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Coexpression cluster:C647: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=1.13027,0.329487,0.585688,0.320418,0.509452,0.854581,0.385011,0.628761,0.621506,1.30663,0.293498,0.423573,0.231404,0.37489,0.169864,0.187326,0.587543,0.131867,0.534957,0.463992,0.585797,0.779448,0.839779,0.500259,0.670559,0.443987,0.442433,0.310589,0.991108,0.399779,0.275306,0.622056,0.110199,0.234859,0.447686,0.473445,0.868674,0.320003,0.127608,0.570628,0.144976,1.33439,0.171949,0.16875,0.360234,0.226447,0.385972,0.284438,0.312409,0.173249,0.456831,0.396393,0.126438,0.694739,0.841347,0.377467,0.176395,0.348876,0.177537,0.348003,0.660716,0.388062,0.299793,0.561703,1.04233,0.529794,0.927044,1.28869,0.612294,1.12869,0.251183,0.0939573,0.542218,0.839414,0.840426,0.787787,0.416738,0.546008,0.609242,0.233499,0.074278,0.560705,0.403653,0.636937,0.789807,0.914491,1.08786,0.386942,0.480498,1.38705,1.01818,0.763867,0.637885,0.368116,0.171417,0.390718,0.248364,0.67819,0.484706,0.622302,0.12852,0.632556,0.672898,0.590971,0.519171,0.788465,0.576179,0.371864,0.238217,0.15924,1.14185,0.670274,0.198172,0.814965,0.971251,0.439271,0.523438,1.38019,0.527634,0.116746,0.831412,0.478284,0.316671,0.413695,1.0796,0.546713,0.988587,0.642598,0.872646,0.124214,0.76453,1.39251,0.886589,0.410725,1.03079,1.02457,0.270369,0.311068,0.989273,1.83943,1.43902,0.95284,0.38094,0.674844,0.52079,0.341558,0.505455,1.68078,0.259186,0.732681,0.500211,0.539661,0.764896,0.286124,0.387634,1.15881,0.465765,0.939934,0.670668,1.15936,0.951654,0.747146,0.608503,1.82534,0.535644,0.402951,0.69704,0.383837,0.275137
|tfbs_overrepresentation_for_novel_motifs=1.13027,0.329487,0.585688,0.320418,0.509452,0.854581,0.385011,0.628761,0.621506,1.30663,0.293498,0.423573,0.231404,0.37489,0.169864,0.187326,0.587543,0.131867,0.534957,0.463992,0.585797,0.779448,0.839779,0.500259,0.670559,0.443987,0.442433,0.310589,0.991108,0.399779,0.275306,0.622056,0.110199,0.234859,0.447686,0.473445,0.868674,0.320003,0.127608,0.570628,0.144976,1.33439,0.171949,0.16875,0.360234,0.226447,0.385972,0.284438,0.312409,0.173249,0.456831,0.396393,0.126438,0.694739,0.841347,0.377467,0.176395,0.348876,0.177537,0.348003,0.660716,0.388062,0.299793,0.561703,1.04233,0.529794,0.927044,1.28869,0.612294,1.12869,0.251183,0.0939573,0.542218,0.839414,0.840426,0.787787,0.416738,0.546008,0.609242,0.233499,0.074278,0.560705,0.403653,0.636937,0.789807,0.914491,1.08786,0.386942,0.480498,1.38705,1.01818,0.763867,0.637885,0.368116,0.171417,0.390718,0.248364,0.67819,0.484706,0.622302,0.12852,0.632556,0.672898,0.590971,0.519171,0.788465,0.576179,0.371864,0.238217,0.15924,1.14185,0.670274,0.198172,0.814965,0.971251,0.439271,0.523438,1.38019,0.527634,0.116746,0.831412,0.478284,0.316671,0.413695,1.0796,0.546713,0.988587,0.642598,0.872646,0.124214,0.76453,1.39251,0.886589,0.410725,1.03079,1.02457,0.270369,0.311068,0.989273,1.83943,1.43902,0.95284,0.38094,0.674844,0.52079,0.341558,0.505455,1.68078,0.259186,0.732681,0.500211,0.539661,0.764896,0.286124,0.387634,1.15881,0.465765,0.939934,0.670668,1.15936,0.951654,0.747146,0.608503,1.82534,0.535644,0.402951,0.69704,0.383837,0.275137
|tfbs_overrepresentation_jaspar=MA0003.1;1.35751,MA0004.1;1.46603,MA0006.1;0.976306,MA0007.1;0.771118,MA0009.1;0.724811,MA0014.1;0.756964,MA0017.1;0.57848,MA0019.1;1.09485,MA0024.1;0.6245,MA0025.1;0.854131,MA0027.1;2.32165,MA0028.1;0.535609,MA0029.1;0.642879,MA0030.1;0.63197,MA0031.1;0.570886,MA0038.1;1.00626,MA0040.1;0.648455,MA0041.1;0.313738,MA0042.1;0.286538,MA0043.1;0.725115,MA0046.1;0.714324,MA0048.1;2.23938,MA0050.1;0.287284,MA0051.1;0.383704,MA0052.1;0.652145,MA0055.1;0.531463,MA0056.1;0,MA0057.1;0.542827,MA0058.1;0.625569,MA0059.1;0.623149,MA0060.1;1.54386,MA0061.1;0.255087,MA0063.1;0,MA0066.1;1.00709,MA0067.1;1.03434,MA0068.1;0.760324,MA0069.1;0.710614,MA0070.1;0.69985,MA0071.1;0.35315,MA0072.1;0.695528,MA0073.1;2.39546,MA0074.1;0.996524,MA0076.1;0.655479,MA0077.1;0.688123,MA0078.1;0.473657,MA0081.1;0.218332,MA0083.1;0.732051,MA0084.1;1.21913,MA0087.1;0.693179,MA0088.1;0.854057,MA0089.1;0,MA0090.1;0.243681,MA0091.1;0.30011,MA0092.1;0.268302,MA0093.1;1.56629,MA0095.1;0,MA0098.1;0,MA0100.1;0.399896,MA0101.1;0.517741,MA0103.1;0.489275,MA0105.1;0.789583,MA0106.1;0.424592,MA0107.1;0.121572,MA0108.2;0.568002,MA0109.1;0,MA0111.1;0.254772,MA0113.1;0.439505,MA0114.1;1.23864,MA0115.1;0.959312,MA0116.1;0.782807,MA0117.1;0.76111,MA0119.1;1.12008,MA0122.1;0.786181,MA0124.1;0.918678,MA0125.1;0.83671,MA0130.1;0,MA0131.1;0.490408,MA0132.1;0,MA0133.1;0,MA0135.1;0.754112,MA0136.1;0.393782,MA0139.1;0.870578,MA0140.1;0.350813,MA0141.1;0.216821,MA0142.1;1.33676,MA0143.1;0.439666,MA0144.1;0.108694,MA0145.1;0.378493,MA0146.1;0.468965,MA0147.1;0.397782,MA0148.1;0.319209,MA0149.1;0.342334,MA0062.2;0.900923,MA0035.2;0.350194,MA0039.2;0.6245,MA0138.2;0.474787,MA0002.2;0.280231,MA0137.2;0.186529,MA0104.2;0.620335,MA0047.2;0.413608,MA0112.2;0.180347,MA0065.2;0.953721,MA0150.1;0.238884,MA0151.1;0,MA0152.1;0.356591,MA0153.1;0.820317,MA0154.1;0.105196,MA0155.1;2.00431,MA0156.1;0.18827,MA0157.1;0.515488,MA0158.1;0,MA0159.1;0.398903,MA0160.1;0.332385,MA0161.1;0,MA0162.1;0.535498,MA0163.1;0.791843,MA0164.1;0.450848,MA0080.2;0.511865,MA0018.2;0.425847,MA0099.2;0.356906,MA0079.2;3.16752,MA0102.2;1.25596,MA0258.1;0.335505,MA0259.1;0.818705,MA0442.1;0
}}
}}

Revision as of 19:20, 22 January 2013


Full id: C647_pineal_cerebellum_pituitary_occipital_parietal_medial_hippocampus



Phase1 CAGE Peaks

Hg19::chr10:133879140..133879164,+p@chr10:133879140..133879164
+
Hg19::chr10:22609986..22610045,+p1@BMI1
Hg19::chr12:1192383..1192475,+p5@ERC1
Hg19::chr16:24621546..24621640,+p@chr16:24621546..24621640
+
Hg19::chr16:24661163..24661168,+p@chr16:24661163..24661168
+
Hg19::chr1:72749352..72749438,-p@chr1:72749352..72749438
-
Hg19::chr1:78444841..78444869,+p6@DNAJB4
Hg19::chr21:17443633..17443652,+p23@LINC00478
Hg19::chr2:73298446..73298468,-p5@SFXN5
Hg19::chr3:47422286..47422316,-p1@BC036224
Hg19::chr5:146762442..146762468,+p2@STK32A
Hg19::chr7:50850523..50850543,-p5@GRB10
Hg19::chrX:49012602..49012631,-p@chrX:49012602..49012631
-


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:0043522leucine zipper domain binding0.0312564375468493
GO:0030275LRR domain binding0.0312564375468493
GO:0007252I-kappaB phosphorylation0.0312564375468493
GO:0008385IkappaB kinase complex0.0338362305696425
GO:0007379segment specification0.0338362305696425
GO:0045768positive regulation of anti-apoptosis0.0338362305696425
GO:0048146positive regulation of fibroblast proliferation0.0338362305696425
GO:0048145regulation of fibroblast proliferation0.0338362305696425
GO:0048144fibroblast proliferation0.0338362305696425
GO:0045767regulation of anti-apoptosis0.0338362305696425
GO:0042734presynaptic membrane0.0338362305696425
GO:0009408response to heat0.0338362305696425



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 organism1.81e-76114
neural tube1.08e-6756
neural rod1.08e-6756
future spinal cord1.08e-6756
neural keel1.08e-6756
regional part of nervous system2.03e-6353
regional part of brain2.03e-6353
central nervous system1.13e-6281
nervous system3.03e-6289
neurectoderm5.40e-5586
neural plate6.10e-5582
presumptive neural plate6.10e-5582
regional part of forebrain7.92e-5541
forebrain7.92e-5541
anterior neural tube7.92e-5541
future forebrain7.92e-5541
brain1.60e-5468
future brain1.60e-5468
brain grey matter1.42e-4434
gray matter1.42e-4434
telencephalon1.97e-4434
ecto-epithelium3.31e-43104
pre-chordal neural plate4.75e-4361
regional part of telencephalon1.09e-4132
cerebral hemisphere1.50e-4132
ectoderm-derived structure2.91e-39171
ectoderm2.91e-39171
presumptive ectoderm2.91e-39171
structure with developmental contribution from neural crest8.81e-37132
cerebral cortex1.01e-3125
pallium1.01e-3125
organ system subdivision1.56e-29223
regional part of cerebral cortex4.74e-2922
neocortex3.16e-2620
anatomical cluster2.98e-21373
tube4.11e-18192
anatomical conduit3.33e-17240
basal ganglion2.92e-149
nuclear complex of neuraxis2.92e-149
aggregate regional part of brain2.92e-149
collection of basal ganglia2.92e-149
cerebral subcortex2.92e-149
neural nucleus3.54e-149
nucleus of brain3.54e-149
posterior neural tube8.35e-1415
chordal neural plate8.35e-1415
organ part2.66e-13218
multi-tissue structure3.05e-12342
diencephalon1.31e-117
future diencephalon1.31e-117
telencephalic nucleus2.15e-117
segmental subdivision of nervous system3.35e-1113
embryo3.49e-11592
epithelium1.08e-10306
cell layer2.22e-10309
multi-cellular organism3.06e-10656
segmental subdivision of hindbrain4.66e-1012
hindbrain4.66e-1012
presumptive hindbrain4.66e-1012
brainstem6.73e-106
germ layer7.64e-10560
germ layer / neural crest7.64e-10560
embryonic tissue7.64e-10560
presumptive structure7.64e-10560
germ layer / neural crest derived structure7.64e-10560
epiblast (generic)7.64e-10560
gyrus1.24e-096
embryonic structure1.52e-09564
developing anatomical structure3.39e-09581
organ3.73e-09503
limbic system9.87e-095
parietal lobe3.16e-085
temporal lobe3.80e-086
anatomical system6.51e-08624
occipital lobe6.53e-085
anatomical group7.58e-08625
gland of diencephalon1.53e-074
neuroendocrine gland1.53e-074
regional part of diencephalon1.90e-074
corpus striatum2.75e-074
striatum2.75e-074
ventral part of telencephalon2.75e-074
future corpus striatum2.75e-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)
MA0003.11.35751
MA0004.11.46603
MA0006.10.976306
MA0007.10.771118
MA0009.10.724811
MA0014.10.756964
MA0017.10.57848
MA0019.11.09485
MA0024.10.6245
MA0025.10.854131
MA0027.12.32165
MA0028.10.535609
MA0029.10.642879
MA0030.10.63197
MA0031.10.570886
MA0038.11.00626
MA0040.10.648455
MA0041.10.313738
MA0042.10.286538
MA0043.10.725115
MA0046.10.714324
MA0048.12.23938
MA0050.10.287284
MA0051.10.383704
MA0052.10.652145
MA0055.10.531463
MA0056.10
MA0057.10.542827
MA0058.10.625569
MA0059.10.623149
MA0060.11.54386
MA0061.10.255087
MA0063.10
MA0066.11.00709
MA0067.11.03434
MA0068.10.760324
MA0069.10.710614
MA0070.10.69985
MA0071.10.35315
MA0072.10.695528
MA0073.12.39546
MA0074.10.996524
MA0076.10.655479
MA0077.10.688123
MA0078.10.473657
MA0081.10.218332
MA0083.10.732051
MA0084.11.21913
MA0087.10.693179
MA0088.10.854057
MA0089.10
MA0090.10.243681
MA0091.10.30011
MA0092.10.268302
MA0093.11.56629
MA0095.10
MA0098.10
MA0100.10.399896
MA0101.10.517741
MA0103.10.489275
MA0105.10.789583
MA0106.10.424592
MA0107.10.121572
MA0108.20.568002
MA0109.10
MA0111.10.254772
MA0113.10.439505
MA0114.11.23864
MA0115.10.959312
MA0116.10.782807
MA0117.10.76111
MA0119.11.12008
MA0122.10.786181
MA0124.10.918678
MA0125.10.83671
MA0130.10
MA0131.10.490408
MA0132.10
MA0133.10
MA0135.10.754112
MA0136.10.393782
MA0139.10.870578
MA0140.10.350813
MA0141.10.216821
MA0142.11.33676
MA0143.10.439666
MA0144.10.108694
MA0145.10.378493
MA0146.10.468965
MA0147.10.397782
MA0148.10.319209
MA0149.10.342334
MA0062.20.900923
MA0035.20.350194
MA0039.20.6245
MA0138.20.474787
MA0002.20.280231
MA0137.20.186529
MA0104.20.620335
MA0047.20.413608
MA0112.20.180347
MA0065.20.953721
MA0150.10.238884
MA0151.10
MA0152.10.356591
MA0153.10.820317
MA0154.10.105196
MA0155.12.00431
MA0156.10.18827
MA0157.10.515488
MA0158.10
MA0159.10.398903
MA0160.10.332385
MA0161.10
MA0162.10.535498
MA0163.10.791843
MA0164.10.450848
MA0080.20.511865
MA0018.20.425847
MA0099.20.356906
MA0079.23.16752
MA0102.21.25596
MA0258.10.335505
MA0259.10.818705
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
USF2#739243.997599195406030.01425460739215360.0499945241933349



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:C647&oldid=2569158"