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Coexpression cluster:C1141: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:38, 17 September 2013


Full id: C1141_argyrophil_pituitary_nonsmall_small_medulla_locus_temporal



Phase1 CAGE Peaks

Hg19::chr11:45918158..45918189,+p8@MAPK8IP1
Hg19::chr15:75488008..75488019,+p@chr15:75488008..75488019
+
Hg19::chr16:8814563..8814603,+p6@ABAT
Hg19::chr1:206223941..206223944,+p1@AVPR1B
Hg19::chr1:240286448..240286474,+p@chr1:240286448..240286474
+
Hg19::chr4:8012461..8012482,-p6@ABLIM2
Hg19::chrX:118608746..118608769,+p@chrX:118608746..118608769
+


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:0019899enzyme binding0.000532460199117048
GO:0019901protein kinase binding0.00275226657247145
GO:0019900kinase binding0.00275226657247145
GO:00038674-aminobutyrate transaminase activity0.00275226657247145
GO:0047298(S)-3-amino-2-methylpropionate transaminase activity0.00275226657247145
GO:0032145succinate-semialdehyde dehydrogenase binding0.00275226657247145
GO:00321444-aminobutyrate transaminase complex0.00275226657247145
GO:0042538hyperosmotic salinity response0.00275226657247145
GO:0009448gamma-aminobutyric acid metabolic process0.00293562138164337
GO:0009651response to salt stress0.00293562138164337
GO:0048148behavioral response to cocaine0.00293562138164337
GO:0019626short-chain fatty acid catabolic process0.00293562138164337
GO:0046359butyrate catabolic process0.00293562138164337
GO:0019605butyrate metabolic process0.00293562138164337
GO:0009450gamma-aminobutyric acid catabolic process0.00293562138164337
GO:0001992regulation of systemic arterial blood pressure by vasopressin0.00330242822745582
GO:0006972hyperosmotic response0.00330242822745582
GO:0005078MAP-kinase scaffold activity0.00330242822745582
GO:0042220response to cocaine0.00330242822745582
GO:0014073response to tropane0.00330242822745582
GO:0046459short-chain fatty acid metabolic process0.00419337448417358
GO:0009062fatty acid catabolic process0.00500323725885042
GO:0006970response to osmotic stress0.00647334823424654
GO:0042135neurotransmitter catabolic process0.00647334823424654
GO:0043279response to alkaloid0.00647334823424654
GO:0050886endocrine process0.00647334823424654
GO:0001990regulation of systemic arterial blood pressure by hormone0.00647334823424654
GO:0019894kinesin binding0.00647334823424654
GO:0017046peptide hormone binding0.00647334823424654
GO:0005000vasopressin receptor activity0.00647334823424654
GO:0046395carboxylic acid catabolic process0.00647334823424654
GO:0016054organic acid catabolic process0.00647334823424654
GO:0005080protein kinase C binding0.00647334823424654
GO:0001603vasopressin-like receptor activity0.00647334823424654
GO:0014070response to organic cyclic substance0.00691692952418288
GO:0003044regulation of systemic arterial blood pressure mediated by a chemical signal0.0073358134288381
GO:0042219amino acid derivative catabolic process0.00832640416780392
GO:0008092cytoskeletal protein binding0.00880142132979071
GO:0007202phospholipase C activation0.00880142132979071
GO:0003073regulation of systemic arterial blood pressure0.00880142132979071
GO:0030159receptor signaling complex scaffold activity0.00965924344639748
GO:0046328regulation of JNK cascade0.00995266979920516
GO:0005737cytoplasm0.00999984862400368
GO:0032947protein complex scaffold0.00999984862400368
GO:0019439aromatic compound catabolic process0.0102660578907856
GO:0042562hormone binding0.0124313000723987
GO:0030534adult behavior0.0126342003787232
GO:0042133neurotransmitter metabolic process0.0146586743863171
GO:0004860protein kinase inhibitor activity0.0179430566270281
GO:0005515protein binding0.0180997788971695
GO:0019210kinase inhibitor activity0.0180997788971695
GO:0008483transaminase activity0.0194389104962489
GO:0044242cellular lipid catabolic process0.0198996041632521
GO:0008217regulation of blood pressure0.0223724594128333
GO:0016769transferase activity, transferring nitrogenous groups0.0243116360946388
GO:0010033response to organic substance0.0243116360946388
GO:0007254JNK cascade0.0250375296718024
GO:0031098stress-activated protein kinase signaling pathway0.025609662230631
GO:0051480cytosolic calcium ion homeostasis0.025609662230631
GO:0007204elevation of cytosolic calcium ion concentration0.025609662230631
GO:0051345positive regulation of hydrolase activity0.0273417127902622
GO:0001505regulation of neurotransmitter levels0.0276061920576986
GO:0043229intracellular organelle0.0294816676800128
GO:0043226organelle0.0294816676800128
GO:0007200G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)0.029694844998741
GO:0006575amino acid derivative metabolic process0.0299069380436163
GO:0003008system process0.0323096681837383
GO:0019887protein kinase regulator activity0.0338427757439054
GO:0006874cellular calcium ion homeostasis0.0360979764961657
GO:0055074calcium ion homeostasis0.0360979764961657
GO:0030170pyridoxal phosphate binding0.0360979764961657
GO:0019207kinase regulator activity0.0364010246706387
GO:0006875cellular metal ion homeostasis0.0364010246706387
GO:0055065metal ion homeostasis0.0364010246706387
GO:0048015phosphoinositide-mediated signaling0.0376576776302515
GO:0007154cell communication0.0378359583518643
GO:0016042lipid catabolic process0.0409821848022357
GO:0001653peptide receptor activity0.0409821848022357
GO:0008528peptide receptor activity, G-protein coupled0.0409821848022357
GO:0000165MAPKKK cascade0.0410131733915982
GO:0042803protein homodimerization activity0.0416457691005139
GO:0007242intracellular signaling cascade0.0416457691005139
GO:0008015blood circulation0.0416457691005139
GO:0003013circulatory system process0.0416457691005139
GO:0009628response to abiotic stimulus0.04243256151255
GO:0030005cellular di-, tri-valent inorganic cation homeostasis0.0439236533691728
GO:0044424intracellular part0.0439236533691728
GO:0031980mitochondrial lumen0.0439236533691728
GO:0055066di-, tri-valent inorganic cation homeostasis0.0439236533691728
GO:0006725aromatic compound metabolic process0.0439236533691728
GO:0005759mitochondrial matrix0.0439236533691728
GO:0006631fatty acid metabolic process0.0453076123791525
GO:0005768endosome0.0453076123791525
GO:0030003cellular cation homeostasis0.0464370468193041
GO:0055080cation homeostasis0.0466312757290864
GO:0042277peptide binding0.0472716745516595



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 tube9.79e-5256
neural rod9.79e-5256
future spinal cord9.79e-5256
neural keel9.79e-5256
regional part of nervous system5.11e-4753
regional part of brain5.11e-4753
brain1.56e-3768
future brain1.56e-3768
regional part of forebrain1.59e-3641
forebrain1.59e-3641
anterior neural tube1.59e-3641
future forebrain1.59e-3641
central nervous system8.08e-3681
neural plate2.73e-3382
presumptive neural plate2.73e-3382
adult organism7.36e-32114
nervous system1.34e-3189
neurectoderm1.96e-3186
brain grey matter2.98e-2834
gray matter2.98e-2834
telencephalon3.64e-2834
ecto-epithelium7.87e-25104
pre-chordal neural plate4.65e-2361
regional part of telencephalon4.93e-2332
cerebral hemisphere5.10e-2332
structure with developmental contribution from neural crest5.35e-23132
regional part of cerebral cortex8.69e-2222
neocortex4.58e-2020
cerebral cortex5.62e-1925
pallium5.62e-1925
organ system subdivision9.13e-17223
brainstem1.00e-166
posterior neural tube6.64e-1615
chordal neural plate6.64e-1615
tube9.44e-15192
ectoderm-derived structure2.50e-13171
ectoderm2.50e-13171
presumptive ectoderm2.50e-13171
pons1.57e-123
segmental subdivision of hindbrain2.03e-1112
hindbrain2.03e-1112
presumptive hindbrain2.03e-1112
neural nucleus5.93e-119
nucleus of brain5.93e-119
segmental subdivision of nervous system1.72e-1013
anatomical conduit2.65e-10240
gyrus3.10e-106
diencephalon5.62e-107
future diencephalon5.62e-107
pituitary gland7.22e-102
anatomical cluster1.59e-09373
temporal lobe2.59e-096
dorsal plus ventral thalamus2.74e-092
thalamic complex2.74e-092
locus ceruleus2.86e-092
brainstem nucleus2.86e-092
hindbrain nucleus2.86e-092
multi-tissue structure6.53e-09342
epithelium1.18e-08306
cell layer1.71e-08309
limbic system7.96e-085
organ part1.65e-07218
parietal lobe2.10e-075
regional part of metencephalon4.23e-079
basal ganglion4.23e-079
nuclear complex of neuraxis4.23e-079
aggregate regional part of brain4.23e-079
metencephalon4.23e-079
collection of basal ganglia4.23e-079
cerebral subcortex4.23e-079
future metencephalon4.23e-079


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)
MA0003.10.546816
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.10.187674
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.12.46653
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.13.04735
MA0056.10
MA0057.10.744639
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.10.575931
MA0063.10
MA0066.11.47685
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.00958848
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.0723293
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.88373
MA0105.10.695228
MA0106.10.648997
MA0107.10.752965
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.741402
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.11.00897
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.10.186511
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.980834
MA0146.10.0610556
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.20.0170091
MA0138.20.704862
MA0002.20.213296
MA0137.20.36398
MA0104.20.223944
MA0047.20.636643
MA0112.22.55032
MA0065.20.591589
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.335384
MA0155.10.534073
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.12.15752
MA0160.10.543522
MA0161.10
MA0162.10.0249953
MA0163.10.632664
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.20.361922
MA0102.21.51913
MA0258.11.97124
MA0259.10.289405
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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