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Coexpression cluster:C1839: Difference between revisions

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{{Coexpression_clusters
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8942,0.343014,0.270094,0.000355808,0.156279,0.313647,0.461742,0.422872,0.336468,0.13327,0.313545,0.17149,0.0877361,0.0880065,0.238969,0.126615,0.0669467,0.0879453,0.000536708,0.396935,0.326779,0.292869,9.8978e-05,3.28664e-05,0.131776,0.158116,0.104606,0.194814,0.104167,0.168186,0.108081,0.123829,0.205215,4.92422e-05,0.0724304,6.76134e-06,0.0110362,0.0604892,0.000117203,0.316879,0.000350296,0.430541,0.508546,0.224871,0.398887,0.00166177,0.310732,0.349611,0.000367311,0.385709,0.278202,0.426488,0.00190533,0.209809,0.253154,0.319519,0.309489,0.430805,0.362154,0.480785,0.185476,0.336314,0.344469,0.184651,0.303359,0.297596,0.42392,0.425912,0.380826,0.259046,0.345068,0.151046,0.483953,0.347171,0.321735,0.15463,0.13907,0.470121,0.269432,0.250466,0.409882,0.115686,0.408975,0.162633,0.342661,0.27567,0.248127,0.33299,0.384731,0.319112,0.526476|tfbs_overrepresentation_for_novel_motifs=2.1885,0.205703,0.500341,0.654974,1.15291,0.653236,0.733342,0.324142,0.321368,0.345702,0.621241,0.778743,0.274093,0.721271,0.453496,1.20439,0.963929,0.395009,0.287891,0.501863,0.500405,0.770467,0.645033,0.44943,2.3241,0.802434,0.25115,0.642741,0.458349,1.90917,1.45697,1.00172,0.359091,1.38854,0.417272,4.0451,0.413782,0.654459,0.388123,0.301779,0.415749,0.580638,0.132849,0.451846,0.476793,4.50619,0.734485,0.609718,0.124583,2.02272,0.817229,0.746838,0.191745,1.08035,1.2359,1.72052,0.4631,1.64902,1.90851,0.688844,1.04369,1.74665,0.86107,2.15436,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,1.66643,1.23387,4.77915,5.64478,0.240727,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,0.0719601,0.963115,1.88098,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,1.15465,0.381528,0.28626,1.06255,0.849074,5.13318,0.389604,1.01316,1.05685,0.967698,0.88799,1.49565,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,1.05995,5.65192,0.596731,0.897476,0.968277,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,2.83049,0.995523,1.15483,0.601055,1.28328,0.763715,1.43285,0.629991,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,2.0258,2.09294,0.577088,3.51312,0.526389,0.79475,1.15522,0.840171,2.9234,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,0.443702|tfbs_overrepresentation_jaspar=MA0003.1;0.737422,MA0004.1;0.626788,MA0006.1;1.14863,MA0007.1;1.47524,MA0009.1;1.11255,MA0014.1;0.660087,MA0017.1;1.24112,MA0019.1;0.784036,MA0024.1;1.00439,MA0025.1;1.24931,MA0027.1;2.73598,MA0028.1;0.470679,MA0029.1;1.02437,MA0030.1;1.01252,MA0031.1;0.945567,MA0038.1;0.736268,MA0040.1;1.03042,MA0041.1;0.64667,MA0042.1;0.612397,MA0043.1;1.11288,MA0046.1;1.10134,MA0048.1;0.195817,MA0050.1;0.613347,MA0051.1;0.731787,MA0052.1;1.03442,MA0055.1;0.0853006,MA0056.1;0,MA0057.1;2.36624,MA0058.1;0.523638,MA0059.1;0.522232,MA0060.1;0.321781,MA0061.1;3.99021,MA0063.1;0,MA0066.1;0.736721,MA0067.1;1.43651,MA0068.1;0.247962,MA0069.1;1.09737,MA0070.1;1.08584,MA0071.1;0.695094,MA0072.1;1.0812,MA0073.1;12.9425,MA0074.1;0.730989,MA0076.1;0.540943,MA0077.1;1.07324,MA0078.1;0.836493,MA0081.1;0.522409,MA0083.1;1.12028,MA0084.1;1.62584,MA0087.1;1.07867,MA0088.1;0.132006,MA0089.1;0,MA0090.1;0.556637,MA0091.1;0.629594,MA0092.1;0.588959,MA0093.1;0.456342,MA0095.1;0,MA0098.1;0,MA0100.1;2.96921,MA0101.1;0.459973,MA0103.1;0.442769,MA0105.1;1.58771,MA0106.1;0.779931,MA0107.1;0.378225,MA0108.2;0.94238,MA0109.1;0,MA0111.1;0.5713,MA0113.1;0.797251,MA0114.1;4.61085,MA0115.1;1.35895,MA0116.1;1.76306,MA0117.1;1.1512,MA0119.1;0.504689,MA0122.1;1.17777,MA0124.1;1.31673,MA0125.1;1.23103,MA0130.1;0,MA0131.1;0.855546,MA0132.1;0,MA0133.1;0,MA0135.1;1.14377,MA0136.1;0.743749,MA0139.1;0.277033,MA0140.1;0.692258,MA0141.1;0.520334,MA0142.1;0.912455,MA0143.1;0.797437,MA0144.1;0.356507,MA0145.1;0.143698,MA0146.1;0.0359558,MA0147.1;0.386018,MA0148.1;0.653474,MA0149.1;0.681935,MA0062.2;0.284987,MA0035.2;0.691506,MA0039.2;4.57923,MA0138.2;0.837782,MA0002.2;0.30855,MA0137.2;0.47779,MA0104.2;0.320919,MA0047.2;0.767096,MA0112.2;0.425004,MA0065.2;2.73531,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;0.172764,MA0155.1;0.409315,MA0156.1;0.480289,MA0157.1;0.883854,MA0158.1;0,MA0159.1;0.386729,MA0160.1;0.669748,MA0161.1;0,MA0162.1;0.81299,MA0163.1;0.0439995,MA0164.1;10.8652,MA0080.2;0.456437,MA0018.2;0.781393,MA0099.2;2.8068,MA0079.2;6.20913,MA0102.2;1.66336,MA0258.1;0.345771,MA0259.1;0.395396,MA0442.1;0}}
|full_id=C1839_Mast_immature_Fibroblast_Mesenchymal_Hair_tenocyte_Keratocytes
|id=C1839
}}

Latest revision as of 11:53, 17 September 2013


Full id: C1839_Mast_immature_Fibroblast_Mesenchymal_Hair_tenocyte_Keratocytes



Phase1 CAGE Peaks

Hg19::chr1:156084491..156084510,+p1@LMNA
Hg19::chr1:156084522..156084529,+p5@LMNA
Hg19::chr1:156084534..156084545,+p4@LMNA
Hg19::chr1:156084552..156084561,+p3@LMNA
Hg19::chr1:156084564..156084580,+p2@LMNA


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><br>

Uber Anatomy
Ontology termp-valuen
epithelial vesicle8.38e-1978
mesoderm2.39e-18315
mesoderm-derived structure2.39e-18315
presumptive mesoderm2.39e-18315
somite4.18e-1771
presomitic mesoderm4.18e-1771
presumptive segmental plate4.18e-1771
dermomyotome4.18e-1771
trunk paraxial mesoderm4.18e-1771
multilaminar epithelium6.05e-1783
dense mesenchyme tissue1.37e-1673
musculoskeletal system2.46e-16167
paraxial mesoderm2.68e-1672
presumptive paraxial mesoderm2.68e-1672
artery6.69e-1542
arterial blood vessel6.69e-1542
arterial system6.69e-1542
epithelial tube open at both ends1.46e-1459
blood vessel1.46e-1459
blood vasculature1.46e-1459
vascular cord1.46e-1459
splanchnic layer of lateral plate mesoderm2.53e-1483
vasculature6.67e-1478
vascular system6.67e-1478
vessel9.48e-1468
skeletal muscle tissue4.39e-1362
striated muscle tissue4.39e-1362
myotome4.39e-1362
unilaminar epithelium2.50e-12148
muscle tissue2.71e-1264
musculature2.71e-1264
musculature of body2.71e-1264
lateral plate mesoderm4.25e-12203
epithelial tube4.34e-12117
trunk mesenchyme2.58e-11122
systemic artery4.67e-1133
systemic arterial system4.67e-1133
surface structure6.64e-1199
integument8.76e-1146
integumental system8.76e-1146
mesenchyme1.53e-10160
entire embryonic mesenchyme1.53e-10160
anatomical system8.28e-10624
trunk8.92e-10199
anatomical group1.22e-09625
skin of body1.26e-0941
multi-cellular organism1.72e-09656
organism subdivision1.93e-09264
cardiovascular system1.88e-08109
circulatory system4.79e-08112


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)
MA0003.10.737422
MA0004.10.626788
MA0006.11.14863
MA0007.11.47524
MA0009.11.11255
MA0014.10.660087
MA0017.11.24112
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.12.36624
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.13.99021
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.112.9425
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.12.96921
MA0101.10.459973
MA0103.10.442769
MA0105.11.58771
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.14.61085
MA0115.11.35895
MA0116.11.76306
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.10.0359558
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.24.57923
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.425004
MA0065.22.73531
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.409315
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.81299
MA0163.10.0439995
MA0164.110.8652
MA0080.20.456437
MA0018.20.781393
MA0099.22.8068
MA0079.26.20913
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
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
CCNT2#90556.336201576962639.78880505817628e-050.00139111853513522
E2F6#187655.017155731697390.0003144978599297790.00322904463165613
EGR1#195854.988179094810140.0003237398000590710.0033092944091582
FOS#235358.99795530889441.69470025615156e-050.000389251814497939
FOSL1#8061539.7135797163731.01017090471068e-087.64501732732457e-07
FOSL2#2355516.93020060456177.18315284751475e-073.20873096767148e-05
GTF2F1#2962512.73966087675772.97806917252935e-060.000101081107023007
HEY1#2346254.040111043105710.0009288852205177990.00674536528616732
HMGN3#932458.178547723350592.73180911341838e-050.000582260024482249
IRF1#365957.63716375356393.84754333311872e-050.000724677327624142
JUN#3725512.51282919233633.25800591331781e-060.000109128569461514
JUND#372756.994663941871035.97069468343598e-050.000984641373824996
MAX#414956.452555509007128.93743970843928e-050.00130694100491415
MXI1#460159.96157162875931.01894348670516e-050.000266576750521042
MYC#460955.22228187160940.0002573944848850610.00276564018589618
NFYB#4801516.75979325353657.55590255814554e-073.32545683636815e-05
NR3C1#290838.983813998703820.002687995788940450.0147971532891183
POU2F2#545259.106124057742521.59639992500654e-050.000369763610041602
REST#597859.650028716128021.19441074361324e-050.000301530248132035
RFX5#5993512.04791082719513.93714721313598e-060.0001275013078427
SIN3A#2594255.408884726815140.0002159522671657270.0024819895268539
SMARCA4#65975156.7659033078881.04731463528549e-111.30681592825068e-09
SMARCB1#6598414.60217262492594.30486693344344e-050.000768540166943417
SMARCC1#6599543.66335931963156.28653634995012e-094.97393613524577e-07
STAT1#6772416.56526999775942.61308619905866e-050.00056385973046175
TAF1#687253.343046285745290.002394600090870310.0135439826098242
TAF7#6879511.43306940492395.11611886715123e-060.000157431449135653
TBP#690853.706770687096390.001428755106721120.00919224755688088
TCF12#6938510.63446490218647.34844389925727e-060.00021113181083756
TFAP2C#702248.647382887888180.0003390518878174050.00344860149121172



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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