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Coexpression cluster:C393: Difference between revisions

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{{Coexpression_clusters
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type XII!0.0282266369397579!1303$GO:0030020!extracellular matrix structural constituent conferring tensile strength!0.0282266369397579!1303$GO:0005861!troponin complex!0.0344718141264407!7140$GO:0005593!FACIT collagen!0.0344718141264407!1303$GO:0006942!regulation of striated muscle contraction!0.0344718141264407!7140$GO:0030934!anchoring collagen!0.0344718141264407!1303$GO:0005515!protein binding!0.0344718141264407!6274;1607;144568;7140;8581;1303$GO:0030199!collagen fibril organization!0.0344718141264407!1303$GO:0005865!striated muscle thin 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646696,0.333698,0.464036,0.570413,0.286047,0.728807,0.00131044,0.0156344,0.361856,0.895648,0.747292,0.144385,0.277306,0.144591,0.00984487,0.617826,0.270834,0.00938437,0.185119,0.521868,0.719617,0.793248,0.34463,0.593925,0.362418,0.0122865,0.282007,0.303832,0.18335,0.00245918,0.100058,0.580851,0.126589,0.571895,0.184207,0.730405,0.0247455,0.197693,0.22176,0.00381761,0.669785,0.160672,0.596305,0.554522,0.00873872,0.505274,0.789198,0.159896,0.485157,0.53999,0.0165465,0.0281628,0.000453662,0.00504789,0.642183,0.050728,0.614052,0.220644|tfbs_overrepresentation_for_novel_motifs=0.0627807,0.232343,0.059802,0.407729,0.169673,0.806284,0.175095,0.858655,0.333785,0.0158681,0.36231,0.203538,0.110027,0.167821,0.679085,0.193751,0.33472,0.516758,0.125731,0.0648405,1.24175,0.306,0.124907,1.03538,0.0793696,0.219025,0.0861865,0.123702,0.172973,0.291216,0.332129,0.363981,0.221705,0.039496,0.0333798,0.0833409,0.0324544,0.129917,0.498551,0.0105076,0.5728,0.0931052,0.0733551,0.0433557,0.0354666,0.0726529,0.175791,0.106932,0.861064,0.17311,0.228909,0.183375,0.0940165,0.427029,0.558863,0.506501,0.706938,0.45661,0.698608,0.148912,0.397292,0.177305,0.335035,0.313136,0.188939,0.286902,0.638114,0.983449,0.355656,0.828977,0.0867459,2.08119,0.010572,0.557091,0.0361178,0.195864,1.01651,0.300172,0.353062,1.41983,0.271469,0.312308,0.552797,0.347399,0.511911,0.00106619,1.95452,0.276936,0.691411,1.07932,0.723727,0.488513,0.377556,0.721432,0.0445871,1.13035,0.123822,0.412519,0.250711,0.231873,0.0264522,0.372975,0.407897,0.337605,0.762448,0.110252,0.325192,0.496667,0.0792544,0.039073,0.229701,0.405608,0.0576237,0.117734,0.679489,0.130124,0.00200222,0.676965,0.285144,0.452122,2.32459,1.27372,0.799469,0.196148,0.782053,0.300752,0.171066,0.381614,0.587649,0.258343,0.489108,0.102719,0.600533,0.56539,0.735665,1.51618,0.665613,0.391857,0.696441,1.52541,1.13019,0.662221,0.987058,0.409595,0.765437,0.144474,0.737169,1.36826,0.633502,0.0913429,0.270424,0.000259436,0.489437,0.0581938,0.52441,0.857896,1.23673,0.155139,0.272485,0.236668,0.661111,0.47352,0.929056,0.240572,0.792924,0.551548,0.0818622,0.174248,0.0158993|tfbs_overrepresentation_jaspar=MA0003.1;0.0016508,MA0004.1;0.115462,MA0006.1;0.043712,MA0007.1;0.105458,MA0009.1;1.14995,MA0014.1;1.09125e-06,MA0017.1;0.211842,MA0019.1;0.206961,MA0024.1;0.366071,MA0025.1;0.570597,MA0027.1;2.00534,MA0028.1;0.185296,MA0029.1;0.381857,MA0030.1;0.372472,MA0031.1;0.320773,MA0038.1;0.176878,MA0040.1;1.0045,MA0041.1;0.396379,MA0042.1;0.350711,MA0043.1;0.453881,MA0046.1;0.444311,MA0048.1;0.0119659,MA0050.1;0.108721,MA0051.1;0.517477,MA0052.1;0.389861,MA0055.1;0.000405343,MA0056.1;0,MA0057.1;0.0910637,MA0058.1;0.0687016,MA0059.1;0.0681464,MA0060.1;0.0636033,MA0061.1;0.26696,MA0063.1;0,MA0066.1;1.00733,MA0067.1;0.739032,MA0068.1;0.0831041,MA0069.1;0.441028,MA0070.1;0.431528,MA0071.1;0.152483,MA0072.1;0.427724,MA0073.1;0.755125,MA0074.1;0.173668,MA0076.1;0.0757217,MA0077.1;0.421218,MA0078.1;0.242013,MA0081.1;0.0682163,MA0083.1;0.460049,MA0084.1;0.916043,MA0087.1;0.425657,MA0088.1;0.138004,MA0089.1;0,MA0090.1;0.589151,MA0091.1;0.373385,MA0092.1;0.32063,MA0093.1;0.0447606,MA0095.1;0,MA0098.1;0,MA0100.1;0.185942,MA0101.1;0.174575,MA0103.1;0.361926,MA0105.1;0.150085,MA0106.1;0.590188,MA0107.1;0.251383,MA0108.2;0.318371,MA0109.1;0,MA0111.1;0.0888583,MA0113.1;0.617,MA0114.1;0.0980889,MA0115.1;0.668285,MA0116.1;0.105451,MA0117.1;0.486035,MA0119.1;0.0614144,MA0122.1;0.50863,MA0124.1;0.630319,MA0125.1;0.554615,MA0130.1;0,MA0131.1;0.255226,MA0132.1;0,MA0133.1;0,MA0135.1;0.479757,MA0136.1;0.535282,MA0139.1;0.0397016,MA0140.1;0.150858,MA0141.1;0.0674008,MA0142.1;0.296096,MA0143.1;1.15972,MA0144.1;0.683441,MA0145.1;0.278707,MA0146.1;0.0959237,MA0147.1;0.0256229,MA0148.1;0.405671,MA0149.1;0.145006,MA0062.2;0.00844267,MA0035.2;0.458892,MA0039.2;0.0578507,MA0138.2;0.242899,MA0002.2;0.518047,MA0137.2;0.750127,MA0104.2;0.0132287,MA0047.2;0.196083,MA0112.2;0.25238,MA0065.2;0.0436892,MA0150.1;0.273149,MA0151.1;0,MA0152.1;0.47,MA0153.1;0.539635,MA0154.1;2.0452,MA0155.1;0.354736,MA0156.1;0.195153,MA0157.1;0.275302,MA0158.1;0,MA0159.1;0.49489,MA0160.1;0.138224,MA0161.1;0,MA0162.1;7.7782e-05,MA0163.1;0.000608073,MA0164.1;0.224291,MA0080.2;0.171095,MA0018.2;0.592438,MA0099.2;0.470547,MA0079.2;2.03752e-08,MA0102.2;0.951693,MA0258.1;0.95914,MA0259.1;0.116092,MA0442.1;0}}
|full_id=C393_amniotic_Placental_Amniotic_clear_Basophils_pharyngeal_tonsil
|id=C393
}}

Latest revision as of 11:22, 17 September 2013


Full id: C393_amniotic_Placental_Amniotic_clear_Basophils_pharyngeal_tonsil



Phase1 CAGE Peaks

Hg19::chr11:1946152..1946161,+p12@TNNT3
Hg19::chr12:83148856..83148864,+p@chr12:83148856..83148864
+
Hg19::chr12:8975061..8975072,+p5@A2ML1
Hg19::chr13:30415684..30415696,-p@chr13:30415684..30415696
-
Hg19::chr16:70740254..70740259,-p@chr16:70740254..70740259
-
Hg19::chr1:153520959..153520976,-p6@S100A3
Hg19::chr21:39670082..39670093,+p@chr21:39670082..39670093
+
Hg19::chr21:39670125..39670140,+p@chr21:39670125..39670140
+
Hg19::chr3:134044856..134044890,+p@chr3:134044856..134044890
+
Hg19::chr3:146323019..146323049,-p1@PLSCR5
Hg19::chr3:24339226..24339231,-p@chr3:24339226..24339231
-
Hg19::chr3:54925405..54925424,+p@chr3:54925405..54925424
+
Hg19::chr3:54925431..54925442,+p@chr3:54925431..54925442
+
Hg19::chr3:55513517..55513530,-p@chr3:55513517..55513530
-
Hg19::chr4:38062660..38062664,+p@chr4:38062660..38062664
+
Hg19::chr5:170210042..170210086,-p@chr5:170210042..170210086
-
Hg19::chr5:170210721..170210734,+p1@GABRP
Hg19::chr5:170238215..170238225,+p@chr5:170238215..170238225
+
Hg19::chr5:170239966..170239982,+p@chr5:170239966..170239982
+
Hg19::chr5:170241044..170241049,-p@chr5:170241044..170241049
-
Hg19::chr6:75828835..75828850,-p21@COL12A1
Hg19::chr6:75828851..75828864,-p20@COL12A1
Hg19::chr6:75828867..75828885,-p10@COL12A1
Hg19::chr7:114542043..114542046,-p@chr7:114542043..114542046
-
Hg19::chr7:14880892..14880938,-p16@DGKB
Hg19::chr8:143867355..143867390,-p2@LY6D
Hg19::chr8:8318890..8318903,-p1@ENST00000521218


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:0005595collagen type XII0.0282266369397579
GO:0030020extracellular matrix structural constituent conferring tensile strength0.0282266369397579
GO:0005861troponin complex0.0344718141264407
GO:0005593FACIT collagen0.0344718141264407
GO:0006942regulation of striated muscle contraction0.0344718141264407
GO:0030934anchoring collagen0.0344718141264407
GO:0005515protein binding0.0344718141264407
GO:0030199collagen fibril organization0.0344718141264407
GO:0005865striated muscle thin filament0.0344718141264407



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>

Uber Anatomy
Ontology termp-valuen
extraembryonic membrane6.51e-12714
membranous layer6.51e-12714
extraembryonic structure5.85e-7424
amnion2.31e-647
chorion9.73e-647
somatic layer of lateral plate mesoderm2.27e-568
placenta6.60e-414
allantois6.60e-414
organ component layer1.17e-2666
acellular anatomical structure7.93e-253
egg chorion7.93e-253
uterus2.38e-0821
embryonic uterus5.39e-0822
internal female genitalia5.39e-0822
organ part1.44e-07218
internal genitalia4.23e-0725


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)
MA0003.10.0016508
MA0004.10.115462
MA0006.10.043712
MA0007.10.105458
MA0009.11.14995
MA0014.11.09125e-06
MA0017.10.211842
MA0019.10.206961
MA0024.10.366071
MA0025.10.570597
MA0027.12.00534
MA0028.10.185296
MA0029.10.381857
MA0030.10.372472
MA0031.10.320773
MA0038.10.176878
MA0040.11.0045
MA0041.10.396379
MA0042.10.350711
MA0043.10.453881
MA0046.10.444311
MA0048.10.0119659
MA0050.10.108721
MA0051.10.517477
MA0052.10.389861
MA0055.10.000405343
MA0056.10
MA0057.10.0910637
MA0058.10.0687016
MA0059.10.0681464
MA0060.10.0636033
MA0061.10.26696
MA0063.10
MA0066.11.00733
MA0067.10.739032
MA0068.10.0831041
MA0069.10.441028
MA0070.10.431528
MA0071.10.152483
MA0072.10.427724
MA0073.10.755125
MA0074.10.173668
MA0076.10.0757217
MA0077.10.421218
MA0078.10.242013
MA0081.10.0682163
MA0083.10.460049
MA0084.10.916043
MA0087.10.425657
MA0088.10.138004
MA0089.10
MA0090.10.589151
MA0091.10.373385
MA0092.10.32063
MA0093.10.0447606
MA0095.10
MA0098.10
MA0100.10.185942
MA0101.10.174575
MA0103.10.361926
MA0105.10.150085
MA0106.10.590188
MA0107.10.251383
MA0108.20.318371
MA0109.10
MA0111.10.0888583
MA0113.10.617
MA0114.10.0980889
MA0115.10.668285
MA0116.10.105451
MA0117.10.486035
MA0119.10.0614144
MA0122.10.50863
MA0124.10.630319
MA0125.10.554615
MA0130.10
MA0131.10.255226
MA0132.10
MA0133.10
MA0135.10.479757
MA0136.10.535282
MA0139.10.0397016
MA0140.10.150858
MA0141.10.0674008
MA0142.10.296096
MA0143.11.15972
MA0144.10.683441
MA0145.10.278707
MA0146.10.0959237
MA0147.10.0256229
MA0148.10.405671
MA0149.10.145006
MA0062.20.00844267
MA0035.20.458892
MA0039.20.0578507
MA0138.20.242899
MA0002.20.518047
MA0137.20.750127
MA0104.20.0132287
MA0047.20.196083
MA0112.20.25238
MA0065.20.0436892
MA0150.10.273149
MA0151.10
MA0152.10.47
MA0153.10.539635
MA0154.12.0452
MA0155.10.354736
MA0156.10.195153
MA0157.10.275302
MA0158.10
MA0159.10.49489
MA0160.10.138224
MA0161.10
MA0162.17.7782e-05
MA0163.10.000608073
MA0164.10.224291
MA0080.20.171095
MA0018.20.592438
MA0099.20.470547
MA0079.22.03752e-08
MA0102.20.951693
MA0258.10.95914
MA0259.10.116092
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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