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Coexpression cluster:C358: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,

Latest revision as of 11:21, 17 September 2013


Full id: C358_cerebellum_middle_occipital_parietal_pineal_medial_amygdala



Phase1 CAGE Peaks

Hg19::chr11:12189656..12189676,+p@chr11:12189656..12189676
+
Hg19::chr11:132711753..132711754,-p@chr11:132711753..132711754
-
Hg19::chr11:132795109..132795151,-p@chr11:132795109..132795151
-
Hg19::chr11:133818054..133818066,-p@chr11:133818054..133818066
-
Hg19::chr11:133818091..133818133,-p@chr11:133818091..133818133
-
Hg19::chr11:64411144..64411154,-p14@NRXN2
Hg19::chr12:121676126..121676137,-p@chr12:121676126..121676137
-
Hg19::chr12:41233225..41233247,+p@chr12:41233225..41233247
+
Hg19::chr12:41233525..41233536,+p@chr12:41233525..41233536
+
Hg19::chr12:41234328..41234338,+p@chr12:41234328..41234338
+
Hg19::chr13:102919100..102919109,-p@chr13:102919100..102919109
-
Hg19::chr15:91806292..91806298,+p@chr15:91806292..91806298
+
Hg19::chr16:335698..335702,+p@chr16:335698..335702
+
Hg19::chr17:77408529..77408544,-p@chr17:77408529..77408544
-
Hg19::chr19:23507286..23507309,-p@chr19:23507286..23507309
-
Hg19::chr19:36443560..36443561,+p@chr19:36443560..36443561
+
Hg19::chr1:102433144..102433146,-p@chr1:102433144..102433146
-
Hg19::chr1:203015803..203015809,+p@chr1:203015803..203015809
+
Hg19::chr2:180503950..180503954,-p@chr2:180503950..180503954
-
Hg19::chr3:121013244..121013255,+p@chr3:121013244..121013255
+
Hg19::chr4:21558541..21558544,-p@chr4:21558541..21558544
-
Hg19::chr5:136319305..136319309,-p@chr5:136319305..136319309
-
Hg19::chr5:19774915..19774916,-p@chr5:19774915..19774916
-
Hg19::chr8:85139312..85139316,+p@chr8:85139312..85139316
+
Hg19::chr8:85348805..85348809,+p@chr8:85348805..85348809
+
Hg19::chrX:49054728..49054739,-p@chrX:49054728..49054739
-
Hg19::chrX:49054890..49054899,-p@chrX:49054890..49054899
-
Hg19::chrX:49055058..49055077,-p@chrX:49055058..49055077
-
Hg19::chrX:49055109..49055167,-p@chrX:49055109..49055167
-
Hg19::chrX:49055219..49055236,-p@chrX:49055219..49055236
-
Hg19::chrX:49055296..49055306,-p@chrX:49055296..49055306
-


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 system7.34e-9453
regional part of brain7.34e-9453
neural tube1.28e-8856
neural rod1.28e-8856
future spinal cord1.28e-8856
neural keel1.28e-8856
brain4.77e-8168
future brain4.77e-8168
brain grey matter1.02e-7234
gray matter1.02e-7234
regional part of forebrain1.09e-7141
forebrain1.09e-7141
anterior neural tube1.09e-7141
future forebrain1.09e-7141
cerebral hemisphere3.71e-7032
central nervous system2.00e-6781
telencephalon6.83e-6634
regional part of telencephalon1.50e-6332
neural plate3.12e-6382
presumptive neural plate3.12e-6382
nervous system3.01e-6089
neurectoderm4.71e-6086
regional part of cerebral cortex6.93e-5922
neocortex1.35e-5620
cerebral cortex1.06e-5125
pallium1.06e-5125
pre-chordal neural plate3.22e-5161
ecto-epithelium9.70e-49104
structure with developmental contribution from neural crest5.74e-40132
adult organism2.31e-38114
ectoderm-derived structure5.36e-29171
ectoderm5.36e-29171
presumptive ectoderm5.36e-29171
organ system subdivision3.84e-24223
gyrus2.07e-236
brainstem6.91e-236
segmental subdivision of hindbrain3.19e-2212
hindbrain3.19e-2212
presumptive hindbrain3.19e-2212
neural nucleus5.04e-229
nucleus of brain5.04e-229
tube5.51e-22192
segmental subdivision of nervous system1.90e-2013
temporal lobe4.79e-206
occipital lobe4.78e-185
posterior neural tube1.32e-1715
chordal neural plate1.32e-1715
pons2.67e-173
anatomical conduit2.16e-16240
regional part of metencephalon9.43e-169
metencephalon9.43e-169
future metencephalon9.43e-169
organ part9.74e-16218
basal ganglion1.21e-159
nuclear complex of neuraxis1.21e-159
aggregate regional part of brain1.21e-159
collection of basal ganglia1.21e-159
cerebral subcortex1.21e-159
corpus striatum2.49e-134
striatum2.49e-134
ventral part of telencephalon2.49e-134
future corpus striatum2.49e-134
telencephalic nucleus4.18e-137
multi-tissue structure1.09e-12342
epithelium1.26e-12306
middle temporal gyrus1.49e-122
cell layer1.92e-12309
locus ceruleus2.95e-122
brainstem nucleus2.95e-122
hindbrain nucleus2.95e-122
anatomical cluster5.47e-12373
limbic system7.01e-115
parietal lobe1.36e-105
frontal cortex1.06e-083
caudate-putamen1.06e-083
dorsal striatum1.06e-083
medulla oblongata2.91e-083
myelencephalon2.91e-083
future myelencephalon2.91e-083
diencephalon7.74e-087
future diencephalon7.74e-087
olfactory region3.36e-071
primary subdivision of skull3.36e-071
cranium3.36e-071
neurocranium3.36e-071
chondrocranium3.36e-071
cartilaginous neurocranium3.36e-071
head paraxial mesoderm3.36e-071
putamen4.01e-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)
MA0003.14.09555e-07
MA0004.10.303232
MA0006.10.0304162
MA0007.10.0818413
MA0009.10.406485
MA0014.10.0037669
MA0017.10.162552
MA0019.11.57239
MA0024.10.322368
MA0025.10.520106
MA0027.11.94566
MA0028.10.0349277
MA0029.10.895805
MA0030.10.328486
MA0031.10.279263
MA0038.10.145356
MA0040.10.342075
MA0041.11.11479
MA0042.10.59843
MA0043.11.04839
MA0046.10.397506
MA0048.10.124274
MA0050.10.600435
MA0051.10.865123
MA0052.10.345132
MA0055.10.0420572
MA0056.10
MA0057.11.49339
MA0058.10.0506385
MA0059.10.418621
MA0060.10.116876
MA0061.10.0287117
MA0063.10
MA0066.12.72573
MA0067.10.685278
MA0068.10.231182
MA0069.10.394339
MA0070.11.00123
MA0071.10.390117
MA0072.10.993189
MA0073.10.294221
MA0074.12.0065
MA0076.10.206609
MA0077.10.37525
MA0078.10.592477
MA0081.10.187827
MA0083.10.412707
MA0084.10.860109
MA0087.10.988819
MA0088.10.14141
MA0089.10
MA0090.10.223118
MA0091.10.0917987
MA0092.10.0745182
MA0093.10.127599
MA0095.10
MA0098.10
MA0100.10.153602
MA0101.10.130624
MA0103.10.28031
MA0105.10.0148964
MA0106.10.170405
MA0107.10.0711943
MA0108.20.759502
MA0109.10
MA0111.10.0675805
MA0113.10.180801
MA0114.10.585362
MA0115.10.615724
MA0116.10.0735945
MA0117.10.437859
MA0119.10.0446378
MA0122.10.459779
MA0124.10.578498
MA0125.10.50452
MA0130.10
MA0131.10.621676
MA0132.10
MA0133.10
MA0135.10.431776
MA0136.10.149526
MA0139.10.00413026
MA0140.10.121887
MA0141.10.0495619
MA0142.10.711177
MA0143.10.180914
MA0144.10.157126
MA0145.10.0014943
MA0146.19.21829e-06
MA0147.10.0760571
MA0148.10.33621
MA0149.10.372761
MA0062.20.178074
MA0035.20.385357
MA0039.20.017743
MA0138.20.594441
MA0002.20.103088
MA0137.20.0368453
MA0104.20.0408112
MA0047.20.162866
MA0112.20.250412
MA0065.20.596841
MA0150.10.472127
MA0151.10
MA0152.10.125496
MA0153.10.489927
MA0154.10.0870334
MA0155.10.484592
MA0156.10.0375332
MA0157.10.236372
MA0158.10
MA0159.10.196704
MA0160.10.356941
MA0161.10
MA0162.10.000546668
MA0163.10.000137003
MA0164.11.66354
MA0080.20.127678
MA0018.21.56329
MA0099.20.125694
MA0079.20.0789439
MA0102.20.895427
MA0258.10.292686
MA0259.10.208795
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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