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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0,

Latest revision as of 11:31, 17 September 2013


Full id: C791_salivary_epididymis_submaxillary_ductus_seminal_parotid_colon



Phase1 CAGE Peaks

Hg19::chr11:111176214..111176228,-p5@C11orf92
Hg19::chr11:70021323..70021345,-p@chr11:70021323..70021345
-
Hg19::chr17:26800592..26800609,+p5@SLC13A2
Hg19::chr1:1266654..1266669,+p1@TAS1R3
Hg19::chr1:17846690..17846694,+p11@ARHGEF10L
Hg19::chr3:46491385..46491395,-p@chr3:46491385..46491395
-
Hg19::chr7:25702754..25702765,-p3@ENST00000446840
p3@uc003sxp.1
Hg19::chr8:107630226..107630237,+p18@OXR1
Hg19::chr8:107630282..107630302,+p13@OXR1
Hg19::chr8:107630313..107630329,+p10@OXR1


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:0015361low affinity sodium:dicarboxylate symporter activity0.00513341279036033
GO:0050916sensory perception of sweet taste0.00513341279036033
GO:0050917sensory perception of umami taste0.00513341279036033
GO:0033041sweet taste receptor activity0.00513341279036033
GO:0001582detection of chemical stimulus during sensory perception of sweet taste0.00513341279036033
GO:0050907detection of chemical stimulus during sensory perception0.012830698841576
GO:0050912detection of chemical stimulus during sensory perception of taste0.012830698841576
GO:0042221response to chemical stimulus0.0170977803924141
GO:0008527taste receptor activity0.0170977803924141
GO:0017153sodium:dicarboxylate symporter activity0.0170977803924141
GO:0005310dicarboxylic acid transmembrane transporter activity0.0170977803924141
GO:0009593detection of chemical stimulus0.0170977803924141
GO:0016998cell wall catabolic process0.0170977803924141
GO:0010382cell wall metabolic process0.0170977803924141
GO:0007047cell wall organization and biogenesis0.0170977803924141
GO:0045229external encapsulating structure organization and biogenesis0.0176305288148319
GO:0005343organic acid:sodium symporter activity0.0277605898821897
GO:0015296anion:cation symporter activity0.0277605898821897
GO:0050909sensory perception of taste0.0283187928199733
GO:0050906detection of stimulus during sensory perception0.0294598247841548
GO:0008067metabotropic glutamate, GABA-B-like receptor activity0.0347493661867851
GO:0051606detection of stimulus0.0465069031538146
GO:0015370solute:sodium symporter activity0.0468551172588897
GO:0008066glutamate receptor activity0.0468551172588897
GO:0031402sodium ion binding0.0468551172588897
GO:0046943carboxylic acid transmembrane transporter activity0.0468551172588897
GO:0005342organic acid transmembrane transporter activity0.0468551172588897
GO:0046982protein heterodimerization activity0.0479073059231907



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 organism2.00e-28114
male genital duct3.11e-213
internal male genitalia3.11e-213
gland of gut2.03e-1610
duct of male reproductive system4.56e-164
major salivary gland1.03e-142
open tracheal system trachea1.89e-142
saliva-secreting gland7.28e-116
gland of oral region7.28e-116
gland of foregut7.28e-116
oral gland7.28e-116
oral cavity7.28e-116
subdivision of digestive tract9.42e-11118
chordate pharynx1.69e-1010
pharyngeal region of foregut1.69e-1010
respiratory system1.87e-1074
male reproductive organ4.70e-1011
pharynx1.48e-0911
anatomical space3.52e-0995
foregut1.47e-0887
epididymis2.70e-081
submandibular gland2.89e-081
submandibular gland primordium2.89e-081
orifice2.97e-0836
respiratory tract2.98e-0854
seminal vesicle3.32e-081
seminal fluid secreting gland3.32e-081
digestive system3.51e-08145
digestive tract3.51e-08145
primitive gut3.51e-08145
vas deferens3.55e-081
spermatic cord3.55e-081
parotid gland3.80e-081
cheek3.80e-081
parotid gland primordium3.80e-081
lower lobe of right lung6.52e-081
right lung lobe6.52e-081
lower lobe of lung6.52e-081
lobe of lung6.52e-081
right lung6.52e-081
tonsil7.45e-081
mucosa-associated lymphoid tissue7.45e-081
lymphoid tissue7.45e-081
tonsillar ring7.45e-081
uterus or analog1.04e-071
male organism1.69e-0722
male reproductive system1.69e-0722
oral opening1.82e-0722
thymus3.23e-074
hemolymphoid system gland3.23e-074
thymic region3.23e-074
pharyngeal gland3.23e-074
thymus primordium3.23e-074
endoderm-derived structure3.95e-07160
endoderm3.95e-07160
presumptive endoderm3.95e-07160
immaterial anatomical entity5.39e-07117


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)
MA0003.10.0586157
MA0004.10.380329
MA0006.10.236135
MA0007.12.55746
MA0009.10.828613
MA0014.10.0679667
MA0017.10.270554
MA0019.10.520264
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.10.25013
MA0029.10.744375
MA0030.10.733118
MA0031.11.60734
MA0038.10.477043
MA0040.10.750125
MA0041.10.397617
MA0042.10.367902
MA0043.10.828925
MA0046.10.817858
MA0048.10.220931
MA0050.10.965046
MA0051.10.473017
MA0052.10.753928
MA0055.10.344701
MA0056.10
MA0057.10.0580131
MA0058.10.293055
MA0059.10.291897
MA0060.10.138988
MA0061.10.118318
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.10.304755
MA0069.10.814052
MA0070.10.803003
MA0071.10.440254
MA0072.10.798564
MA0073.10.000749839
MA0074.10.4723
MA0076.10.307383
MA0077.10.790956
MA0078.10.568317
MA0081.10.292043
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.10.0309101
MA0089.10
MA0090.10.320494
MA0091.10.382762
MA0092.10.347826
MA0093.10.238771
MA0095.10
MA0098.10
MA0100.10.49029
MA0101.10.241637
MA0103.10.646502
MA0105.10.422512
MA0106.10.516528
MA0107.10.529721
MA0108.20.666881
MA0109.10
MA0111.10.33284
MA0113.10.532314
MA0114.10.174997
MA0115.11.06753
MA0116.11.02702
MA0117.10.865782
MA0119.10.760742
MA0122.10.891407
MA0124.11.0263
MA0125.10.942948
MA0130.10
MA0131.10.585907
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.10.483775
MA0139.11.72746
MA0140.10.437738
MA0141.10.290336
MA0142.10.638837
MA0143.10.532484
MA0144.10.491079
MA0145.10.14293
MA0146.10.4029
MA0147.10.184931
MA0148.10.403564
MA0149.10.428597
MA0062.20.366815
MA0035.20.437071
MA0039.20.0721026
MA0138.20.569505
MA0002.20.407187
MA0137.20.710884
MA0104.20.138396
MA0047.21.25985
MA0112.20.133417
MA0065.21.37627
MA0150.10.315136
MA0151.10
MA0152.10.443956
MA0153.12.13564
MA0154.10.185581
MA0155.10.296882
MA0156.10.715501
MA0157.10.612166
MA0158.10
MA0159.12.33654
MA0160.11.07255
MA0161.10
MA0162.10.00711618
MA0163.11.30834
MA0164.10.544294
MA0080.20.671553
MA0018.20.517858
MA0099.20.444294
MA0079.24.32523e-06
MA0102.21.36707
MA0258.10.155735
MA0259.10.191914
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
RAD21#588544.142013558182530.01132276475674040.0415289983645026



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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