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Coexpression cluster:C876: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.312007,0.279194,0.305225,0.440628,0.267236,0.439064,0.511871,0.164003,0.161941,0.119197,0.410439,2.33761,1.30067,0.500805,0.266007,0.287179,0.728104,0.218596,0.137566,0.216842,0.305279,0.0355541,0.431698,0.262652,0.918075,0.575764,0.36063,0.429643,0.74357,0.329945,0.389837,0.764231,0.190489,0.807612,0.23642,0.261421,1.22823,0.440165,0.213144,0.14756,0.235191,0.374544,0.366128,0.731232,0.0550925,0.333541,0.51292,0.4002,0.615516,0.270138,0.589559,0.524278,0.0739421,0.839846,0.99088,0.503626,0.273964,0.472204,0.329728,0.47124,0.804523,0.5152,0.162346,0.700946,0.532513,0.667267,1.07848,1.44489,0.754027,1.28328,0.362234,0.168734,1.37801,0.988898,0.392686,0.114787,0.105027,0.684401,0.750836,0.341765,0.141333,0.699894,0.532172,0.498312,0.937974,1.24697,0.468577,0.659731,0.614883,1.54397,1.17124,0.911274,0.78075,1.08517,2.08725,1.12954,0.136404,0.82268,0.619373,0.0858425,0.214313,0.775192,0.817185,0.731699,0.656016,0.406162,0.716172,0.49749,0.917554,0.252953,0.315525,0.814459,0.300169,0.41935,1.12352,0.656078,0.218696,0.388709,0.664981,1.09481,0.980696,0.612519,2.90223,1.34104,1.23356,0.685145,0.50576,0.785662,1.02292,0.208774,0.911957,0.39253,1.03718,0.539846,1.18405,0.0922077,0.999117,0.430179,1.14186,1.99816,1.59626,1.10478,0.507423,0.819206,0.657732,0.464114,0.641461,1.83907,0.37143,0.565137,1.3062,2.39813,0.912334,1.47041,0.514733,1.31376,0.599133,0.254737,0.347536,0.320853,1.10357,0.894035,0.750062,0.323817,0.673453,0.531409,1.03307,0.510589,0.333592
|tfbs_overrepresentation_for_novel_motifs=0.312007,0.279194,0.305225,0.440628,0.267236,0.439064,0.511871,0.164003,0.161941,0.119197,0.410439,2.33761,1.30067,0.500805,0.266007,0.287179,0.728104,0.218596,0.137566,0.216842,0.305279,0.0355541,0.431698,0.262652,0.918075,0.575764,0.36063,0.429643,0.74357,0.329945,0.389837,0.764231,0.190489,0.807612,0.23642,0.261421,1.22823,0.440165,0.213144,0.14756,0.235191,0.374544,0.366128,0.731232,0.0550925,0.333541,0.51292,0.4002,0.615516,0.270138,0.589559,0.524278,0.0739421,0.839846,0.99088,0.503626,0.273964,0.472204,0.329728,0.47124,0.804523,0.5152,0.162346,0.700946,0.532513,0.667267,1.07848,1.44489,0.754027,1.28328,0.362234,0.168734,1.37801,0.988898,0.392686,0.114787,0.105027,0.684401,0.750836,0.341765,0.141333,0.699894,0.532172,0.498312,0.937974,1.24697,0.468577,0.659731,0.614883,1.54397,1.17124,0.911274,0.78075,1.08517,2.08725,1.12954,0.136404,0.82268,0.619373,0.0858425,0.214313,0.775192,0.817185,0.731699,0.656016,0.406162,0.716172,0.49749,0.917554,0.252953,0.315525,0.814459,0.300169,0.41935,1.12352,0.656078,0.218696,0.388709,0.664981,1.09481,0.980696,0.612519,2.90223,1.34104,1.23356,0.685145,0.50576,0.785662,1.02292,0.208774,0.911957,0.39253,1.03718,0.539846,1.18405,0.0922077,0.999117,0.430179,1.14186,1.99816,1.59626,1.10478,0.507423,0.819206,0.657732,0.464114,0.641461,1.83907,0.37143,0.565137,1.3062,2.39813,0.912334,1.47041,0.514733,1.31376,0.599133,0.254737,0.347536,0.320853,1.10357,0.894035,0.750062,0.323817,0.673453,0.531409,1.03307,0.510589,0.333592
|tfbs_overrepresentation_jaspar=MA0003.1;0.0913842,MA0004.1;0.415381,MA0006.1;0.265592,MA0007.1;1.02827,MA0009.1;0.870971,MA0014.1;0.580022,MA0017.1;0.301634,MA0019.1;0.558663,MA0024.1;0.766783,MA0025.1;1.00397,MA0027.1;2.48103,MA0028.1;0.280275,MA0029.1;0.785955,MA0030.1;0.774581,MA0031.1;0.710608,MA0038.1;0.514558,MA0040.1;0.791764,MA0041.1;0.433167,MA0042.1;0.402577,MA0043.1;0.871285,MA0046.1;0.860127,MA0048.1;0.264106,MA0050.1;0.403421,MA0051.1;0.510444,MA0052.1;0.795605,MA0055.1;1.40898,MA0056.1;0,MA0057.1;0.253359,MA0058.1;0.325084,MA0059.1;0.323879,MA0060.1;0.162248,MA0061.1;0.139804,MA0063.1;0,MA0066.1;0.514973,MA0067.1;1.18766,MA0068.1;0.109867,MA0069.1;0.856287,MA0070.1;0.845142,MA0071.1;0.47692,MA0072.1;0.840664,MA0073.1;0.987536,MA0074.1;1.27017,MA0076.1;0.339975,MA0077.1;1.94461,MA0078.1;0.607575,MA0081.1;0.324031,MA0083.1;0.878452,MA0084.1;1.37471,MA0087.1;0.838229,MA0088.1;0.158781,MA0089.1;0,MA0090.1;0.353576,MA0091.1;0.417885,MA0092.1;0.381858,MA0093.1;0.26836,MA0095.1;0,MA0098.1;0,MA0100.1;0.528088,MA0101.1;0.271368,MA0103.1;0.257174,MA0105.1;0.229733,MA0106.1;0.554855,MA0107.1;0.205358,MA0108.2;0.707575,MA0109.1;0,MA0111.1;0.959847,MA0113.1;3.50747,MA0114.1;0.200901,MA0115.1;1.11137,MA0116.1;0.208403,MA0117.1;0.908433,MA0119.1;0.308914,MA0122.1;0.934245,MA0124.1;1.06995,MA0125.1;0.986127,MA0130.1;0,MA0131.1;0.625452,MA0132.1;0,MA0133.1;0,MA0135.1;0.90122,MA0136.1;0.521435,MA0139.1;0.406919,MA0140.1;1.19454,MA0141.1;0.322254,MA0142.1;0.679161,MA0143.1;0.571113,MA0144.1;0.1885,MA0145.1;0.706237,MA0146.1;0.0794051,MA0147.1;0.211483,MA0148.1;0.439278,MA0149.1;0.464973,MA0062.2;0.135498,MA0035.2;1.19307,MA0039.2;0.909157,MA0138.2;0.608783,MA0002.2;0.152495,MA0137.2;0.28622,MA0104.2;0.161609,MA0047.2;0.542971,MA0112.2;0.166662,MA0065.2;0.0483532,MA0150.1;0.34802,MA0151.1;0,MA0152.1;0.480711,MA0153.1;5.19916,MA0154.1;0.062786,MA0155.1;0.359913,MA0156.1;0.288314,MA0157.1;0.652111,MA0158.1;0,MA0159.1;0.212043,MA0160.1;1.15068,MA0161.1;0,MA0162.1;0.294626,MA0163.1;0.034916,MA0164.1;0.583138,MA0080.2;0.268439,MA0018.2;0.556211,MA0099.2;0.481058,MA0079.2;0.893499,MA0102.2;1.41188,MA0258.1;0.180288,MA0259.1;0.218904,MA0442.1;0
}}
}}

Revision as of 19:31, 22 January 2013


Full id: C876_skeletal_spinal_medulla_hippocampus_parietal_thalamus_occipital



Phase1 CAGE Peaks

Hg19::chr10:94001015..94001051,-p@chr10:94001015..94001051
-
Hg19::chr15:93632396..93632407,-p3@RGMA
Hg19::chr1:160103394..160103410,+p@chr1:160103394..160103410
+
Hg19::chr1:160103559..160103576,+p@chr1:160103559..160103576
+
Hg19::chr1:160103656..160103669,+p@chr1:160103656..160103669
+
Hg19::chr1:160103687..160103724,+p@chr1:160103687..160103724
+
Hg19::chr1:160103733..160103769,+p@chr1:160103733..160103769
+
Hg19::chr1:160107625..160107629,+p@chr1:160107625..160107629
+
Hg19::chrX:135849340..135849399,-p6@ARHGEF6


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:0001843neural tube closure0.010383953248564
GO:0014020primary neural tube formation0.010383953248564
GO:0001839neural plate morphogenesis0.010383953248564
GO:0001841neural tube formation0.010383953248564
GO:0001840neural plate development0.010383953248564
GO:0001838embryonic epithelial tube formation0.010383953248564
GO:0021915neural tube development0.010383953248564
GO:0016331morphogenesis of embryonic epithelium0.0105201195496108
GO:0002009morphogenesis of an epithelium0.0236325170582736
GO:0007254JNK cascade0.0236325170582736
GO:0031098stress-activated protein kinase signaling pathway0.0236325170582736
GO:0035239tube morphogenesis0.0242021142259976
GO:0048598embryonic morphogenesis0.0242021142259976
GO:0009792embryonic development ending in birth or egg hatching0.0242021142259976
GO:0043009chordate embryonic development0.0242021142259976
GO:0035295tube development0.0274244371401497
GO:0048503GPI anchor binding0.0274244371401497
GO:0009986cell surface0.0274244371401497
GO:0000165MAPKKK cascade0.0274244371401497
GO:0005089Rho guanyl-nucleotide exchange factor activity0.0274244371401497
GO:0035023regulation of Rho protein signal transduction0.0274244371401497
GO:0005088Ras guanyl-nucleotide exchange factor activity0.0274244371401497
GO:0032502developmental process0.0274244371401497
GO:0007266Rho protein signal transduction0.0298931627822005
GO:0009790embryonic development0.0358469119443389
GO:0035091phosphoinositide binding0.0368062548747997
GO:0005085guanyl-nucleotide exchange factor activity0.0435957043134591
GO:0005543phospholipid binding0.0441627868691779
GO:0016337cell-cell adhesion0.0441627868691779
GO:0005096GTPase activator activity0.0441627868691779
GO:0046578regulation of Ras protein signal transduction0.044715327201792
GO:0007243protein kinase cascade0.044715327201792
GO:0007265Ras protein signal transduction0.049776947180899



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 organism2.51e-95114
neural tube4.01e-8356
neural rod4.01e-8356
future spinal cord4.01e-8356
neural keel4.01e-8356
regional part of nervous system2.33e-7653
regional part of brain2.33e-7653
central nervous system1.42e-6581
regional part of forebrain1.05e-6141
forebrain1.05e-6141
anterior neural tube1.05e-6141
future forebrain1.05e-6141
brain1.28e-6168
future brain1.28e-6168
neural plate1.90e-6082
presumptive neural plate1.90e-6082
nervous system1.18e-5789
neurectoderm5.58e-5786
brain grey matter6.98e-5534
gray matter6.98e-5534
telencephalon7.26e-5534
regional part of telencephalon1.90e-5032
cerebral hemisphere2.13e-5032
ecto-epithelium1.16e-44104
structure with developmental contribution from neural crest3.63e-42132
regional part of cerebral cortex1.42e-4122
pre-chordal neural plate9.03e-4161
neocortex6.83e-3720
cerebral cortex5.07e-3625
pallium5.07e-3625
ectoderm-derived structure1.80e-32171
ectoderm1.80e-32171
presumptive ectoderm1.80e-32171
organ system subdivision4.56e-25223
posterior neural tube2.01e-2115
chordal neural plate2.01e-2115
neural nucleus1.42e-209
nucleus of brain1.42e-209
basal ganglion1.96e-209
nuclear complex of neuraxis1.96e-209
aggregate regional part of brain1.96e-209
collection of basal ganglia1.96e-209
cerebral subcortex1.96e-209
tube1.26e-19192
anatomical conduit1.26e-19240
telencephalic nucleus3.62e-167
anatomical cluster7.24e-16373
segmental subdivision of hindbrain3.01e-1512
hindbrain3.01e-1512
presumptive hindbrain3.01e-1512
brainstem9.69e-156
gyrus3.81e-146
segmental subdivision of nervous system6.45e-1413
multi-tissue structure1.55e-13342
limbic system6.01e-135
parietal lobe2.48e-125
temporal lobe7.26e-126
epithelium5.98e-11306
cell layer1.05e-10309
organ part1.73e-10218
organ2.65e-10503
regional part of diencephalon6.34e-104
corpus striatum6.80e-104
striatum6.80e-104
ventral part of telencephalon6.80e-104
future corpus striatum6.80e-104
regional part of metencephalon1.90e-099
metencephalon1.90e-099
future metencephalon1.90e-099
embryo5.54e-09592
germ layer1.96e-08560
germ layer / neural crest1.96e-08560
embryonic tissue1.96e-08560
presumptive structure1.96e-08560
germ layer / neural crest derived structure1.96e-08560
epiblast (generic)1.96e-08560
diencephalon2.40e-087
future diencephalon2.40e-087
multi-cellular organism2.43e-08656
pons2.50e-083
spinal cord3.02e-083
dorsal region element3.02e-083
dorsum3.02e-083
embryonic structure3.07e-08564
medulla oblongata4.31e-083
myelencephalon4.31e-083
future myelencephalon4.31e-083
frontal cortex5.09e-083
developing anatomical structure6.34e-08581
occipital lobe9.51e-085
caudate-putamen1.31e-073
dorsal striatum1.31e-073
anatomical system4.75e-07624
anatomical group5.24e-07625
male genital duct8.84e-073
internal male genitalia8.84e-073


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)
MA0003.10.0913842
MA0004.10.415381
MA0006.10.265592
MA0007.11.02827
MA0009.10.870971
MA0014.10.580022
MA0017.10.301634
MA0019.10.558663
MA0024.10.766783
MA0025.11.00397
MA0027.12.48103
MA0028.10.280275
MA0029.10.785955
MA0030.10.774581
MA0031.10.710608
MA0038.10.514558
MA0040.10.791764
MA0041.10.433167
MA0042.10.402577
MA0043.10.871285
MA0046.10.860127
MA0048.10.264106
MA0050.10.403421
MA0051.10.510444
MA0052.10.795605
MA0055.11.40898
MA0056.10
MA0057.10.253359
MA0058.10.325084
MA0059.10.323879
MA0060.10.162248
MA0061.10.139804
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.10.109867
MA0069.10.856287
MA0070.10.845142
MA0071.10.47692
MA0072.10.840664
MA0073.10.987536
MA0074.11.27017
MA0076.10.339975
MA0077.11.94461
MA0078.10.607575
MA0081.10.324031
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.10.158781
MA0089.10
MA0090.10.353576
MA0091.10.417885
MA0092.10.381858
MA0093.10.26836
MA0095.10
MA0098.10
MA0100.10.528088
MA0101.10.271368
MA0103.10.257174
MA0105.10.229733
MA0106.10.554855
MA0107.10.205358
MA0108.20.707575
MA0109.10
MA0111.10.959847
MA0113.13.50747
MA0114.10.200901
MA0115.11.11137
MA0116.10.208403
MA0117.10.908433
MA0119.10.308914
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.10.406919
MA0140.11.19454
MA0141.10.322254
MA0142.10.679161
MA0143.10.571113
MA0144.10.1885
MA0145.10.706237
MA0146.10.0794051
MA0147.10.211483
MA0148.10.439278
MA0149.10.464973
MA0062.20.135498
MA0035.21.19307
MA0039.20.909157
MA0138.20.608783
MA0002.20.152495
MA0137.20.28622
MA0104.20.161609
MA0047.20.542971
MA0112.20.166662
MA0065.20.0483532
MA0150.10.34802
MA0151.10
MA0152.10.480711
MA0153.15.19916
MA0154.10.062786
MA0155.10.359913
MA0156.10.288314
MA0157.10.652111
MA0158.10
MA0159.10.212043
MA0160.11.15068
MA0161.10
MA0162.10.294626
MA0163.10.034916
MA0164.10.583138
MA0080.20.268439
MA0018.20.556211
MA0099.20.481058
MA0079.20.893499
MA0102.21.41188
MA0258.10.180288
MA0259.10.218904
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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C876&oldid=2569387"