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Coexpression cluster:C4553: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.699513,1.40091,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,1.18351,0.820209,0.985163,0.436625,0.925331,0.639839,1.60265,1.17594,0.575162,0.452865,0.305559,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.427404,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.259059,0.63803,0.461452,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.893117,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,1.7986,0.502203,1.5923,1.45054,1.10051,0.414196,0.396746,1.12884,1.20029,0.73687,1.16162,1.14559,0.960908,0.498519,1.39759,0.507157,0.303648,1.76229,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,1.54991,1.37703,1.14422,1.27663,1.05794,1.68795,1.39614,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,1.44883,1.66424,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,1.96632,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,2.04753,1.08214,2.31409,0.773313,0.539692,0.318511,1.29196,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.56135
|tfbs_overrepresentation_jaspar=MA0003.1;0.178364,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;0.118426,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;1.21731,MA0025.1;1.46617,MA0027.1;2.95767,MA0028.1;0.658629,MA0029.1;1.23771,MA0030.1;1.22561,MA0031.1;1.15713,MA0038.1;0.94098,MA0040.1;1.24388,MA0041.1;0.847069,MA0042.1;0.810843,MA0043.1;1.32783,MA0046.1;1.31611,MA0048.1;0.341392,MA0050.1;0.81185,MA0051.1;2.15619,MA0052.1;1.24796,MA0055.1;2.37507,MA0056.1;0,MA0057.1;0.333427,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;0.492218,MA0061.1;0.456531,MA0063.1;0,MA0066.1;0.941452,MA0067.1;1.65513,MA0068.1;1.84332,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;0.668628,MA0074.1;0.935474,MA0076.1;0.734647,MA0077.1;1.28751,MA0078.1;1.04495,MA0081.1;1.70054,MA0083.1;1.33535,MA0084.1;1.84562,MA0087.1;1.29304,MA0088.1;0.257905,MA0089.1;0,MA0090.1;0.751469,MA0091.1;0.829044,MA0092.1;0.785956,MA0093.1;0.642957,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;0.646932,MA0103.1;0.628063,MA0105.1;0.31555,MA0106.1;0.986396,MA0107.1;0.556367,MA0108.2;1.15387,MA0109.1;0,MA0111.1;0.767139,MA0113.1;1.00436,MA0114.1;0.549955,MA0115.1;1.57693,MA0116.1;0.560723,MA0117.1;1.36676,MA0119.1;0.695578,MA0122.1;1.39371,MA0124.1;1.53432,MA0125.1;1.44766,MA0130.1;0,MA0131.1;1.06461,MA0132.1;0,MA0133.1;0,MA0135.1;1.35921,MA0136.1;0.948776,MA0139.1;0.440097,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;2.29531,MA0144.1;0.531867,MA0145.1;0.273764,MA0146.1;0.107247,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;0.0526989,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;0.264678,MA0065.2;0.277623,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.312019,MA0155.1;3.71118,MA0156.1;1.60572,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.149099,MA0163.1;3.96434,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.311277,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0
}}
}}

Revision as of 22:08, 22 January 2013


Full id: C4553_peripheral_cerebellum_neuroectodermal_neuroblastoma_occipital_cerebral_duodenum



Phase1 CAGE Peaks

Hg19::chr6:123317372..123317398,+p1@CLVS2
Hg19::chr6:123318814..123318860,+p@chr6:123318814..123318860
+
Hg19::chr6:123318862..123318892,+p@chr6:123318862..123318892
+


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><br>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
neural tube2.43e-8156
neural rod2.43e-8156
future spinal cord2.43e-8156
neural keel2.43e-8156
regional part of nervous system1.44e-7353
regional part of brain1.44e-7353
nervous system2.02e-7089
neurectoderm6.86e-6586
central nervous system7.41e-6581
brain3.12e-6168
future brain3.12e-6168
neural plate2.96e-5582
presumptive neural plate2.96e-5582
regional part of forebrain3.01e-5341
forebrain3.01e-5341
anterior neural tube3.01e-5341
future forebrain3.01e-5341
adult organism1.12e-50114
brain grey matter8.75e-4434
gray matter8.75e-4434
telencephalon1.21e-4334
ecto-epithelium2.06e-41104
ectoderm-derived structure1.43e-40171
ectoderm1.43e-40171
presumptive ectoderm1.43e-40171
cerebral hemisphere4.21e-3932
regional part of telencephalon9.50e-3932
pre-chordal neural plate4.89e-3661
regional part of cerebral cortex3.11e-3422
structure with developmental contribution from neural crest6.98e-34132
neocortex2.83e-3320
cerebral cortex9.00e-3025
pallium9.00e-3025
posterior neural tube1.34e-2815
chordal neural plate1.34e-2815
organ system subdivision1.08e-27223
segmental subdivision of hindbrain5.97e-2112
hindbrain5.97e-2112
presumptive hindbrain5.97e-2112
segmental subdivision of nervous system3.41e-1913
brainstem4.81e-196
gyrus3.84e-186
tube1.20e-16192
neural nucleus1.55e-159
nucleus of brain1.55e-159
regional part of metencephalon4.84e-139
metencephalon4.84e-139
future metencephalon4.84e-139
anatomical cluster2.12e-12373
anatomical conduit3.32e-12240
sympathetic nervous system2.01e-115
autonomic nervous system2.01e-115
basal ganglion3.44e-119
nuclear complex of neuraxis3.44e-119
aggregate regional part of brain3.44e-119
collection of basal ganglia3.44e-119
cerebral subcortex3.44e-119
diencephalon8.28e-117
future diencephalon8.28e-117
temporal lobe1.29e-106
pons1.98e-103
telencephalic nucleus2.13e-107
medulla oblongata2.47e-103
myelencephalon2.47e-103
future myelencephalon2.47e-103
parietal lobe3.60e-105
frontal cortex4.76e-103
spinal cord1.27e-093
dorsal region element1.27e-093
dorsum1.27e-093
organ part1.96e-08218
epithelium4.36e-08306
cell layer6.48e-08309
gland of diencephalon7.30e-084
neuroendocrine gland7.30e-084
pituitary gland8.98e-082
locus ceruleus2.68e-072
brainstem nucleus2.68e-072
hindbrain nucleus2.68e-072
middle frontal gyrus3.44e-072
corpus striatum3.50e-074
striatum3.50e-074
ventral part of telencephalon3.50e-074
future corpus striatum3.50e-074
middle temporal gyrus5.15e-072
meninx5.65e-072
membrane organ5.65e-072
meningeal cluster5.65e-072
germ layer8.82e-07560
germ layer / neural crest8.82e-07560
embryonic tissue8.82e-07560
presumptive structure8.82e-07560
germ layer / neural crest derived structure8.82e-07560
epiblast (generic)8.82e-07560
Disease
Ontology termp-valuen
neuroectodermal tumor5.23e-2110
neuroendocrine tumor1.65e-096
germ cell and embryonal cancer1.06e-0822
germ cell cancer1.06e-0822


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)
MA0003.10.178364
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.12.15619
MA0052.11.24796
MA0055.12.37507
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.84332
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.668628
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.11.70054
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.12.29531
MA0144.10.531867
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.13.71118
MA0156.11.60572
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.13.96434
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.311277
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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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