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Coexpression cluster:C1048: Difference between revisions

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{{Coexpression_clusters
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,0.54956,0.554803,0.455388,0.473509,0.462252,0.335015,0.435559,0.53418,0.28015,0.492484,0.0409505,0.397471,0.449258,0.330704,0.443138,0.519779,0.364755,0.312488,0.547073,0.48939,0.395736,0.0959524,0.238065,0.452384,0.62882,0.585012,0.481224,0.204547,0.452254,0.259924,0.136638,0.137048,0.353983,0.194753,0.104944,0.136955,0.274587,0.554772,0.469052,0.425619,0.50814,0.429061,0.202353,0.240717,0.162041,0.292976,0.161384,0.255196,0.167238,0.190639,0.307532,0.265287,0.113346,0.168727,0.221472,0.095012,0.320667,0.456504,0.607439,0.5938,0.679098,0.334729,0.557075,0.187049,0.120389,0.497569,0.611294,0.541437,0.406439,0.0611493,0.559083,0.313926,0.373141,0.459861,0.447066,0.594101,0.512982,0.649607,0.279812,0.481032,0.491197,0.278645,0.439191,0.431751,0.586217,0.588503,0.535591,0.381036,0.491941,0.230489,0.285747,0.494548,0.128913,0.23568,0.213047,0.638022,0.394858,0.369527,0.207064,0.178571,0.568909,0.247225,0.00497628,0.403105,0.366377,0.476867,0.540268,0.459344,0.335957|tfbs_overrepresentation_for_novel_motifs=0.348717,0.183537,0.341646,1.21028,0.816074,1.20684,0.554663,0.561282,0.555925,0.0394821,0.450635,1.45571,0.152895,0.543352,0.81316,0.863056,0.774423,1.29227,0.163559,0.0766963,1.62225,0.715078,0.472508,0.805193,0.385586,0.619829,0.135503,0.470396,0.304828,0.122648,0.429397,0.810962,0.220667,0.154814,0.269459,0.0649851,0.266487,0.481208,0.244807,0.174436,0.739305,0.413601,0.0547276,0.299183,0.0775086,0.371118,0.555735,0.440085,0.0498256,0.822946,0.63387,0.567337,0.309329,0.887323,1.03948,0.546236,0.831988,0.514077,0.388089,0.513089,0.85167,0.558065,0.556977,0.746929,0.575742,0.712797,1.12756,1.49516,0.800646,1.33315,0.400869,0.573519,0.0911419,1.03748,0.149081,0.138565,0.401476,0.730167,0.797419,0.379656,0.167664,0.745864,0.575394,0.19474,0.986227,0.0220225,0.0757344,0.118789,0.659621,1.59442,1.22073,0.959334,0.827657,0.227232,0.302606,0.672575,0.946574,0.87,0.664183,0.106284,0.246049,0.822041,0.864454,0.778061,0.701386,0.446229,0.762347,0.539961,0.385342,0.286892,0.352381,0.861701,0.336372,0.459808,1.17281,0.265019,0.0278613,0.428232,0.710479,0.229841,1.02923,0.657218,0.477387,0.586509,1.28328,0.730921,0.548418,0.83262,1.07171,0.240162,0.960022,0.432175,1.08604,0.583225,1.23359,0.113443,0.423593,0.470947,1.19123,2.04907,1.64679,1.15398,0.550118,0.866494,0.703126,1.2618,0.686615,1.88987,1.86008,0.224241,0.0833399,0.0510299,0.960402,0.183004,0.557588,1.36372,0.643609,0.288769,0.385642,0.357927,1.15277,0.941964,0.796636,0.36101,0.71907,0.574616,0.213234,0.553354,0.0203307|tfbs_overrepresentation_jaspar=MA0003.1;0.00101002,MA0004.1;0.455723,MA0006.1;0.300178,MA0007.1;0.437331,MA0009.1;0.918715,MA0014.1;0.00962431,MA0017.1;2.43637,MA0019.1;0.602411,MA0024.1;0.813542,MA0025.1;1.05265,MA0027.1;2.5321,MA0028.1;0.315574,MA0029.1;0.832916,MA0030.1;0.821423,MA0031.1;0.756713,MA0038.1;0.557409,MA0040.1;0.838784,MA0041.1;0.474018,MA0042.1;0.442535,MA0043.1;0.919032,MA0046.1;0.90778,MA0048.1;0.0955945,MA0050.1;0.443405,MA0051.1;0.553205,MA0052.1;0.842664,MA0055.1;0.028436,MA0056.1;0,MA0057.1;0.0912556,MA0058.1;0.362328,MA0059.1;0.361075,MA0060.1;0.190336,MA0061.1;0.497495,MA0063.1;0,MA0066.1;0.557833,MA0067.1;1.23721,MA0068.1;0.133123,MA0069.1;0.903908,MA0070.1;2.06698,MA0071.1;0.518907,MA0072.1;0.888148,MA0073.1;9.20286e-05,MA0074.1;0.552456,MA0076.1;0.377799,MA0077.1;0.880402,MA0078.1;0.652193,MA0081.1;0.948525,MA0083.1;0.926258,MA0084.1;1.42483,MA0087.1;0.885691,MA0088.1;0.054222,MA0089.1;0,MA0090.1;0.391903,MA0091.1;6.44543,MA0092.1;0.421159,MA0093.1;0.303084,MA0095.1;0,MA0098.1;0,MA0100.1;0.571227,MA0101.1;0.30624,MA0103.1;0.291333,MA0105.1;0.0818021,MA0106.1;0.59853,MA0107.1;0.236528,MA0108.2;0.753643,MA0109.1;0,MA0111.1;0.405141,MA0113.1;1.49247,MA0114.1;1.89851,MA0115.1;1.1606,MA0116.1;0.239768,MA0117.1;0.956472,MA0119.1;0.345493,MA0122.1;0.982472,MA0124.1;1.11898,MA0125.1;1.0347,MA0130.1;0,MA0131.1;0.670358,MA0132.1;0,MA0133.1;0,MA0135.1;0.949204,MA0136.1;1.38624,MA0139.1;0.155155,MA0140.1;1.28413,MA0141.1;0.944441,MA0142.1;0.724856,MA0143.1;0.615094,MA0144.1;1.17059,MA0145.1;0.220937,MA0146.1;0.00761723,MA0147.1;0.243042,MA0148.1;3.1027,MA0149.1;0.506665,MA0062.2;1.50503,MA0035.2;2.21238,MA0039.2;0.00915579,MA0138.2;0.653421,MA0002.2;0.179788,MA0137.2;0.321796,MA0104.2;0.189646,MA0047.2;3.5755,MA0112.2;0.458158,MA0065.2;0.490252,MA0150.1;0.386144,MA0151.1;0,MA0152.1;1.29801,MA0153.1;1.01778,MA0154.1;0.0799828,MA0155.1;0.0535085,MA0156.1;2.36842,MA0157.1;0.697424,MA0158.1;0,MA0159.1;0.243637,MA0160.1;0.495355,MA0161.1;0,MA0162.1;0.0163939,MA0163.1;0.0104024,MA0164.1;0.627336,MA0080.2;2.26549,MA0018.2;0.599912,MA0099.2;0.523145,MA0079.2;1.41562e-07,MA0102.2;1.46209,MA0258.1;0.603127,MA0259.1;0.25092,MA0442.1;0}}
|full_id=C1048_signet_small_colon_duodenum_temporal_trachea_gall
|id=C1048
}}

Latest revision as of 11:36, 17 September 2013


Full id: C1048_signet_small_colon_duodenum_temporal_trachea_gall



Phase1 CAGE Peaks

Hg19::chr17:34328588..34328597,-p2@CCL15
Hg19::chr2:201242699..201242710,+p23@SPATS2L
Hg19::chr2:201242715..201242739,+p12@SPATS2L
Hg19::chr2:27669034..27669075,-p3@IFT172
Hg19::chr4:165675319..165675335,+p1@LOC100505989
Hg19::chr4:165675340..165675345,+p5@LOC100505989
Hg19::chr4:165675379..165675390,+p4@LOC100505989
Hg19::chr4:165675511..165675518,+p6@LOC100505989


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:0008201heparin binding0.0273314247674389
GO:0008009chemokine activity0.0273314247674389
GO:0042379chemokine receptor binding0.0273314247674389
GO:0001664G-protein-coupled receptor binding0.0273314247674389
GO:0005539glycosaminoglycan binding0.0273314247674389
GO:0006874cellular calcium ion homeostasis0.0273314247674389
GO:0030247polysaccharide binding0.0273314247674389
GO:0055074calcium ion homeostasis0.0273314247674389
GO:0006875cellular metal ion homeostasis0.0273314247674389
GO:0055065metal ion homeostasis0.0273314247674389
GO:0001871pattern binding0.0273314247674389
GO:0042330taxis0.0273314247674389
GO:0006935chemotaxis0.0273314247674389
GO:0030005cellular di-, tri-valent inorganic cation homeostasis0.0278028021233909
GO:0007626locomotory behavior0.0278028021233909
GO:0055066di-, tri-valent inorganic cation homeostasis0.0278028021233909
GO:0030003cellular cation homeostasis0.0278028021233909
GO:0055080cation homeostasis0.0278028021233909
GO:0055082cellular chemical homeostasis0.0291988233652572
GO:0006873cellular ion homeostasis0.0291988233652572
GO:0050801ion homeostasis0.0313145728501302
GO:0007610behavior0.031792812417562
GO:0048878chemical homeostasis0.031792812417562
GO:0005125cytokine activity0.031792812417562
GO:0019725cellular homeostasis0.036885202050857
GO:0030246carbohydrate binding0.0436478611125488
GO:0042592homeostatic process0.0436478611125488
GO:0005615extracellular space0.046264968808301
GO:0042221response to chemical stimulus0.0497852317519475



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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
gastrointestinal system1.21e-2125
intestine1.14e-2017
small intestine7.57e-204
subdivision of digestive tract1.02e-17118
digestive system3.12e-15145
digestive tract3.12e-15145
primitive gut3.12e-15145
endoderm-derived structure2.20e-13160
endoderm2.20e-13160
presumptive endoderm2.20e-13160
open tracheal system trachea2.55e-132
throat8.53e-132
biliary system9.37e-119
biliary tree9.37e-119
biliary bud9.37e-119
bile duct2.38e-096
digestive system duct2.38e-096
duodenum6.86e-092
organ system subdivision3.60e-08223
vermiform appendix2.23e-071
caecum2.23e-071
midgut2.23e-071
adult organism2.30e-07114
submandibular gland2.84e-071
submandibular gland primordium2.84e-071
lower lobe of right lung3.02e-071
right lung lobe3.02e-071
lower lobe of lung3.02e-071
lobe of lung3.02e-071
right lung3.02e-071
hepatopancreatic ampulla5.50e-071
extrahepatic bile duct5.50e-071
common bile duct5.50e-071
duodenal papilla5.50e-071
colon9.81e-079
Disease
Ontology termp-valuen
signet ring cell adenocarcinoma3.06e-132


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)
MA0003.10.00101002
MA0004.10.455723
MA0006.10.300178
MA0007.10.437331
MA0009.10.918715
MA0014.10.00962431
MA0017.12.43637
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.315574
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.10.0955945
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.10.028436
MA0056.10
MA0057.10.0912556
MA0058.10.362328
MA0059.10.361075
MA0060.10.190336
MA0061.10.497495
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.133123
MA0069.10.903908
MA0070.12.06698
MA0071.10.518907
MA0072.10.888148
MA0073.19.20286e-05
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.948525
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.054222
MA0089.10
MA0090.10.391903
MA0091.16.44543
MA0092.10.421159
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.30624
MA0103.10.291333
MA0105.10.0818021
MA0106.10.59853
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.11.49247
MA0114.11.89851
MA0115.11.1606
MA0116.10.239768
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.11.38624
MA0139.10.155155
MA0140.11.28413
MA0141.10.944441
MA0142.10.724856
MA0143.10.615094
MA0144.11.17059
MA0145.10.220937
MA0146.10.00761723
MA0147.10.243042
MA0148.13.1027
MA0149.10.506665
MA0062.21.50503
MA0035.22.21238
MA0039.20.00915579
MA0138.20.653421
MA0002.20.179788
MA0137.20.321796
MA0104.20.189646
MA0047.23.5755
MA0112.20.458158
MA0065.20.490252
MA0150.10.386144
MA0151.10
MA0152.11.29801
MA0153.11.01778
MA0154.10.0799828
MA0155.10.0535085
MA0156.12.36842
MA0157.10.697424
MA0158.10
MA0159.10.243637
MA0160.10.495355
MA0161.10
MA0162.10.0163939
MA0163.10.0104024
MA0164.10.627336
MA0080.22.26549
MA0018.20.599912
MA0099.20.523145
MA0079.21.41562e-07
MA0102.21.46209
MA0258.10.603127
MA0259.10.25092
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
FOXA1#316945.540709874692730.003444272925946160.0175223547232155
GATA3#2625413.6182581786030.0001128396522810840.00154677260068042



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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