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{{Coexpression_clusters
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|full_id=C3049_thyroid_epididymis_ductus_pituitary_seminal_renal_throat
|gostat_on_coexpression_clusters=GO:0030159!receptor signaling complex scaffold activity!0.0241307749547345!9231$GO:0032947!protein complex scaffold!0.0241307749547345!9231
|id=C3049
}}

Latest revision as of 12:18, 17 September 2013


Full id: C3049_thyroid_epididymis_ductus_pituitary_seminal_renal_throat



Phase1 CAGE Peaks

Hg19::chr10:79602040..79602046,-p22@DLG5
Hg19::chr1:26551833..26551845,+p4@ENST00000451482
p4@uc001blq.2
Hg19::chr9:139847065..139847079,+p3@LCN12


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

GO IDGO nameFDR corrected p-value
GO:0030159receptor signaling complex scaffold activity0.0241307749547345
GO:0032947protein complex scaffold0.0241307749547345



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
adult organism4.15e-63114
neural tube2.00e-6056
neural rod2.00e-6056
future spinal cord2.00e-6056
neural keel2.00e-6056
regional part of nervous system3.40e-5653
regional part of brain3.40e-5653
neural plate1.04e-4982
presumptive neural plate1.04e-4982
neurectoderm5.62e-4786
brain3.68e-4468
future brain3.68e-4468
regional part of forebrain8.33e-4441
forebrain8.33e-4441
anterior neural tube8.33e-4441
future forebrain8.33e-4441
central nervous system8.78e-4481
nervous system1.37e-3889
ecto-epithelium2.92e-37104
structure with developmental contribution from neural crest5.06e-35132
pre-chordal neural plate1.48e-3261
brain grey matter5.67e-3034
gray matter5.67e-3034
telencephalon1.24e-2934
regional part of telencephalon4.80e-2532
cerebral hemisphere7.70e-2532
ectoderm-derived structure3.07e-21171
ectoderm3.07e-21171
presumptive ectoderm3.07e-21171
brainstem1.10e-206
tube2.35e-18192
regional part of cerebral cortex3.05e-1822
neural nucleus5.58e-189
nucleus of brain5.58e-189
diencephalon1.37e-177
future diencephalon1.37e-177
posterior neural tube4.30e-1715
chordal neural plate4.30e-1715
neocortex6.01e-1720
cerebral cortex7.95e-1625
pallium7.95e-1625
anatomical conduit8.66e-16240
organ system subdivision7.18e-14223
gyrus1.38e-136
segmental subdivision of hindbrain3.68e-1312
hindbrain3.68e-1312
presumptive hindbrain3.68e-1312
basal ganglion5.68e-139
nuclear complex of neuraxis5.68e-139
aggregate regional part of brain5.68e-139
collection of basal ganglia5.68e-139
cerebral subcortex5.68e-139
anatomical cluster9.01e-13373
segmental subdivision of nervous system4.57e-1213
male genital duct5.54e-123
internal male genitalia5.54e-123
telencephalic nucleus6.31e-127
epithelium8.59e-12306
cell layer1.41e-11309
pons1.83e-113
medulla oblongata5.89e-113
myelencephalon5.89e-113
future myelencephalon5.89e-113
multi-tissue structure7.60e-11342
duct of male reproductive system4.48e-094
organ6.90e-09503
gland of diencephalon8.38e-094
neuroendocrine gland8.38e-094
regional part of diencephalon2.00e-084
throat2.17e-082
pituitary gland2.17e-082
locus ceruleus2.50e-082
brainstem nucleus2.50e-082
hindbrain nucleus2.50e-082
corpus striatum4.22e-084
striatum4.22e-084
ventral part of telencephalon4.22e-084
future corpus striatum4.22e-084
dorsal plus ventral thalamus7.11e-082
thalamic complex7.11e-082
temporal lobe1.28e-076
middle temporal gyrus1.40e-072
organ part5.82e-07218


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
MA0048.11.62115
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
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
MA0073.10.407479
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
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
MA0111.10.767139
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
MA0141.11.6959
MA0142.11.12317
MA0143.11.00455
MA0144.11.31729
MA0145.10.752137
MA0146.11.70974
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.195278
MA0138.21.04628
MA0002.21.20011
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
MA0155.10.711948
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
MA0079.20.181755
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

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

TF#promotersEnrichmentp-valueq-value
ESR1#2099330.76860329615453.43136389821584e-050.000673497865374486



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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