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Coexpression cluster:C629: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;0.135551,MA0004.1;0.275994,MA0006.1;0.152601,MA0007.1;0.260673,MA0009.1;0.695988,MA0014.1;0.0165986,MA0017.1;0.181071,MA0019.1;0.403106,MA0024.1;0.59663,MA0025.1;0.824398,MA0027.1;2.28954,MA0028.1;0.164086,MA0029.1;0.614815,MA0030.1;0.604021,MA0031.1;1.34227,MA0038.1;0.363295,MA0040.1;0.620334,MA0041.1;1.44251,MA0042.1;0.264992,MA0043.1;0.69629,MA0046.1;0.685589,MA0048.1;0.110534,MA0050.1;0.265714,MA0051.1;0.359609,MA0052.1;0.623986,MA0055.1;0.276748,MA0056.1;0,MA0057.1;0.0243088,MA0058.1;0.200063,MA0059.1;0.199079,MA0060.1;0.266757,MA0061.1;0.487876,MA0063.1;0,MA0066.1;0.363668,MA0067.1;1.00375,MA0068.1;0.385025,MA0069.1;0.681911,MA0070.1;0.671241,MA0071.1;0.878639,MA0072.1;0.666958,MA0073.1;0.0345424,MA0074.1;0.358953,MA0076.1;0.212295,MA0077.1;0.65962,MA0078.1;0.447828,MA0081.1;0.199203,MA0083.1;0.703169,MA0084.1;1.18798,MA0087.1;0.664629,MA0088.1;0.0514785,MA0089.1;0,MA0090.1;0.223576,MA0091.1;0.278153,MA0092.1;0.691297,MA0093.1;0.154754,MA0095.1;0,MA0098.1;0,MA0100.1;0.375452,MA0101.1;0.475507,MA0103.1;0.448026,MA0105.1;0.430023,MA0106.1;0.399649,MA0107.1;0.708233,MA0108.2;0.540797,MA0109.1;0,MA0111.1;0.234271,MA0113.1;0.414278,MA0114.1;0.104181,MA0115.1;0.929032,MA0116.1;0.718336,MA0117.1;0.732,MA0119.1;0.18693,MA0122.1;0.756889,MA0124.1;0.888592,MA0125.1;0.807083,MA0130.1;0,MA0131.1;0.464307,MA0132.1;0,MA0133.1;0,MA0135.1;0.725055,MA0136.1;0.369468,MA0139.1;0.0564547,MA0140.1;0.873545,MA0141.1;0.197753,MA0142.1;0.514195,MA0143.1;0.414436,MA0144.1;0.652118,MA0145.1;1.16117,MA0146.1;0.0782306,MA0147.1;0.111828,MA0148.1;0.296708,MA0149.1;0.319221,MA0062.2;0.0599644,MA0035.2;0.326883,MA0039.2;0.498555,MA0138.2;0.44894,MA0002.2;0.531015,MA0137.2;0.168782,MA0104.2;0.0769208,MA0047.2;0.388882,MA0112.2;0.0113102,MA0065.2;0.16797,MA0150.1;1.8297,MA0151.1;0,MA0152.1;0.333125,MA0153.1;0.790794,MA0154.1;1.01572,MA0155.1;0.283527,MA0156.1;0.170442,MA0157.1;1.22595,MA0158.1;0,MA0159.1;0.361202,MA0160.1;0.30953,MA0161.1;0,MA0162.1;0.00136062,MA0163.1;0.106785,MA0164.1;1.08899,MA0080.2;0.154815,MA0018.2;0.400879,MA0099.2;1.59306,MA0079.2;0.000723295,MA0102.2;1.22472,MA0258.1;0.300766,MA0259.1;0.374338,MA0442.1;0
}}
}}

Revision as of 19:19, 22 January 2013


Full id: C629_esophagus_amniotic_tongue_throat_tonsil_uterus_salivary



Phase1 CAGE Peaks

Hg19::chr12:8975206..8975223,+p1@A2ML1
Hg19::chr13:78109854..78109865,+p3@SCEL
Hg19::chr13:78109875..78109882,+p4@SCEL
Hg19::chr13:78109884..78109902,+p2@SCEL
Hg19::chr17:8301132..8301150,-p1@RNF222
Hg19::chr18:28682130..28682137,-p7@DSC2
Hg19::chr18:28682227..28682238,-p8@DSC2
Hg19::chr18:28682263..28682280,-p4@DSC2
Hg19::chr3:188889737..188889767,+p4@TPRG1
Hg19::chr3:188889775..188889786,+p13@TPRG1
Hg19::chr4:144275173..144275206,+p@chr4:144275173..144275206
+
Hg19::chr4:69313145..69313164,+p2@TMPRSS11E
Hg19::chr5:175838453..175838465,-p@chr5:175838453..175838465
-
Hg19::chr8:22435762..22435782,+p9@PDLIM2


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
extraembryonic membrane4.63e-1914
membranous layer4.63e-1914
respiratory system1.38e-1874
oral opening5.11e-1822
endoderm-derived structure7.64e-16160
endoderm7.64e-16160
presumptive endoderm7.64e-16160
anterior region of body1.60e-1562
craniocervical region1.60e-1562
mouth7.29e-1529
stomodeum7.29e-1529
orifice1.59e-1436
neck9.28e-1310
surface structure3.76e-1299
head7.91e-1256
chorion1.06e-117
respiratory tract1.03e-1054
organ component layer2.85e-1066
mouth mucosa3.98e-1013
extraembryonic structure5.28e-1024
digestive system8.64e-10145
digestive tract8.64e-10145
primitive gut8.64e-10145
subdivision of head1.08e-0949
mucosa1.29e-0920
amnion4.26e-097
foregut7.11e-0987
mucosa of oral region1.29e-084
respiratory system mucosa1.29e-084
gingival epithelium1.89e-083
lower respiratory tract epithelium4.39e-083
epithelium of bronchus4.39e-083
tongue5.06e-083
gustatory system5.06e-083
future tongue5.06e-083
chordate pharynx5.53e-0810
pharyngeal region of foregut5.53e-0810
somatic layer of lateral plate mesoderm6.82e-088
gland of gut1.35e-0710
acellular anatomical structure1.65e-073
egg chorion1.65e-073
organ part2.84e-07218
pharyngeal arch system3.44e-0718
pharynx3.48e-0711
organ5.32e-07503
tracheobronchial tree5.81e-0715
lower respiratory tract5.81e-0715
subdivision of digestive tract6.54e-07118
Disease
Ontology termp-valuen
squamous cell carcinoma8.27e-1114


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)
MA0003.10.135551
MA0004.10.275994
MA0006.10.152601
MA0007.10.260673
MA0009.10.695988
MA0014.10.0165986
MA0017.10.181071
MA0019.10.403106
MA0024.10.59663
MA0025.10.824398
MA0027.12.28954
MA0028.10.164086
MA0029.10.614815
MA0030.10.604021
MA0031.11.34227
MA0038.10.363295
MA0040.10.620334
MA0041.11.44251
MA0042.10.264992
MA0043.10.69629
MA0046.10.685589
MA0048.10.110534
MA0050.10.265714
MA0051.10.359609
MA0052.10.623986
MA0055.10.276748
MA0056.10
MA0057.10.0243088
MA0058.10.200063
MA0059.10.199079
MA0060.10.266757
MA0061.10.487876
MA0063.10
MA0066.10.363668
MA0067.11.00375
MA0068.10.385025
MA0069.10.681911
MA0070.10.671241
MA0071.10.878639
MA0072.10.666958
MA0073.10.0345424
MA0074.10.358953
MA0076.10.212295
MA0077.10.65962
MA0078.10.447828
MA0081.10.199203
MA0083.10.703169
MA0084.11.18798
MA0087.10.664629
MA0088.10.0514785
MA0089.10
MA0090.10.223576
MA0091.10.278153
MA0092.10.691297
MA0093.10.154754
MA0095.10
MA0098.10
MA0100.10.375452
MA0101.10.475507
MA0103.10.448026
MA0105.10.430023
MA0106.10.399649
MA0107.10.708233
MA0108.20.540797
MA0109.10
MA0111.10.234271
MA0113.10.414278
MA0114.10.104181
MA0115.10.929032
MA0116.10.718336
MA0117.10.732
MA0119.10.18693
MA0122.10.756889
MA0124.10.888592
MA0125.10.807083
MA0130.10
MA0131.10.464307
MA0132.10
MA0133.10
MA0135.10.725055
MA0136.10.369468
MA0139.10.0564547
MA0140.10.873545
MA0141.10.197753
MA0142.10.514195
MA0143.10.414436
MA0144.10.652118
MA0145.11.16117
MA0146.10.0782306
MA0147.10.111828
MA0148.10.296708
MA0149.10.319221
MA0062.20.0599644
MA0035.20.326883
MA0039.20.498555
MA0138.20.44894
MA0002.20.531015
MA0137.20.168782
MA0104.20.0769208
MA0047.20.388882
MA0112.20.0113102
MA0065.20.16797
MA0150.11.8297
MA0151.10
MA0152.10.333125
MA0153.10.790794
MA0154.11.01572
MA0155.10.283527
MA0156.10.170442
MA0157.11.22595
MA0158.10
MA0159.10.361202
MA0160.10.30953
MA0161.10
MA0162.10.00136062
MA0163.10.106785
MA0164.11.08899
MA0080.20.154815
MA0018.20.400879
MA0099.21.59306
MA0079.20.000723295
MA0102.21.22472
MA0258.10.300766
MA0259.10.374338
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
NR3C1#290844.278006666049440.01156838455163820.0422887824357206



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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