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{{Coexpression_clusters
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|full_id=C4285_medial_medulla_trachea_caudate_middle_insula_putamen
|id=C4285
|ontology_enrichment_celltype=CL:0000791!8.50e-08!18;CL:0000789!8.50e-08!18;CL:0002420!8.50e-08!18;CL:0002419!8.50e-08!18;CL:0000790!8.50e-08!18;CL:0000084!7.07e-07!25;CL:0000827!7.07e-07!25;CL:0000625!9.09e-07!11
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!1.46e-42!57;UBERON:0005068!1.46e-42!57;UBERON:0006241!1.46e-42!57;UBERON:0007135!1.46e-42!57;UBERON:0007023!1.26e-40!115;UBERON:0001017!5.76e-40!82;UBERON:0005743!1.32e-39!86;UBERON:0000955!4.88e-39!69;UBERON:0006238!4.88e-39!69;UBERON:0002616!4.55e-36!59;UBERON:0000073!2.06e-35!94;UBERON:0001016!2.06e-35!94;UBERON:0002780!2.75e-34!41;UBERON:0001890!2.75e-34!41;UBERON:0006240!2.75e-34!41;UBERON:0003080!4.69e-33!42;UBERON:0003075!2.06e-31!86;UBERON:0007284!2.06e-31!86;UBERON:0002020!6.66e-29!34;UBERON:0003528!6.66e-29!34;UBERON:0002346!6.98e-29!90;UBERON:0001893!7.37e-29!34;UBERON:0002791!6.61e-28!33;UBERON:0001869!3.78e-27!32;UBERON:0000153!8.37e-26!129;UBERON:0007811!8.37e-26!129;UBERON:0000033!2.97e-24!123;UBERON:0003056!3.62e-24!61;UBERON:0002619!8.02e-21!22;UBERON:0000956!2.04e-20!25;UBERON:0000203!2.04e-20!25;UBERON:0001950!5.68e-19!20;UBERON:0004121!5.19e-17!169;UBERON:0000924!5.50e-16!173;UBERON:0006601!5.50e-16!173;UBERON:0003076!1.86e-10!15;UBERON:0003057!1.86e-10!15;UBERON:0002308!5.60e-10!9;UBERON:0000125!5.60e-10!9;UBERON:0002420!6.85e-10!9;UBERON:0007245!6.85e-10!9;UBERON:0010009!6.85e-10!9;UBERON:0010011!6.85e-10!9;UBERON:0000454!6.85e-10!9;UBERON:0004111!5.23e-09!241;UBERON:0000025!1.18e-08!194;UBERON:0009663!4.07e-08!7;UBERON:0000475!4.47e-08!365;UBERON:0004733!5.01e-08!12;UBERON:0002028!5.01e-08!12;UBERON:0007277!5.01e-08!12;UBERON:0000477!1.26e-07!286;UBERON:0000200!1.26e-07!6;UBERON:0004732!3.84e-07!13;UBERON:0001871!7.07e-07!7;UBERON:0002298!8.47e-07!8;UBERON:0001894!8.73e-07!7;UBERON:0006222!8.73e-07!7
}}

Latest revision as of 12:42, 17 September 2013


Full id: C4285_medial_medulla_trachea_caudate_middle_insula_putamen



Phase1 CAGE Peaks

Hg19::chr3:138048631..138048651,-p3@NME9
Hg19::chr3:138048653..138048677,-p1@NME9
Hg19::chr3:138048682..138048698,-p2@NME9


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 tube1.07e-6156
neural rod1.07e-6156
future spinal cord1.07e-6156
neural keel1.07e-6156
regional part of nervous system1.06e-5753
regional part of brain1.06e-5753
central nervous system1.76e-5181
brain5.38e-5168
future brain5.38e-5168
regional part of forebrain5.94e-4841
forebrain5.94e-4841
anterior neural tube5.94e-4841
future forebrain5.94e-4841
nervous system3.73e-4689
adult organism1.07e-45114
telencephalon4.48e-4434
brain grey matter4.62e-4434
gray matter4.62e-4434
neural plate1.85e-4382
presumptive neural plate1.85e-4382
cerebral hemisphere3.08e-4132
regional part of telencephalon5.29e-4132
neurectoderm1.28e-4086
pre-chordal neural plate8.29e-3561
regional part of cerebral cortex7.98e-3322
ecto-epithelium7.46e-32104
cerebral cortex1.82e-3025
pallium1.82e-3025
neocortex1.06e-2920
structure with developmental contribution from neural crest8.89e-26132
ectoderm-derived structure2.94e-21171
ectoderm2.94e-21171
presumptive ectoderm2.94e-21171
organ system subdivision1.20e-18223
neural nucleus4.92e-159
nucleus of brain4.92e-159
basal ganglion6.58e-159
nuclear complex of neuraxis6.58e-159
aggregate regional part of brain6.58e-159
collection of basal ganglia6.58e-159
cerebral subcortex6.58e-159
posterior neural tube2.08e-1415
chordal neural plate2.08e-1415
tube3.53e-13192
telencephalic nucleus4.65e-127
gyrus3.67e-116
segmental subdivision of hindbrain8.26e-1112
hindbrain8.26e-1112
presumptive hindbrain8.26e-1112
brainstem9.15e-116
anatomical conduit6.94e-10240
segmental subdivision of nervous system8.55e-1013
limbic system3.59e-095
anatomical cluster4.16e-09373
organ part4.32e-09218
temporal lobe5.51e-096
parietal lobe5.95e-095
occipital lobe1.01e-085
epithelium2.51e-08306
corpus striatum3.61e-084
striatum3.61e-084
ventral part of telencephalon3.61e-084
future corpus striatum3.61e-084
cell layer4.46e-08309
multi-tissue structure3.90e-07342
organ7.20e-07503


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)
MA0003.10.0471418
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
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.12.13518
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.12.89432
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
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
MA0101.11.55947
MA0103.10.628063
MA0105.10.846801
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.11.35563
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
MA0144.14.49708
MA0145.10.273764
MA0146.10.707589
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.21.15986
MA0138.21.04628
MA0002.20.476938
MA0137.22.70092
MA0104.20.491226
MA0047.20.973066
MA0112.21.34467
MA0065.22.13692
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
MA0162.10.455568
MA0163.10.776149
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.09178
MA0102.21.88331
MA0258.12.22591
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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
MAX#414936.452555509007120.003721913834265510.0187052095152714
SP1#666735.69838137814090.005403962701712170.0247255086569753
SREBF1#6720347.00584944048839.62099323994382e-060.000255221466341502
STAT3#6774310.51946499715420.0008589184530415310.00644244357348495
TCF7L2#6934310.77017656313730.0008003181298398380.00615813933267095
USF1#739136.361499277207960.00388404057290560.0190838028506628



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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