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{{Coexpression_clusters
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196,0.167238,0.190639,0.307532,0.265287,0.113346,0.168727,0.221472,0.095012,0.320667,0.456504,0.607439,0.5938,0.679098,0.334729,0.557075,0.187049,0.448658,0.151747,0.611294,0.541437,0.406439,0.589165,0.559083,0.313926,0.373141,0.127174,0.447066,0.594101,0.512982,0.649607,0.279812,0.481032,0.491197,0.278645,0.439191,0.431751,0.586217,0.588503,0.535591,0.381036,0.491941,0.230489,0.285747,0.494548,0.462673,0.23568,0.213047,0.638022,0.394858,0.369527,0.569966,0.178571,0.568909,0.247225,0.48895,0.403105,0.366377,0.476867,0.540268,0.459344,0.697624|tfbs_overrepresentation_for_novel_motifs=0.348717,0.0704539,0.341646,1.21028,1.48054,0.480078,0.554663,0.19223,0.555925,0.154405,0.450635,0.597407,0.152895,0.543352,0.300614,0.322799,0.774423,0.250594,0.163559,0.0766963,1.62225,0.180463,0.472508,0.29709,1.00212,0.619829,0.135503,0.470396,0.304828,0.122648,0.429397,0.810962,0.220667,0.154814,0.269459,0.171488,0.266487,0.481208,0.244807,0.174436,0.739305,0.413601,0.775279,0.809926,0.198862,0.371118,0.555735,0.440085,0.416595,0.304949,0.63387,0.567337,0.309329,0.887323,1.03948,0.546236,0.308962,0.514077,0.388089,0.513089,0.85167,0.558065,0.190442,0.746929,0.575742,0.712797,1.12756,1.49516,0.800646,1.33315,0.400869,0.573519,0.0911419,1.03748,0.149081,0.429044,1.88626,0.730167,0.797419,0.379656,0.50159,0.745864,0.575394,0.567311,0.986227,0.0220225,0.26222,0.118789,0.659621,1.59442,1.22073,0.959334,0.827657,0.644398,0.302606,1.24975,0.488357,0.87,0.664183,0.345507,0.246049,0.822041,0.864454,0.778061,0.701386,0.446229,0.762347,0.539961,0.385342,0.286892,0.352381,0.861701,0.336372,0.459808,1.17281,0.265019,0.0278613,0.428232,0.710479,0.229841,1.02923,0.657218,0.477387,0.586509,1.28328,0.730921,0.548418,0.83262,1.07171,0.674618,0.960022,0.432175,1.08604,0.583225,1.23359,0.364369,0.423593,1.18725,1.19123,2.04907,1.64679,1.15398,1.35598,0.866494,0.703126,0.505785,0.686615,1.88987,1.05631,0.224241,0.0833399,0.0510299,0.960402,0.183004,0.557588,1.36372,0.643609,0.786331,0.385642,0.357927,1.15277,0.941964,0.796636,0.36101,0.71907,0.574616,0.611402,0.553354,0.0203307|tfbs_overrepresentation_jaspar=MA0003.1;0.00718652,MA0004.1;0.455723,MA0006.1;0.300178,MA0007.1;0.437331,MA0009.1;0.918715,MA0014.1;0.00962431,MA0017.1;0.337901,MA0019.1;0.602411,MA0024.1;0.813542,MA0025.1;1.05265,MA0027.1;2.5321,MA0028.1;0.315574,MA0029.1;0.832916,MA0030.1;0.821423,MA0031.1;0.756713,MA0038.1;0.557409,MA0040.1;1.95652,MA0041.1;2.07464,MA0042.1;1.12605,MA0043.1;0.919032,MA0046.1;0.90778,MA0048.1;0.316923,MA0050.1;0.443405,MA0051.1;0.553205,MA0052.1;0.842664,MA0055.1;0.524515,MA0056.1;0,MA0057.1;0.0912556,MA0058.1;0.362328,MA0059.1;0.361075,MA0060.1;0.190336,MA0061.1;0.497495,MA0063.1;0,MA0066.1;1.3723,MA0067.1;1.23721,MA0068.1;0.133123,MA0069.1;0.903908,MA0070.1;0.892666,MA0071.1;2.22338,MA0072.1;0.888148,MA0073.1;9.20286e-05,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;0.054222,MA0089.1;0,MA0090.1;1.79681,MA0091.1;0.458301,MA0092.1;0.421159,MA0093.1;0.303084,MA0095.1;0,MA0098.1;0,MA0100.1;0.571227,MA0101.1;0.30624,MA0103.1;0.291333,MA0105.1;0.279181,MA0106.1;0.59853,MA0107.1;0.666147,MA0108.2;0.753643,MA0109.1;0,MA0111.1;0.405141,MA0113.1;0.614917,MA0114.1;0.231781,MA0115.1;1.1606,MA0116.1;0.673701,MA0117.1;0.956472,MA0119.1;0.913661,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;0.155155,MA0140.1;0.516266,MA0141.1;0.359385,MA0142.1;0.724856,MA0143.1;0.615094,MA0144.1;0.218541,MA0145.1;0.0613434,MA0146.1;0.00761723,MA0147.1;0.243042,MA0148.1;1.20731,MA0149.1;0.506665,MA0062.2;0.485915,MA0035.2;0.515566,MA0039.2;0.0817047,MA0138.2;0.653421,MA0002.2;1.01797,MA0137.2;0.86081,MA0104.2;0.189646,MA0047.2;0.586412,MA0112.2;0.0572179,MA0065.2;0.0631316,MA0150.1;0.386144,MA0151.1;0,MA0152.1;0.52279,MA0153.1;1.01778,MA0154.1;0.274121,MA0155.1;0.43752,MA0156.1;0.865715,MA0157.1;0.697424,MA0158.1;0,MA0159.1;0.243637,MA0160.1;0.495355,MA0161.1;0,MA0162.1;0.0163939,MA0163.1;0.0517199,MA0164.1;0.627336,MA0080.2;0.303167,MA0018.2;0.599912,MA0099.2;0.523145,MA0079.2;1.80475e-05,MA0102.2;1.46209,MA0258.1;0.209744,MA0259.1;0.25092,MA0442.1;0}}
|full_id=C1033_locus_medulla_spinal_globus_amygdala_pineal_hippocampus
|id=C1033
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!9.72e-36!57;UBERON:0005068!9.72e-36!57;UBERON:0006241!9.72e-36!57;UBERON:0007135!9.72e-36!57;UBERON:0001017!4.04e-32!82;UBERON:0007023!8.98e-31!115;UBERON:0005743!2.49e-30!86;UBERON:0000955!5.04e-30!69;UBERON:0006238!5.04e-30!69;UBERON:0002616!8.45e-30!59;UBERON:0002346!2.98e-29!90;UBERON:0000073!4.75e-29!94;UBERON:0001016!4.75e-29!94;UBERON:0003075!2.88e-28!86;UBERON:0007284!2.88e-28!86;UBERON:0003080!1.47e-25!42;UBERON:0002780!9.13e-25!41;UBERON:0001890!9.13e-25!41;UBERON:0006240!9.13e-25!41;UBERON:0002020!1.06e-20!34;UBERON:0003528!1.06e-20!34;UBERON:0001893!2.54e-20!34;UBERON:0002791!1.48e-19!33;UBERON:0001869!1.39e-18!32;UBERON:0000924!1.49e-17!173;UBERON:0006601!1.49e-17!173;UBERON:0003056!4.79e-17!61;UBERON:0004121!1.21e-16!169;UBERON:0000033!1.64e-14!123;UBERON:0002619!3.14e-14!22;UBERON:0000153!3.27e-14!129;UBERON:0007811!3.27e-14!129;UBERON:0000956!9.27e-13!25;UBERON:0000203!9.27e-13!25;UBERON:0001950!2.31e-12!20;UBERON:0003076!3.44e-11!15;UBERON:0003057!3.44e-11!15;UBERON:0002308!4.57e-10!9;UBERON:0000125!4.57e-10!9;UBERON:0002420!6.78e-10!9;UBERON:0007245!6.78e-10!9;UBERON:0010009!6.78e-10!9;UBERON:0010011!6.78e-10!9;UBERON:0000454!6.78e-10!9;UBERON:0002298!2.18e-09!8;UBERON:0000025!1.39e-08!194;UBERON:0004733!2.42e-08!12;UBERON:0002028!2.42e-08!12;UBERON:0007277!2.42e-08!12;UBERON:0009663!5.30e-08!7;UBERON:0004732!2.00e-07!13;UBERON:0000483!4.60e-07!309;UBERON:0004111!5.32e-07!241;UBERON:0000119!5.53e-07!312
}}

Latest revision as of 11:36, 17 September 2013


Full id: C1033_locus_medulla_spinal_globus_amygdala_pineal_hippocampus



Phase1 CAGE Peaks

Hg19::chr14:62044439..62044441,-p@chr14:62044439..62044441
-
Hg19::chr1:110564357..110564369,+p@chr1:110564357..110564369
+
Hg19::chr2:234077635..234077640,+p@chr2:234077635..234077640
+
Hg19::chr2:234077675..234077686,+p@chr2:234077675..234077686
+
Hg19::chr3:167375550..167375561,-p@chr3:167375550..167375561
-
Hg19::chr4:83551428..83551439,-p@chr4:83551428..83551439
-
Hg19::chr4:83551445..83551463,-p@chr4:83551445..83551463
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Hg19::chr8:82355027..82355036,-p5@PMP2


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
neural tube1.39e-9456
neural rod1.39e-9456
future spinal cord1.39e-9456
neural keel1.39e-9456
regional part of nervous system8.79e-8753
regional part of brain8.79e-8753
central nervous system4.82e-7281
brain1.78e-7068
future brain1.78e-7068
nervous system1.87e-6489
neural plate3.00e-6382
presumptive neural plate3.00e-6382
regional part of forebrain3.60e-6341
forebrain3.60e-6341
anterior neural tube3.60e-6341
future forebrain3.60e-6341
neurectoderm4.34e-6086
brain grey matter2.01e-5134
gray matter2.01e-5134
telencephalon1.07e-5034
ecto-epithelium7.68e-49104
adult organism9.86e-48114
regional part of telencephalon1.28e-4232
cerebral hemisphere2.20e-4232
neural nucleus1.16e-419
nucleus of brain1.16e-419
pre-chordal neural plate2.46e-4161
structure with developmental contribution from neural crest3.67e-40132
brainstem1.81e-366
basal ganglion1.60e-319
nuclear complex of neuraxis1.60e-319
aggregate regional part of brain1.60e-319
collection of basal ganglia1.60e-319
cerebral subcortex1.60e-319
posterior neural tube1.86e-3115
chordal neural plate1.86e-3115
ectoderm-derived structure2.02e-31171
ectoderm2.02e-31171
presumptive ectoderm2.02e-31171
telencephalic nucleus4.90e-307
organ system subdivision1.74e-24223
regional part of cerebral cortex4.39e-2422
tube5.34e-24192
segmental subdivision of hindbrain5.79e-2412
hindbrain5.79e-2412
presumptive hindbrain5.79e-2412
segmental subdivision of nervous system4.69e-2213
cerebral cortex4.22e-2125
pallium4.22e-2125
limbic system1.97e-195
pons3.90e-193
medulla oblongata3.90e-193
myelencephalon3.90e-193
future myelencephalon3.90e-193
anatomical conduit4.53e-18240
neocortex8.59e-1720
gyrus1.15e-156
regional part of diencephalon7.24e-144
locus ceruleus1.15e-132
brainstem nucleus1.15e-132
hindbrain nucleus1.15e-132
diencephalon1.21e-137
future diencephalon1.21e-137
Ammon's horn1.77e-132
lobe parts of cerebral cortex1.77e-132
hippocampal formation1.77e-132
limbic lobe1.77e-132
corpus striatum1.82e-134
striatum1.82e-134
ventral part of telencephalon1.82e-134
future corpus striatum1.82e-134
globus pallidus2.00e-132
pallidum2.00e-132
epithelium6.29e-13306
middle temporal gyrus8.53e-132
cell layer9.57e-13309
pineal body1.22e-122
regional part of epithalamus1.22e-122
secretory circumventricular organ1.22e-122
circumventricular organ1.22e-122
epithalamus1.22e-122
anatomical cluster2.21e-12373
regional part of metencephalon6.71e-119
metencephalon6.71e-119
future metencephalon6.71e-119
organ part9.90e-11218
multi-tissue structure7.41e-10342
spinal cord2.84e-093
dorsal region element2.84e-093
dorsum2.84e-093
caudate-putamen1.06e-083
dorsal striatum1.06e-083
temporal lobe3.47e-086
substantia nigra1.85e-071
midbrain nucleus1.85e-071
regional part of midbrain1.85e-071
midbrain1.85e-071
presumptive midbrain1.85e-071
midbrain neural tube1.85e-071
olfactory region2.67e-071


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)
MA0003.10.00718652
MA0004.10.455723
MA0006.10.300178
MA0007.10.437331
MA0009.10.918715
MA0014.10.00962431
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.315574
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.11.95652
MA0041.12.07464
MA0042.11.12605
MA0043.10.919032
MA0046.10.90778
MA0048.10.316923
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.10.524515
MA0056.10
MA0057.10.0912556
MA0058.10.362328
MA0059.10.361075
MA0060.10.190336
MA0061.10.497495
MA0063.10
MA0066.11.3723
MA0067.11.23721
MA0068.10.133123
MA0069.10.903908
MA0070.10.892666
MA0071.12.22338
MA0072.10.888148
MA0073.19.20286e-05
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.054222
MA0089.10
MA0090.11.79681
MA0091.10.458301
MA0092.10.421159
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.30624
MA0103.10.291333
MA0105.10.279181
MA0106.10.59853
MA0107.10.666147
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.10.231781
MA0115.11.1606
MA0116.10.673701
MA0117.10.956472
MA0119.10.913661
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.155155
MA0140.10.516266
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.10.218541
MA0145.10.0613434
MA0146.10.00761723
MA0147.10.243042
MA0148.11.20731
MA0149.10.506665
MA0062.20.485915
MA0035.20.515566
MA0039.20.0817047
MA0138.20.653421
MA0002.21.01797
MA0137.20.86081
MA0104.20.189646
MA0047.20.586412
MA0112.20.0572179
MA0065.20.0631316
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.274121
MA0155.10.43752
MA0156.10.865715
MA0157.10.697424
MA0158.10
MA0159.10.243637
MA0160.10.495355
MA0161.10
MA0162.10.0163939
MA0163.10.0517199
MA0164.10.627336
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.21.80475e-05
MA0102.21.46209
MA0258.10.209744
MA0259.10.25092
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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