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Coexpression cluster:C653: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.599307,1.27624,1.10792,0.320418,0.17087,0.319017,0.385011,0.0904943,0.298989,1.30663,0.797059,0.423573,0.231404,0.37489,0.169864,0.187326,0.587543,0.412009,0.534957,0.463992,0.202464,0.148689,0.839779,0.167123,0.238419,0.443987,0.20034,0.310589,0.991108,0.177695,0.275306,0.622056,1.18646,0.234859,0.447686,0.473445,0.442053,0.320003,0.127608,3.2542,0.144976,2.05637,0.065193,0.16875,0.548753,0.642555,1.00297,1.41723,0.0578104,0.173249,0.456831,0.396393,0.300076,0.694739,0.841347,0.984299,0.176395,0.348876,0.177537,0.348003,0.660716,1.00755,0.0892869,1.38047,0.403967,0.529794,0.927044,1.28869,0.612294,1.12869,0.251183,0.0939573,2.71318,0.839414,0.487306,0.452565,0.0498505,0.546008,0.609242,0.233499,0.074278,0.560705,0.403653,0.307716,0.789807,5.99704,1.48951,0.687175,0.480498,1.38705,1.01818,1.80226,0.637885,0.368116,0.171417,0.390718,0.53079,0.67819,0.484706,1.86339,0.12852,1.52942,0.672898,0.590971,0.519171,1.43641,0.576179,0.371864,0.238217,0.480814,0.211112,0.670274,0.198172,0.814965,0.971251,0.142611,1.05642,0.274314,0.527634,0.116746,0.831412,0.478284,0.316671,0.413695,1.0796,1.34877,0.988587,0.642598,0.872646,0.124214,0.76453,0.761072,0.886589,1.05706,1.03079,0.369137,0.270369,0.311068,0.989273,1.83943,1.43902,0.95284,0.38094,0.674844,1.29375,0.341558,0.505455,1.68078,0.259186,0.732681,0.500211,2.41674,0.764896,0.286124,0.387634,1.15881,0.465765,0.939934,1.24665,1.15936,0.951654,0.747146,0.608503,0.623024,0.535644,0.402951,0.10496,0.998288,1.81316
|tfbs_overrepresentation_jaspar=MA0003.1;6.73009,MA0004.1;0.297884,MA0006.1;0.506155,MA0007.1;0.771118,MA0009.1;0.724811,MA0014.1;6.16728,MA0017.1;0.199401,MA0019.1;0.428118,MA0024.1;0.6245,MA0025.1;0.854131,MA0027.1;2.32165,MA0028.1;1.02527,MA0029.1;0.642879,MA0030.1;0.63197,MA0031.1;0.570886,MA0038.1;0.387473,MA0040.1;0.648455,MA0041.1;0.313738,MA0042.1;0.286538,MA0043.1;0.725115,MA0046.1;0.714324,MA0048.1;0.30948,MA0050.1;0.287284,MA0051.1;0.383704,MA0052.1;0.652145,MA0055.1;0.3329,MA0056.1;0,MA0057.1;5.26285,MA0058.1;0.219229,MA0059.1;0.218203,MA0060.1;0.0892161,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;4.36386,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;0.682802,MA0091.1;0.30011,MA0092.1;0.268302,MA0093.1;0.171791,MA0095.1;0,MA0098.1;0,MA0100.1;0.399896,MA0101.1;0.17426,MA0103.1;0.162663,MA0105.1;1.56723,MA0106.1;0.424592,MA0107.1;0.385539,MA0108.2;0.568002,MA0109.1;0,MA0111.1;0.708492,MA0113.1;0.439505,MA0114.1;0.757044,MA0115.1;0.959312,MA0116.1;3.21805,MA0117.1;0.76111,MA0119.1;0.205526,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;1.31319,MA0140.1;0.925465,MA0141.1;0.216821,MA0142.1;0.541045,MA0143.1;0.439666,MA0144.1;0.108694,MA0145.1;1.70801,MA0146.1;1.14469,MA0147.1;0.126316,MA0148.1;0.319209,MA0149.1;0.342334,MA0062.2;0.527542,MA0035.2;0.350194,MA0039.2;4.75477,MA0138.2;0.474787,MA0002.2;0.0821804,MA0137.2;0.186529,MA0104.2;0.298328,MA0047.2;0.413608,MA0112.2;0.888079,MA0065.2;0.953721,MA0150.1;0.238884,MA0151.1;0,MA0152.1;0.356591,MA0153.1;0.820317,MA0154.1;0.7755,MA0155.1;1.57183,MA0156.1;0.18827,MA0157.1;0.515488,MA0158.1;0,MA0159.1;1.29394,MA0160.1;0.332385,MA0161.1;0,MA0162.1;5.43109,MA0163.1;7.4957,MA0164.1;0.450848,MA0080.2;0.171855,MA0018.2;1.91268,MA0099.2;0.356906,MA0079.2;18.9595,MA0102.2;1.25596,MA0258.1;0.102521,MA0259.1;0.132107,MA0442.1;0
}}
}}

Revision as of 19:20, 22 January 2013


Full id: C653_cerebellum_pituitary_pineal_nonsmall_somatostatinoma_occipital_small



Phase1 CAGE Peaks

Hg19::chr11:17498348..17498431,-p1@ABCC8
Hg19::chr17:2652834..2652899,-p@chr17:2652834..2652899
-
Hg19::chr17:2652910..2652993,-p@chr17:2652910..2652993
-
Hg19::chr1:39734131..39734171,+p3@MACF1
Hg19::chr20:10199329..10199356,-p@chr20:10199329..10199356
-
Hg19::chr20:5892121..5892131,+p3@CHGB
Hg19::chr5:140201183..140201218,+p1@PCDHA5
Hg19::chr7:153790099..153790127,+p@chr7:153790099..153790127
+
Hg19::chr7:82792120..82792150,-p3@PCLO
Hg19::chr8:104512123..104512154,+p@chr8:104512123..104512154
+
Hg19::chr8:104512157..104512199,+p@chr8:104512157..104512199
+
Hg19::chr8:104512807..104512822,+p12@RIMS2
Hg19::chr8:104512831..104512852,+p5@RIMS2


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:0015079potassium ion transmembrane transporter activity0.0412124876932546
GO:0005522profilin binding0.0412124876932546
GO:0016079synaptic vesicle exocytosis0.0412124876932546
GO:0008281sulfonylurea receptor activity0.0412124876932546
GO:0005509calcium ion binding0.0412124876932546



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
embryonic stem cell2.79e-075
Uber Anatomy
Ontology termp-valuen
central nervous system3.66e-7181
nervous system3.46e-6989
neural tube4.11e-6856
neural rod4.11e-6856
future spinal cord4.11e-6856
neural keel4.11e-6856
regional part of nervous system3.96e-6453
regional part of brain3.96e-6453
brain2.22e-5968
future brain2.22e-5968
regional part of forebrain5.37e-5541
forebrain5.37e-5541
anterior neural tube5.37e-5541
future forebrain5.37e-5541
neural plate4.05e-4582
presumptive neural plate4.05e-4582
telencephalon6.10e-4434
brain grey matter7.75e-4434
gray matter7.75e-4434
neurectoderm3.28e-4286
cerebral hemisphere1.43e-4132
regional part of telencephalon4.58e-4132
adult organism9.11e-41114
pre-chordal neural plate8.61e-3761
regional part of cerebral cortex3.33e-3622
ecto-epithelium6.18e-35104
neocortex2.27e-3320
organ system subdivision6.07e-33223
cerebral cortex4.42e-3125
pallium4.42e-3125
ectoderm-derived structure1.05e-30171
ectoderm1.05e-30171
presumptive ectoderm1.05e-30171
structure with developmental contribution from neural crest8.05e-25132
tube2.38e-15192
anatomical cluster5.10e-15373
basal ganglion2.27e-149
nuclear complex of neuraxis2.27e-149
aggregate regional part of brain2.27e-149
collection of basal ganglia2.27e-149
cerebral subcortex2.27e-149
neural nucleus4.23e-149
nucleus of brain4.23e-149
posterior neural tube5.15e-1415
chordal neural plate5.15e-1415
diencephalon2.51e-127
future diencephalon2.51e-127
temporal lobe7.59e-126
telencephalic nucleus1.97e-117
gyrus5.60e-116
embryo6.89e-11592
anatomical conduit1.42e-10240
segmental subdivision of hindbrain1.74e-1012
hindbrain1.74e-1012
presumptive hindbrain1.74e-1012
brainstem1.19e-096
segmental subdivision of nervous system1.66e-0913
parietal lobe2.29e-095
occipital lobe3.98e-095
limbic system7.21e-095
gland of diencephalon1.94e-084
neuroendocrine gland1.94e-084
organ part3.37e-08218
corpus striatum7.76e-084
striatum7.76e-084
ventral part of telencephalon7.76e-084
future corpus striatum7.76e-084
multi-cellular organism9.03e-08656
regional part of diencephalon1.00e-074
developing anatomical structure1.10e-07581
organ1.27e-07503
epithelium1.64e-07306
germ layer2.36e-07560
germ layer / neural crest2.36e-07560
embryonic tissue2.36e-07560
presumptive structure2.36e-07560
germ layer / neural crest derived structure2.36e-07560
epiblast (generic)2.36e-07560
multi-tissue structure2.41e-07342
cell layer2.77e-07309
embryonic structure4.05e-07564
regional part of metencephalon5.86e-079
metencephalon5.86e-079
future metencephalon5.86e-079
anatomical system7.54e-07624
anatomical group8.57e-07625


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)
MA0003.16.73009
MA0004.10.297884
MA0006.10.506155
MA0007.10.771118
MA0009.10.724811
MA0014.16.16728
MA0017.10.199401
MA0019.10.428118
MA0024.10.6245
MA0025.10.854131
MA0027.12.32165
MA0028.11.02527
MA0029.10.642879
MA0030.10.63197
MA0031.10.570886
MA0038.10.387473
MA0040.10.648455
MA0041.10.313738
MA0042.10.286538
MA0043.10.725115
MA0046.10.714324
MA0048.10.30948
MA0050.10.287284
MA0051.10.383704
MA0052.10.652145
MA0055.10.3329
MA0056.10
MA0057.15.26285
MA0058.10.219229
MA0059.10.218203
MA0060.10.0892161
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
MA0073.14.36386
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
MA0090.10.682802
MA0091.10.30011
MA0092.10.268302
MA0093.10.171791
MA0095.10
MA0098.10
MA0100.10.399896
MA0101.10.17426
MA0103.10.162663
MA0105.11.56723
MA0106.10.424592
MA0107.10.385539
MA0108.20.568002
MA0109.10
MA0111.10.708492
MA0113.10.439505
MA0114.10.757044
MA0115.10.959312
MA0116.13.21805
MA0117.10.76111
MA0119.10.205526
MA0122.10.786181
MA0124.10.918678
MA0125.10.83671
MA0130.10
MA0131.10.490408
MA0132.10
MA0133.10
MA0135.10.754112
MA0136.10.393782
MA0139.11.31319
MA0140.10.925465
MA0141.10.216821
MA0142.10.541045
MA0143.10.439666
MA0144.10.108694
MA0145.11.70801
MA0146.11.14469
MA0147.10.126316
MA0148.10.319209
MA0149.10.342334
MA0062.20.527542
MA0035.20.350194
MA0039.24.75477
MA0138.20.474787
MA0002.20.0821804
MA0137.20.186529
MA0104.20.298328
MA0047.20.413608
MA0112.20.888079
MA0065.20.953721
MA0150.10.238884
MA0151.10
MA0152.10.356591
MA0153.10.820317
MA0154.10.7755
MA0155.11.57183
MA0156.10.18827
MA0157.10.515488
MA0158.10
MA0159.11.29394
MA0160.10.332385
MA0161.10
MA0162.15.43109
MA0163.17.4957
MA0164.10.450848
MA0080.20.171855
MA0018.21.91268
MA0099.20.356906
MA0079.218.9595
MA0102.21.25596
MA0258.10.102521
MA0259.10.132107
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
REST#597853.711549506203090.007520350077139610.0310074157799599
ZNF263#1012763.794696140158770.002585173580546710.0142982017464766



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:C653&oldid=2569164"