.85e-0825
neuron4.72e-076
neuroblast4.72e-076
electrically signaling cell4.72e-076
oligodendrocyte9.79e-077
macroglial cell9.79e-077
astrocyte9.79e-077
oligodendrocyte precursor cell9.79e-077
Uber Anatomy
Ontology termp-valuen
central nervous system7.74e-6981
nervous system2.67e-6589
neural tube3.20e-6456
neural rod3.20e-6456
future spinal cord3.20e-6456
neural keel3.20e-6456
regional part of nervous system2.43e-6053
regional part of brain2.43e-6053
brain5.97e-5468
future brain5.97e-5468
neural plate1.99e-5082
presumptive neural plate1.99e-5082
neurectoderm8.83e-4986
regional part of forebrain4.33e-4841
forebrain4.33e-4841
anterior neural tube4.33e-4841
future forebrain4.33e-4841
adult organism6.12e-46114
telencephalon1.56e-4234
brain grey matter1.88e-4234
gray matter1.88e-4234
cerebral hemisphere5.32e-4032
regional part of telencephalon6.24e-4032
ecto-epithelium5.21e-39104
pre-chordal neural plate3.58e-3761
ectoderm-derived structure1.18e-35171
ectoderm1.18e-35171
presumptive ectoderm1.18e-35171
structure with developmental contribution from neural crest8.60e-32132
cerebral cortex6.66e-3125
pallium6.66e-3125
organ system subdivision1.14e-29223
regional part of cerebral cortex1.92e-2722
neocortex9.44e-2520
posterior neural tube1.43e-1615
chordal neural plate1.43e-1615
anatomical cluster2.00e-14373
segmental subdivision of nervous system5.52e-1413
basal ganglion3.67e-139
nuclear complex of neuraxis3.67e-139
aggregate regional part of brain3.67e-139
collection of basal ganglia3.67e-139
cerebral subcortex3.67e-139
segmental subdivision of hindbrain5.14e-1312
hindbrain5.14e-1312
presumptive hindbrain5.14e-1312
neural nucleus7.55e-139
nucleus of brain7.55e-139
tube4.10e-12192
organ part1.33e-10218
telencephalic nucleus1.98e-107
regional part of metencephalon2.68e-099
metencephalon2.68e-099
future metencephalon2.68e-099
anatomical conduit3.89e-09240
gyrus4.04e-096
brainstem5.67e-096
limbic system2.34e-085
temporal lobe7.37e-086
epithelium9.35e-08306
parietal lobe9.61e-085
embryo1.08e-07592
multi-cellular organism1.67e-07656
cell layer1.73e-07309
occipital lobe1.76e-075
diencephalon4.89e-077
future diencephalon4.89e-077
multi-tissue structure5.03e-07342
organ5.49e-07503
corpus striatum5.73e-074
striatum5.73e-074
ventral part of telencephalon5.73e-074
future corpus striatum5.73e-074


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)
MA0003.10.0214529
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
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
MA0055.10.125954
MA0056.10
MA0057.10.69331
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.946082
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.02755
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
MA0105.11.22348
MA0106.10.869173
MA0107.11.1497
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
MA0143.12.05538
MA0144.10.430413
MA0145.10.195821
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.0626799
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
POU5F1#5460183.85980036297640.01187154239091560.0432410984467908



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:C2650&oldid=2571161"