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Coexpression cluster:C2342: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.590005,0.620826,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,2.07992,0.706765,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.223552,0.581762,0.169357,0.731221,0.528529,0.632849,0.892087,0.316693,0.728867,0.537869,0.297585,0.682839,1.09415,1.10579,0.911389,0.49475,1.49582,0.491074,0.740899,0.463978,0.371755,0.493145,0.66492,0.183156,0.53106,0.648765,0.61613,0.822818,0.694903,0.173425,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.806003,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,1.03936,0.248021,1.32819,0.336329,0.859396,0.305238,1.00941,1.08,0.62601,0.95118,1.02594,0.844168,1.03184,1.27559,0.353274,0.221873,0.793068,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,0.749003,1.17564,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,1.27972,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.234974,0.521611,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,1.08488,0.820225,0.156682
|tfbs_overrepresentation_jaspar=MA0003.1;2.39007,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;0.25531,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.125954,MA0056.1;0,MA0057.1;1.28333,MA0058.1;0.605914,MA0059.1;0.604454,MA0060.1;0.393285,MA0061.1;1.68681,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;0.380957,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;0.182167,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;3.51257,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;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;1.46638,MA0142.1;1.00381,MA0143.1;2.05538,MA0144.1;1.92815,MA0145.1;0.195821,MA0146.1;1.25938,MA0147.1;1.16748,MA0148.1;1.75269,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;2.52211,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;2.35208,MA0104.2;1.01696,MA0047.2;0.856092,MA0112.2;0.187982,MA0065.2;2.43626,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;2.15942,MA0163.1;1.37853,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;3.12283,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0
}}
}}

Revision as of 20:35, 22 January 2013


Full id: C2342_locus_thalamus_spinal_hippocampus_globus_caudate_medulla



Phase1 CAGE Peaks

Hg19::chr15:65360552..65360574,-p4@RASL12
Hg19::chr15:65360586..65360610,-p2@RASL12
Hg19::chr3:84002765..84002792,+p@chr3:84002765..84002792
+
Hg19::chrX:23352816..23352836,+p4@PTCHD1


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:0008158hedgehog receptor activity0.0197766289344743



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
adult organism3.13e-91114
neural tube3.45e-5856
neural rod3.45e-5856
future spinal cord3.45e-5856
neural keel3.45e-5856
regional part of nervous system1.66e-5353
regional part of brain1.66e-5353
central nervous system3.02e-5081
brain1.55e-4368
future brain1.55e-4368
nervous system2.56e-4389
regional part of forebrain1.12e-4141
forebrain1.12e-4141
anterior neural tube1.12e-4141
future forebrain1.12e-4141
neural plate2.00e-4182
presumptive neural plate2.00e-4182
neurectoderm1.19e-3886
brain grey matter3.27e-3334
gray matter3.27e-3334
telencephalon8.47e-3334
organ system subdivision3.18e-30223
ecto-epithelium3.26e-30104
regional part of telencephalon3.44e-3032
cerebral hemisphere5.58e-3032
structure with developmental contribution from neural crest8.65e-30132
pre-chordal neural plate1.27e-2561
regional part of cerebral cortex2.69e-2422
ectoderm-derived structure5.26e-23171
ectoderm5.26e-23171
presumptive ectoderm5.26e-23171
neocortex2.42e-2120
cerebral cortex1.11e-2025
pallium1.11e-2025
anatomical cluster5.38e-19373
multi-tissue structure1.45e-17342
posterior neural tube4.86e-1715
chordal neural plate4.86e-1715
anatomical conduit7.27e-17240
tube4.36e-16192
neural nucleus1.08e-149
nucleus of brain1.08e-149
basal ganglion1.47e-149
nuclear complex of neuraxis1.47e-149
aggregate regional part of brain1.47e-149
collection of basal ganglia1.47e-149
cerebral subcortex1.47e-149
embryo2.18e-13592
organ part3.22e-13218
organ5.45e-13503
segmental subdivision of hindbrain1.20e-1212
hindbrain1.20e-1212
presumptive hindbrain1.20e-1212
multi-cellular organism1.08e-11656
epithelium1.25e-11306
telencephalic nucleus1.42e-117
segmental subdivision of nervous system1.89e-1113
embryonic structure1.93e-11564
cell layer2.63e-11309
germ layer3.45e-11560
germ layer / neural crest3.45e-11560
embryonic tissue3.45e-11560
presumptive structure3.45e-11560
germ layer / neural crest derived structure3.45e-11560
epiblast (generic)3.45e-11560
developing anatomical structure4.32e-11581
brainstem8.11e-116
diencephalon2.43e-107
future diencephalon2.43e-107
anatomical system8.53e-10624
anatomical group1.00e-09625
limbic system7.29e-095
gyrus8.02e-096
regional part of metencephalon2.19e-089
metencephalon2.19e-089
future metencephalon2.19e-089
temporal lobe5.88e-086
parietal lobe2.53e-075
corpus striatum3.95e-074
striatum3.95e-074
ventral part of telencephalon3.95e-074
future corpus striatum3.95e-074
regional part of diencephalon5.45e-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)
MA0003.12.39007
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
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.11.28333
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.11.68681
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.380957
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
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
MA0105.13.51257
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.11.13665
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
MA0141.11.46638
MA0142.11.00381
MA0143.12.05538
MA0144.11.92815
MA0145.10.195821
MA0146.11.25938
MA0147.11.16748
MA0148.11.75269
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.22.52211
MA0138.20.928035
MA0002.20.379056
MA0137.22.35208
MA0104.21.01696
MA0047.20.856092
MA0112.20.187982
MA0065.22.43626
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
MA0162.12.15942
MA0163.11.37853
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.23.12283
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

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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