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Coexpression cluster:C1480: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.44418,1.35536,0.436508,0.58616,1.01854,0.584466,0.662701,0.269608,0.267027,2.54809,0.553339,0.707204,0.223349,0.650887,0.391663,0.415981,0.889639,0.336106,0.236034,0.127969,0.436569,0.0880431,1.41165,0.387783,1.21515,0.730467,0.202389,0.574247,0.396295,0.547818,0.530785,0.92701,0.302275,0.640661,2.52957,2.82399,0.93226,1.43099,0.329602,1.28576,0.355745,0.513952,0.0979105,0.390088,1.41477,0.468392,0.66382,0.542147,0.0909286,0.396429,0.745008,0.675919,0.891214,1.00488,1.15929,0.653901,0.400834,0.62023,0.186533,0.619193,0.968558,0.666252,0.267534,2.00306,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,2.1621,0.275507,4.31331,1.15727,4.28285,1.12235,0.192925,0.84426,0.913168,0.477584,0.240887,0.86037,0.684313,0.272514,1.10535,2.07207,0.126687,0.536262,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,7.09564,0.32338,0.234532,0.987239,0.776336,0.166235,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,2.10687,0.376529,0.44815,0.978783,0.430775,0.563054,1.29401,0.352243,4.18682,0.529546,1.9262,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,1.57878,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,0.175219,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,2.2813,0.424432,7.63078,1.07915,0.258882,0.665754,1.48627,0.755083,0.378604,0.484017,1.15112,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.29379,0.661335,0.307168
|tfbs_overrepresentation_jaspar=MA0003.1;11.3965,MA0004.1;0.558729,MA0006.1;0.391183,MA0007.1;0.539222,MA0009.1;1.03681,MA0014.1;7.9489,MA0017.1;0.432438,MA0019.1;0.7124,MA0024.1;0.929647,MA0025.1;1.17262,MA0027.1;2.65688,MA0028.1;0.408079,MA0029.1;0.949428,MA0030.1;0.937696,MA0031.1;0.871496,MA0038.1;0.665566,MA0040.1;0.955415,MA0041.1;0.578072,MA0042.1;0.544748,MA0043.1;1.03713,MA0046.1;1.02569,MA0048.1;0.152639,MA0050.1;0.545671,MA0051.1;0.661179,MA0052.1;0.959373,MA0055.1;0.465994,MA0056.1;0,MA0057.1;0.147053,MA0058.1;0.458909,MA0059.1;0.457555,MA0060.1;0.267412,MA0061.1;0.23892,MA0063.1;0,MA0066.1;0.66601,MA0067.1;1.35893,MA0068.1;0.199491,MA0069.1;1.02175,MA0070.1;1.01032,MA0071.1;0.625297,MA0072.1;2.29768,MA0073.1;0.0214749,MA0074.1;0.660398,MA0076.1;0.475586,MA0077.1;0.997832,MA0078.1;1.80244,MA0081.1;1.15882,MA0083.1;1.04447,MA0084.1;1.5477,MA0087.1;1.00322,MA0088.1;2.21033,MA0089.1;0,MA0090.1;0.490736,MA0091.1;3.46565,MA0092.1;0.522012,MA0093.1;0.394379,MA0095.1;0,MA0098.1;0,MA0100.1;0.679972,MA0101.1;0.397846,MA0103.1;0.381434,MA0105.1;0.134725,MA0106.1;0.70837,MA0107.1;0.320267,MA0108.2;0.868347,MA0109.1;0,MA0111.1;0.504913,MA0113.1;0.725375,MA0114.1;0.845337,MA0115.1;1.28169,MA0116.1;0.323925,MA0117.1;1.07516,MA0119.1;3.97414,MA0122.1;1.10154,MA0124.1;1.23968,MA0125.1;1.15445,MA0130.1;0,MA0131.1;0.782708,MA0132.1;0,MA0133.1;0,MA0135.1;1.06778,MA0136.1;0.672893,MA0139.1;1.86787,MA0140.1;0.622527,MA0141.1;0.455728,MA0142.1;0.838805,MA0143.1;0.725558,MA0144.1;0.299851,MA0145.1;0.707171,MA0146.1;0.718193,MA0147.1;0.327615,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;0.23336,MA0035.2;0.621793,MA0039.2;2.28878,MA0138.2;0.765223,MA0002.2;0.255126,MA0137.2;0.414885,MA0104.2;0.26661,MA0047.2;0.695777,MA0112.2;2.25875,MA0065.2;0.718489,MA0150.1;2.10974,MA0151.1;0,MA0152.1;0.629368,MA0153.1;1.13732,MA0154.1;1.3291,MA0155.1;1.09123,MA0156.1;0.417278,MA0157.1;0.810597,MA0158.1;0,MA0159.1;0.328286,MA0160.1;0.600559,MA0161.1;0,MA0162.1;1.87239,MA0163.1;15.1517,MA0164.1;0.738243,MA0080.2;0.394469,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;4.76174,MA0102.2;1.58513,MA0258.1;4.97441,MA0259.1;0.336472,MA0442.1;0
}}
}}

Revision as of 19:57, 22 January 2013


Full id: C1480_optic_neuroectodermal_corpus_cerebellum_diencephalon_occipital_Astrocyte



Phase1 CAGE Peaks

Hg19::chr20:24449821..24449843,+p4@SYNDIG1
Hg19::chr20:24449953..24450011,+p2@SYNDIG1
Hg19::chr20:24450118..24450148,+p3@SYNDIG1
Hg19::chr20:24450259..24450346,+p1@SYNDIG1
Hg19::chr20:24450356..24450367,+p5@SYNDIG1
Hg19::chr20:24450498..24450540,+p@chr20:24450498..24450540
+


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 cell2.94e-0925
neurectodermal cell5.10e-0959
ectodermal cell8.35e-0772
Uber Anatomy
Ontology termp-valuen
nervous system1.47e-5589
central nervous system2.03e-5481
brain1.14e-4568
future brain1.14e-4568
neural tube1.29e-4556
neural rod1.29e-4556
future spinal cord1.29e-4556
neural keel1.29e-4556
neurectoderm1.52e-4386
regional part of nervous system7.38e-4353
regional part of brain7.38e-4353
neural plate2.96e-4182
presumptive neural plate2.96e-4182
ecto-epithelium1.62e-35104
adult organism2.51e-35114
ectoderm-derived structure3.22e-35171
ectoderm3.22e-35171
presumptive ectoderm3.22e-35171
regional part of forebrain4.79e-3241
forebrain4.79e-3241
anterior neural tube4.79e-3241
future forebrain4.79e-3241
structure with developmental contribution from neural crest3.49e-31132
telencephalon2.29e-3034
brain grey matter6.66e-3034
gray matter6.66e-3034
pre-chordal neural plate5.97e-2961
cerebral hemisphere2.29e-2832
regional part of telencephalon2.54e-2832
cerebral cortex8.22e-2325
pallium8.22e-2325
regional part of cerebral cortex5.58e-2122
neocortex1.94e-1920
organ system subdivision2.00e-17223
posterior neural tube2.08e-1415
chordal neural plate2.08e-1415
segmental subdivision of nervous system7.73e-1313
segmental subdivision of hindbrain7.64e-1212
hindbrain7.64e-1212
presumptive hindbrain7.64e-1212
anatomical cluster2.76e-10373
regional part of metencephalon2.21e-099
metencephalon2.21e-099
future metencephalon2.21e-099
tube7.94e-09192
basal ganglion1.54e-089
nuclear complex of neuraxis1.54e-089
aggregate regional part of brain1.54e-089
collection of basal ganglia1.54e-089
cerebral subcortex1.54e-089
neural nucleus1.71e-089
nucleus of brain1.71e-089
organ part1.74e-07218
multi-cellular organism1.97e-07656
cerebellum5.54e-076
rhombic lip5.54e-076
telencephalic nucleus5.76e-077
gyrus6.48e-076
temporal lobe6.97e-076


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)
MA0003.111.3965
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.17.9489
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.152639
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.465994
MA0056.10
MA0057.10.147053
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.12.29768
MA0073.10.0214749
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.11.80244
MA0081.11.15882
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.12.21033
MA0089.10
MA0090.10.490736
MA0091.13.46565
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.134725
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.845337
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.13.97414
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.11.86787
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.707171
MA0146.10.718193
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.22.28878
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.22.25875
MA0065.20.718489
MA0150.12.10974
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.11.3291
MA0155.11.09123
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.11.87239
MA0163.115.1517
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.24.76174
MA0102.21.58513
MA0258.14.97441
MA0259.10.336472
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
ESR1#2099315.38430164807720.0006374039095799040.0052269022387418



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:C1480&oldid=2569991"