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Coexpression cluster:C753: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;0.486434,MA0004.1;0.349539,MA0006.1;0.210781,MA0007.1;0.332734,MA0009.1;0.79061,MA0014.1;0.00227771,MA0017.1;0.24363,MA0019.1;0.486183,MA0024.1;0.688373,MA0025.1;0.921763,MA0027.1;2.39404,MA0028.1;0.224112,MA0029.1;0.707146,MA0030.1;0.696006,MA0031.1;0.633489,MA0038.1;1.12886,MA0040.1;0.712837,MA0041.1;0.366339,MA0042.1;0.337481,MA0043.1;0.790919,MA0046.1;0.779945,MA0048.1;0.185335,MA0050.1;0.338274,MA0051.1;0.439895,MA0052.1;0.716602,MA0055.1;0.0496191,MA0056.1;0,MA0057.1;0.0465155,MA0058.1;0.265212,MA0059.1;1.34253,MA0060.1;0.119532,MA0061.1;0.100525,MA0063.1;0,MA0066.1;0.444231,MA0067.1;1.1037,MA0068.1;0.262497,MA0069.1;0.776171,MA0070.1;0.765217,MA0071.1;1.85155,MA0072.1;0.760818,MA0073.1;3.85623e-06,MA0074.1;1.11883,MA0076.1;0.278993,MA0077.1;2.97647,MA0078.1;0.533387,MA0081.1;0.730303,MA0083.1;0.79797,MA0084.1;1.28962,MA0087.1;0.758426,MA0088.1;0.248289,MA0089.1;0,MA0090.1;0.291627,MA0091.1;0.351901,MA0092.1;0.318032,MA0093.1;0.213288,MA0095.1;0,MA0098.1;0,MA0100.1;0.456802,MA0101.1;0.216017,MA0103.1;0.203171,MA0105.1;0.0403209,MA0106.1;0.482519,MA0107.1;0.156959,MA0108.2;0.630531,MA0109.1;0,MA0111.1;0.303543,MA0113.1;0.498009,MA0114.1;0.465415,MA0115.1;1.02805,MA0116.1;0.159642,MA0117.1;0.827487,MA0119.1;1.29122,MA0122.1;0.852927,MA0124.1;0.98702,MA0125.1;0.904129,MA0130.1;0,MA0131.1;0.550695,MA0132.1;0,MA0133.1;0,MA0135.1;0.820382,MA0136.1;0.450422,MA0139.1;0.0922451,MA0140.1;0.405425,MA0141.1;0.726533,MA0142.1;0.602852,MA0143.1;1.24556,MA0144.1;0.142196,MA0145.1;0.822953,MA0146.1;0.0935127,MA0147.1;0.162359,MA0148.1;0.372124,MA0149.1;0.396509,MA0062.2;0.0969238,MA0035.2;0.404774,MA0039.2;0.0194173,MA0138.2;0.534556,MA0002.2;0.358551,MA0137.2;0.229531,MA0104.2;0.118985,MA0047.2;0.47109,MA0112.2;0.106997,MA0065.2;0.28513,MA0150.1;0.286461,MA0151.1;0,MA0152.1;0.411494,MA0153.1;3.39643,MA0154.1;0.153348,MA0155.1;0.0230394,MA0156.1;0.231442,MA0157.1;0.576556,MA0158.1;0,MA0159.1;0.162854,MA0160.1;0.386031,MA0161.1;0,MA0162.1;0.0266618,MA0163.1;0.0519618,MA0164.1;1.2703,MA0080.2;0.611699,MA0018.2;0.483823,MA0099.2;0.411824,MA0079.2;8.76424e-07,MA0102.2;1.32663,MA0258.1;0.420151,MA0259.1;0.504687,MA0442.1;0
}}
}}

Revision as of 19:25, 22 January 2013


Full id: C753_Retinal_retina_eye_kidney_caudate_corpus_putamen



Phase1 CAGE Peaks

Hg19::chr13:51913806..51913817,+p2@SERPINE3
Hg19::chr13:51913819..51913838,+p1@SERPINE3
Hg19::chr13:51913893..51913901,+p@chr13:51913893..51913901
+
Hg19::chr13:51913997..51914020,+p@chr13:51913997..51914020
+
Hg19::chr14:28081776..28081788,+p1@LOC100505967
Hg19::chr14:28081790..28081795,+p2@LOC100505967
Hg19::chr1:75180314..75180323,-p@chr1:75180314..75180323
-
Hg19::chr2:219610770..219610777,+p19@TTLL4
Hg19::chr2:219610813..219610832,+p8@TTLL4
Hg19::chr8:75898210..75898219,+p11@CRISPLD1
Hg19::chr8:75898244..75898255,+p7@CRISPLD1


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:0004835tubulin-tyrosine ligase activity0.0328891110651264



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
retinal pigment epithelial cell1.62e-603
visual pigment cell1.25e-454
pigment cell1.35e-1314
Uber Anatomy
Ontology termp-valuen
pigmented layer of retina1.62e-603
presumptive retinal pigmented epithelium1.62e-603
retina1.81e-536
photoreceptor array1.81e-536
posterior segment of eyeball1.81e-536
layer of retina1.25e-454
eye5.84e-2421
visual system5.84e-2421
sense organ5.35e-2124
sensory system5.35e-2124
entire sense organ system5.35e-2124
pigment epithelium of eye4.11e-1711
camera-type eye2.03e-1620
simple eye2.03e-1620
immature eye2.03e-1620
ocular region2.03e-1620
eyeball of camera-type eye2.03e-1620
optic cup2.03e-1620
optic vesicle2.03e-1620
eye primordium2.03e-1620
face5.77e-1522
pre-chordal neural plate1.72e-1161
neural plate1.74e-1182
presumptive neural plate1.74e-1182
neurectoderm6.03e-1186
ectodermal placode9.89e-1131
ecto-epithelium5.07e-09104
frontal cortex7.76e-083
medulla oblongata8.29e-083
myelencephalon8.29e-083
future myelencephalon8.29e-083
structure with developmental contribution from neural crest4.73e-07132
ectoderm-derived structure6.56e-07171
ectoderm6.56e-07171
presumptive ectoderm6.56e-07171
subdivision of head6.72e-0749


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)
MA0003.10.486434
MA0004.10.349539
MA0006.10.210781
MA0007.10.332734
MA0009.10.79061
MA0014.10.00227771
MA0017.10.24363
MA0019.10.486183
MA0024.10.688373
MA0025.10.921763
MA0027.12.39404
MA0028.10.224112
MA0029.10.707146
MA0030.10.696006
MA0031.10.633489
MA0038.11.12886
MA0040.10.712837
MA0041.10.366339
MA0042.10.337481
MA0043.10.790919
MA0046.10.779945
MA0048.10.185335
MA0050.10.338274
MA0051.10.439895
MA0052.10.716602
MA0055.10.0496191
MA0056.10
MA0057.10.0465155
MA0058.10.265212
MA0059.11.34253
MA0060.10.119532
MA0061.10.100525
MA0063.10
MA0066.10.444231
MA0067.11.1037
MA0068.10.262497
MA0069.10.776171
MA0070.10.765217
MA0071.11.85155
MA0072.10.760818
MA0073.13.85623e-06
MA0074.11.11883
MA0076.10.278993
MA0077.12.97647
MA0078.10.533387
MA0081.10.730303
MA0083.10.79797
MA0084.11.28962
MA0087.10.758426
MA0088.10.248289
MA0089.10
MA0090.10.291627
MA0091.10.351901
MA0092.10.318032
MA0093.10.213288
MA0095.10
MA0098.10
MA0100.10.456802
MA0101.10.216017
MA0103.10.203171
MA0105.10.0403209
MA0106.10.482519
MA0107.10.156959
MA0108.20.630531
MA0109.10
MA0111.10.303543
MA0113.10.498009
MA0114.10.465415
MA0115.11.02805
MA0116.10.159642
MA0117.10.827487
MA0119.11.29122
MA0122.10.852927
MA0124.10.98702
MA0125.10.904129
MA0130.10
MA0131.10.550695
MA0132.10
MA0133.10
MA0135.10.820382
MA0136.10.450422
MA0139.10.0922451
MA0140.10.405425
MA0141.10.726533
MA0142.10.602852
MA0143.11.24556
MA0144.10.142196
MA0145.10.822953
MA0146.10.0935127
MA0147.10.162359
MA0148.10.372124
MA0149.10.396509
MA0062.20.0969238
MA0035.20.404774
MA0039.20.0194173
MA0138.20.534556
MA0002.20.358551
MA0137.20.229531
MA0104.20.118985
MA0047.20.47109
MA0112.20.106997
MA0065.20.28513
MA0150.10.286461
MA0151.10
MA0152.10.411494
MA0153.13.39643
MA0154.10.153348
MA0155.10.0230394
MA0156.10.231442
MA0157.10.576556
MA0158.10
MA0159.10.162854
MA0160.10.386031
MA0161.10
MA0162.10.0266618
MA0163.10.0519618
MA0164.11.2703
MA0080.20.611699
MA0018.20.483823
MA0099.20.411824
MA0079.28.76424e-07
MA0102.21.32663
MA0258.10.420151
MA0259.10.504687
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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