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{{Coexpression_clusters
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0.177664,0.28365,0.0385243,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.0750181|tfbs_overrepresentation_for_novel_motifs=0.699513,0.14394,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,1.18351,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,1.49369,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,1.05396,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.427404,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.259059,0.63803,0.151453,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,1.10051,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.169933,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.188952,0.794219,1.10778,1.35006,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.250511,1.37083,1.21015,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.265282|tfbs_overrepresentation_jaspar=MA0003.1;0.401049,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;0.377374,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;0.936307,MA0052.1;1.24796,MA0055.1;1.06172,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;0.405474,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;0.0834661,MA0074.1;0.935474,MA0076.1;0.734647,MA0077.1;1.28751,MA0078.1;1.04495,MA0081.1;0.714712,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;1.52002,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;1.00455,MA0144.1;0.531867,MA0145.1;0.273764,MA0146.1;0.348055,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;0.195278,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;0.731309,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;0.256269,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.149099,MA0163.1;0.122425,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.09178,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C3120_cerebellum_caudate_putamen_amygdala_middle_nucleus_diencephalon
|id=C3120
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!4.36e-35!94;UBERON:0001016!4.36e-35!94;UBERON:0000955!1.49e-33!69;UBERON:0006238!1.49e-33!69;UBERON:0001049!1.83e-33!57;UBERON:0005068!1.83e-33!57;UBERON:0006241!1.83e-33!57;UBERON:0007135!1.83e-33!57;UBERON:0005743!2.63e-33!86;UBERON:0001017!2.60e-32!82;UBERON:0002616!4.96e-31!59;UBERON:0002780!2.76e-30!41;UBERON:0001890!2.76e-30!41;UBERON:0006240!2.76e-30!41;UBERON:0003080!3.51e-29!42;UBERON:0002346!1.87e-28!90;UBERON:0003075!4.85e-27!86;UBERON:0007284!4.85e-27!86;UBERON:0001893!2.61e-24!34;UBERON:0002020!8.75e-24!34;UBERON:0003528!8.75e-24!34;UBERON:0003056!1.36e-23!61;UBERON:0002791!2.25e-23!33;UBERON:0001869!2.78e-23!32;UBERON:0000033!9.79e-19!123;UBERON:0002619!2.02e-18!22;UBERON:0000924!3.38e-18!173;UBERON:0006601!3.38e-18!173;UBERON:0000153!1.35e-17!129;UBERON:0007811!1.35e-17!129;UBERON:0004121!5.05e-17!169;UBERON:0001950!1.86e-16!20;UBERON:0000956!1.88e-16!25;UBERON:0000203!1.88e-16!25;UBERON:0007023!1.43e-15!115;UBERON:0002420!8.01e-10!9;UBERON:0007245!8.01e-10!9;UBERON:0010009!8.01e-10!9;UBERON:0010011!8.01e-10!9;UBERON:0000454!8.01e-10!9;UBERON:0002308!6.42e-09!9;UBERON:0000125!6.42e-09!9;UBERON:0000025!3.39e-08!194;UBERON:0009663!7.93e-08!7;UBERON:0000200!1.80e-07!6;UBERON:0001894!1.98e-07!7;UBERON:0006222!1.98e-07!7;UBERON:0001871!4.61e-07!7
}}

Latest revision as of 12:19, 17 September 2013


Full id: C3120_cerebellum_caudate_putamen_amygdala_middle_nucleus_diencephalon



Phase1 CAGE Peaks

Hg19::chr11:17172163..17172175,-p@chr11:17172163..17172175
-
Hg19::chr16:89772545..89772566,+p@chr16:89772545..89772566
+
Hg19::chr8:22086151..22086178,-p7@PHYHIP


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
regional part of nervous system7.10e-8153
regional part of brain7.10e-8153
neural tube3.03e-8056
neural rod3.03e-8056
future spinal cord3.03e-8056
neural keel3.03e-8056
brain4.78e-6768
future brain4.78e-6768
regional part of forebrain3.19e-6541
forebrain3.19e-6541
anterior neural tube3.19e-6541
future forebrain3.19e-6541
telencephalon2.90e-6434
central nervous system6.44e-6481
brain grey matter9.29e-6434
gray matter9.29e-6434
cerebral hemisphere1.35e-6332
nervous system2.42e-6289
regional part of telencephalon1.48e-5832
neural plate9.99e-5582
presumptive neural plate9.99e-5582
neurectoderm1.27e-5486
regional part of cerebral cortex1.05e-4822
pre-chordal neural plate2.12e-4461
neocortex1.33e-4220
cerebral cortex1.79e-4225
pallium1.79e-4225
ecto-epithelium4.59e-41104
adult organism5.17e-39114
structure with developmental contribution from neural crest7.95e-34132
ectoderm-derived structure3.28e-29171
ectoderm3.28e-29171
presumptive ectoderm3.28e-29171
basal ganglion9.89e-249
nuclear complex of neuraxis9.89e-249
aggregate regional part of brain9.89e-249
collection of basal ganglia9.89e-249
cerebral subcortex9.89e-249
neural nucleus8.23e-239
nucleus of brain8.23e-239
organ system subdivision4.58e-22223
gyrus3.21e-206
tube5.54e-20192
telencephalic nucleus1.19e-177
limbic system3.28e-175
temporal lobe4.57e-176
segmental subdivision of hindbrain3.69e-1612
hindbrain3.69e-1612
presumptive hindbrain3.69e-1612
posterior neural tube7.26e-1615
chordal neural plate7.26e-1615
segmental subdivision of nervous system8.31e-1513
corpus striatum1.23e-144
striatum1.23e-144
ventral part of telencephalon1.23e-144
future corpus striatum1.23e-144
anatomical conduit6.22e-14240
brainstem1.18e-126
regional part of metencephalon1.27e-129
metencephalon1.27e-129
future metencephalon1.27e-129
caudate-putamen1.44e-113
dorsal striatum1.44e-113
organ part1.78e-11218
parietal lobe3.93e-115
frontal cortex7.00e-113
anatomical cluster4.36e-10373
pons1.44e-093
epithelium1.86e-09306
cell layer2.87e-09309
caudate nucleus2.83e-082
future caudate nucleus2.83e-082
middle temporal gyrus5.78e-082
Ammon's horn5.98e-082
lobe parts of cerebral cortex5.98e-082
hippocampal formation5.98e-082
limbic lobe5.98e-082
amygdala7.07e-082
middle frontal gyrus8.36e-082
globus pallidus8.36e-082
pallidum8.36e-082
locus ceruleus7.39e-072
brainstem nucleus7.39e-072
hindbrain nucleus7.39e-072
meninx7.86e-072
membrane organ7.86e-072
meningeal cluster7.86e-072
multi-tissue structure8.05e-07342


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)
MA0003.10.401049
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
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
MA0051.10.936307
MA0052.11.24796
MA0055.11.06172
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
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0834661
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
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
MA0103.11.52002
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
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.195278
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.09178
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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