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{{Coexpression_clusters
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|full_id=C3988_spinal_brain_putamen_Renal_rectum_hippocampus_skeletal
|id=C3988
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005743!4.28e-50!86;UBERON:0001049!6.83e-50!57;UBERON:0005068!6.83e-50!57;UBERON:0006241!6.83e-50!57;UBERON:0007135!6.83e-50!57;UBERON:0001017!7.91e-49!82;UBERON:0000073!8.31e-49!94;UBERON:0001016!8.31e-49!94;UBERON:0003075!2.68e-43!86;UBERON:0007284!2.68e-43!86;UBERON:0002616!2.89e-42!59;UBERON:0002346!3.40e-40!90;UBERON:0000955!6.83e-39!69;UBERON:0006238!6.83e-39!69;UBERON:0002780!8.41e-39!41;UBERON:0001890!8.41e-39!41;UBERON:0006240!8.41e-39!41;UBERON:0003080!1.74e-37!42;UBERON:0001893!3.95e-35!34;UBERON:0002020!4.31e-35!34;UBERON:0003528!4.31e-35!34;UBERON:0002791!3.68e-34!33;UBERON:0003056!1.17e-33!61;UBERON:0001869!4.98e-33!32;UBERON:0007023!4.01e-30!115;UBERON:0004121!4.39e-29!169;UBERON:0000153!5.71e-28!129;UBERON:0007811!5.71e-28!129;UBERON:0000924!1.10e-27!173;UBERON:0006601!1.10e-27!173;UBERON:0000033!1.62e-27!123;UBERON:0000956!1.98e-25!25;UBERON:0000203!1.98e-25!25;UBERON:0002619!1.14e-23!22;UBERON:0001950!2.13e-21!20;UBERON:0000064!5.68e-15!219;UBERON:0000483!1.48e-13!309;UBERON:0000025!3.41e-13!194;UBERON:0003076!3.98e-13!15;UBERON:0003057!3.98e-13!15;UBERON:0000119!4.08e-13!312;UBERON:0002420!3.18e-11!9;UBERON:0007245!3.18e-11!9;UBERON:0010009!3.18e-11!9;UBERON:0010011!3.18e-11!9;UBERON:0000454!3.18e-11!9;UBERON:0002308!4.84e-11!9;UBERON:0000125!4.84e-11!9;UBERON:0004732!1.42e-10!13;UBERON:0000481!5.59e-10!347;UBERON:0004733!5.99e-10!12;UBERON:0002028!5.99e-10!12;UBERON:0007277!5.99e-10!12;UBERON:0004111!6.71e-10!241;UBERON:0001871!2.93e-09!7;UBERON:0009663!4.55e-09!7;UBERON:0000477!8.35e-09!286;UBERON:0000922!1.41e-08!612;UBERON:0000475!3.67e-08!365;UBERON:0000200!3.33e-07!6;UBERON:0002298!3.61e-07!8;UBERON:0000349!4.47e-07!5;UBERON:0002680!5.16e-07!9;UBERON:0001895!5.16e-07!9;UBERON:0010092!5.16e-07!9
}}

Latest revision as of 12:37, 17 September 2013


Full id: C3988_spinal_brain_putamen_Renal_rectum_hippocampus_skeletal



Phase1 CAGE Peaks

Hg19::chr1:61333622..61333640,-p@chr1:61333622..61333640
-
Hg19::chr20:61885781..61885822,-p1@NKAIN4
Hg19::chr20:61885826..61885844,-p3@NKAIN4


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>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
neuronal stem cell2.69e-088
embryonic stem cell7.36e-075
Uber Anatomy
Ontology termp-valuen
neural tube7.30e-6156
neural rod7.30e-6156
future spinal cord7.30e-6156
neural keel7.30e-6156
central nervous system1.55e-5981
nervous system1.85e-5789
regional part of nervous system3.38e-5653
regional part of brain3.38e-5653
neural plate1.18e-4682
presumptive neural plate1.18e-4682
brain9.77e-4668
future brain9.77e-4668
regional part of forebrain7.92e-4541
forebrain7.92e-4541
anterior neural tube7.92e-4541
future forebrain7.92e-4541
neurectoderm1.31e-4386
telencephalon2.82e-4334
brain grey matter4.28e-4334
gray matter4.28e-4334
cerebral hemisphere1.88e-4032
regional part of telencephalon2.08e-4032
pre-chordal neural plate2.03e-3661
ecto-epithelium8.30e-36104
adult organism6.81e-32114
ectoderm-derived structure4.00e-30171
ectoderm4.00e-30171
presumptive ectoderm4.00e-30171
cerebral cortex4.58e-3025
pallium4.58e-3025
regional part of cerebral cortex1.17e-2922
structure with developmental contribution from neural crest1.57e-27132
neocortex1.36e-2620
organ system subdivision3.24e-23223
posterior neural tube1.64e-1615
chordal neural plate1.64e-1615
basal ganglion7.81e-159
nuclear complex of neuraxis7.81e-159
aggregate regional part of brain7.81e-159
collection of basal ganglia7.81e-159
cerebral subcortex7.81e-159
neural nucleus1.94e-149
nucleus of brain1.94e-149
anatomical cluster8.11e-14373
organ part1.41e-13218
segmental subdivision of hindbrain3.34e-1212
hindbrain3.34e-1212
presumptive hindbrain3.34e-1212
telencephalic nucleus7.31e-127
tube2.58e-11192
segmental subdivision of nervous system4.72e-1113
multi-tissue structure5.62e-10342
brainstem6.13e-106
embryo6.75e-10592
gyrus1.70e-096
epithelium2.17e-09306
limbic system4.01e-095
cell layer4.11e-09309
temporal lobe1.70e-086
parietal lobe4.18e-085
regional part of metencephalon4.49e-089
metencephalon4.49e-089
future metencephalon4.49e-089
occipital lobe6.07e-085
corpus striatum8.53e-084
striatum8.53e-084
ventral part of telencephalon8.53e-084
future corpus striatum8.53e-084
anatomical conduit1.00e-07240
developing anatomical structure2.14e-07581
multi-cellular organism3.14e-07656


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)
MA0003.12.05336
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.758317
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
MA0048.12.45333
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.11.59304
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
MA0073.13.923
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.11.31954
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.11.80901
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.11.3784
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
MA0145.10.752137
MA0146.12.3244
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.21.62945
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.20.731309
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.11.51687
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.12.76014
MA0163.15.63764
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.29.48295
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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