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Coexpression cluster:C982: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.348717,0.600139,0.341646,0.481684,0.301904,0.480078,0.554663,0.19223,0.555925,0.355088,0.450635,0.597407,1.45506,0.543352,0.81316,0.322799,0.774423,0.250594,0.491486,0.950453,0.341703,0.405031,0.472508,0.805193,0.385586,0.619829,0.135503,0.470396,2.27376,0.122648,1.09762,0.810962,0.628961,0.469827,0.742281,1.2001,0.266487,0.481208,0.244807,0.996317,0.268162,0.413601,0.444349,0.299183,0.949078,0.970329,0.555735,0.440085,0.186577,0.304949,0.63387,0.567337,1.06746,0.887323,1.03948,0.546236,0.308962,0.514077,0.776738,0.513089,0.85167,0.558065,0.190442,0.746929,1.4101,0.712797,1.12756,1.49516,0.800646,1.33315,0.400869,0.573519,0.304852,1.03748,1.43212,0.429044,0.127753,0.730167,0.797419,0.379656,0.167664,0.745864,0.575394,0.567311,2.258,0.450611,0.26222,0.759942,0.659621,1.59442,1.22073,0.959334,0.827657,0.227232,1.48306,0.672575,0.488357,0.87,0.664183,2.9884,0.246049,0.822041,0.864454,0.778061,0.701386,1.98154,0.762347,0.539961,1.00159,0.782066,0.352381,0.861701,1.60345,0.459808,1.17281,0.265019,1.199,1.0951,0.710479,0.229841,1.02923,0.657218,0.477387,0.586509,1.28328,0.730921,1.35238,0.83262,1.07171,0.674618,0.960022,1.10364,1.08604,0.583225,1.23359,0.364369,0.423593,0.470947,1.19123,2.04907,1.64679,1.15398,0.550118,0.866494,0.703126,0.505785,0.686615,1.88987,0.410382,0.224241,0.593875,0.423488,0.960402,1.03091,0.557588,1.36372,0.643609,0.288769,0.385642,0.941217,1.15277,0.941964,0.796636,0.948033,0.71907,0.574616,0.213234,0.553354,0.0643507
|tfbs_overrepresentation_jaspar=MA0003.1;0.797136,MA0004.1;0.455723,MA0006.1;0.300178,MA0007.1;1.1148,MA0009.1;0.918715,MA0014.1;0.473479,MA0017.1;0.337901,MA0019.1;0.602411,MA0024.1;0.813542,MA0025.1;1.05265,MA0027.1;2.5321,MA0028.1;0.846854,MA0029.1;0.832916,MA0030.1;0.821423,MA0031.1;0.756713,MA0038.1;0.557409,MA0040.1;0.838784,MA0041.1;0.474018,MA0042.1;0.442535,MA0043.1;0.919032,MA0046.1;0.90778,MA0048.1;2.19172,MA0050.1;0.443405,MA0051.1;0.553205,MA0052.1;0.842664,MA0055.1;0.835832,MA0056.1;0,MA0057.1;0.305162,MA0058.1;0.362328,MA0059.1;0.361075,MA0060.1;0.190336,MA0061.1;0.165998,MA0063.1;0,MA0066.1;0.557833,MA0067.1;1.23721,MA0068.1;0.133123,MA0069.1;0.903908,MA0070.1;0.892666,MA0071.1;0.518907,MA0072.1;0.888148,MA0073.1;0.326687,MA0074.1;0.552456,MA0076.1;0.377799,MA0077.1;0.880402,MA0078.1;0.652193,MA0081.1;0.361233,MA0083.1;0.926258,MA0084.1;1.42483,MA0087.1;0.885691,MA0088.1;0.199853,MA0089.1;0,MA0090.1;0.391903,MA0091.1;0.458301,MA0092.1;1.07975,MA0093.1;0.303084,MA0095.1;0,MA0098.1;0,MA0100.1;0.571227,MA0101.1;0.30624,MA0103.1;0.291333,MA0105.1;0.0818021,MA0106.1;1.45807,MA0107.1;0.236528,MA0108.2;0.753643,MA0109.1;0,MA0111.1;1.04489,MA0113.1;0.614917,MA0114.1;0.231781,MA0115.1;1.1606,MA0116.1;0.673701,MA0117.1;0.956472,MA0119.1;0.345493,MA0122.1;0.982472,MA0124.1;1.11898,MA0125.1;1.0347,MA0130.1;0,MA0131.1;0.670358,MA0132.1;0,MA0133.1;0,MA0135.1;0.949204,MA0136.1;0.564434,MA0139.1;0.916926,MA0140.1;0.516266,MA0141.1;0.359385,MA0142.1;0.724856,MA0143.1;0.615094,MA0144.1;0.623945,MA0145.1;1.7555,MA0146.1;0.65158,MA0147.1;0.243042,MA0148.1;0.480298,MA0149.1;0.506665,MA0062.2;0.485915,MA0035.2;0.515566,MA0039.2;0.44475,MA0138.2;0.653421,MA0002.2;0.179788,MA0137.2;0.86081,MA0104.2;0.189646,MA0047.2;0.586412,MA0112.2;1.69642,MA0065.2;0.0631316,MA0150.1;0.386144,MA0151.1;0,MA0152.1;1.29801,MA0153.1;1.01778,MA0154.1;0.0799828,MA0155.1;0.43752,MA0156.1;0.323987,MA0157.1;0.697424,MA0158.1;0,MA0159.1;0.682702,MA0160.1;0.495355,MA0161.1;0,MA0162.1;0.378102,MA0163.1;0.288263,MA0164.1;0.627336,MA0080.2;0.303167,MA0018.2;0.599912,MA0099.2;0.523145,MA0079.2;0.481761,MA0102.2;1.46209,MA0258.1;1.7796,MA0259.1;0.699589,MA0442.1;0
}}
}}

Revision as of 19:36, 22 January 2013


Full id: C982_pineal_substantia_thalamus_globus_spinal_corpus_medulla



Phase1 CAGE Peaks

Hg19::chr10:75118611..75118626,-p2@TTC18
Hg19::chr15:48010462..48010480,+p8@SEMA6D
Hg19::chr17:20979154..20979174,+p2@ENST00000456235
Hg19::chr17:73472575..73472603,+p3@KIAA0195
Hg19::chr19:35417728..35417761,-p1@BC047554
Hg19::chr3:118753758..118753785,-p4@IGSF11
Hg19::chr4:87855851..87855903,-p1@C4orf36
Hg19::chr7:29519662..29519677,+p4@CHN2


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><br>

Uber Anatomy
Ontology termp-valuen
adult organism5.71e-86114
neural tube6.09e-6656
neural rod6.09e-6656
future spinal cord6.09e-6656
neural keel6.09e-6656
regional part of nervous system2.10e-6153
regional part of brain2.10e-6153
central nervous system2.15e-5881
nervous system2.61e-5489
brain7.78e-5468
future brain7.78e-5468
regional part of forebrain1.56e-5341
forebrain1.56e-5341
anterior neural tube1.56e-5341
future forebrain1.56e-5341
neural plate1.84e-5282
presumptive neural plate1.84e-5282
neurectoderm9.51e-5186
telencephalon4.90e-4334
brain grey matter6.15e-4334
gray matter6.15e-4334
pre-chordal neural plate8.65e-4161
regional part of telencephalon5.10e-4032
ecto-epithelium5.44e-40104
cerebral hemisphere7.34e-4032
structure with developmental contribution from neural crest8.32e-34132
organ system subdivision4.57e-30223
cerebral cortex2.15e-2925
pallium2.15e-2925
regional part of cerebral cortex2.35e-2922
ectoderm-derived structure4.54e-29171
ectoderm4.54e-29171
presumptive ectoderm4.54e-29171
neocortex1.62e-2620
anatomical cluster4.74e-18373
tube5.04e-17192
anatomical conduit4.02e-15240
neural nucleus4.85e-159
nucleus of brain4.85e-159
basal ganglion6.04e-159
nuclear complex of neuraxis6.04e-159
aggregate regional part of brain6.04e-159
collection of basal ganglia6.04e-159
cerebral subcortex6.04e-159
multi-tissue structure2.30e-14342
posterior neural tube2.16e-1315
chordal neural plate2.16e-1315
epithelium1.82e-12306
telencephalic nucleus3.27e-127
cell layer3.96e-12309
diencephalon9.38e-127
future diencephalon9.38e-127
segmental subdivision of nervous system1.17e-1013
organ2.67e-10503
brainstem3.96e-106
gyrus6.18e-106
embryo1.31e-09592
segmental subdivision of hindbrain1.84e-0912
hindbrain1.84e-0912
presumptive hindbrain1.84e-0912
organ part2.49e-09218
limbic system9.50e-095
developing anatomical structure1.42e-08581
embryonic structure1.95e-08564
germ layer2.70e-08560
germ layer / neural crest2.70e-08560
embryonic tissue2.70e-08560
presumptive structure2.70e-08560
germ layer / neural crest derived structure2.70e-08560
epiblast (generic)2.70e-08560
occipital lobe3.84e-085
parietal lobe3.89e-085
multi-cellular organism4.23e-08656
temporal lobe5.00e-086
regional part of diencephalon7.78e-084
corpus striatum1.04e-074
striatum1.04e-074
ventral part of telencephalon1.04e-074
future corpus striatum1.04e-074
gland of diencephalon3.44e-074
neuroendocrine gland3.44e-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)
MA0003.10.797136
MA0004.10.455723
MA0006.10.300178
MA0007.11.1148
MA0009.10.918715
MA0014.10.473479
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.846854
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.12.19172
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.10.835832
MA0056.10
MA0057.10.305162
MA0058.10.362328
MA0059.10.361075
MA0060.10.190336
MA0061.10.165998
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.133123
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.10.326687
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.199853
MA0089.10
MA0090.10.391903
MA0091.10.458301
MA0092.11.07975
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.30624
MA0103.10.291333
MA0105.10.0818021
MA0106.11.45807
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.11.04489
MA0113.10.614917
MA0114.10.231781
MA0115.11.1606
MA0116.10.673701
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.916926
MA0140.10.516266
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.10.623945
MA0145.11.7555
MA0146.10.65158
MA0147.10.243042
MA0148.10.480298
MA0149.10.506665
MA0062.20.485915
MA0035.20.515566
MA0039.20.44475
MA0138.20.653421
MA0002.20.179788
MA0137.20.86081
MA0104.20.189646
MA0047.20.586412
MA0112.21.69642
MA0065.20.0631316
MA0150.10.386144
MA0151.10
MA0152.11.29801
MA0153.11.01778
MA0154.10.0799828
MA0155.10.43752
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.10.682702
MA0160.10.495355
MA0161.10
MA0162.10.378102
MA0163.10.288263
MA0164.10.627336
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.20.481761
MA0102.21.46209
MA0258.11.7796
MA0259.10.699589
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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