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Coexpression cluster:C2309: Difference between revisions

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{{Coexpression_clusters
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201057,0.0130187,0.129351,0.141936,0.0786166,0.276997,0.205513,0.282389,0.251421,0.162089,0.330223,0.387837,0.233244,0.207281,0.327401,0.195748,0.0429696,0.161712,0.237871,0.00277578,0.095257,0.328852,0.332769,0.00372893,0.04166,0.266687,0.0181825,0.0338675,4.93642e-05,0.15156,0.287598,0.00673322,0.223773,0.25788,0.181895,0.00336176,0.30702,0.202977,0.170837,0.0604859,0.28543,0.00220735,0.228479,0.00844447,0.00363597,0.0140513,0.355805,0.279739,0.108118,0.259901,0.139723,0.0708274,0.0710478,0.0206568,0.102645,0.0539258,0.0709978,0.401939,0.332746,0.271338,0.242121,0.298673,0.244395,0.106889,0.128632,0.000107739,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.000543954,0.0583767,0.088258,0.000297685,0.0486914,0.175784,0.262778,0.373453,0.362662,0.433518,0.184359,0.334474,0.000735605,0.257476,0.291176,0.081972,0.00739196,0.229571,0.359036,0.00844265,0.171704,0.208256,0.265058,0.0361085,0.362898,0.00593844,0.00207843,0.151361,0.0433477,0.286696,0.150674,0.0345639,0.246177,0.35674,0.35852,0.318525,0.213257,0.287217,0.000339729,0.410951,0.289049,0.266974,0.125746,0.112897,0.398354,0.222091,0.0228412,0.00915515,0.0936726,0.343425,0.132374,0.285122,0.22741,0.203996,0.276721,0.321965,0.0386145,0.450113|tfbs_overrepresentation_for_novel_motifs=0.590005,0.298605,0.581696,0.741427,1.32255,0.739643,0.821651,0.395818,1.01802,0.151681,0.706765,0.867962,0.341754,1.89595,0.532789,0.559384,2.39977,0.471262,0.356737,0.223552,0.581762,2.95429,0.731221,0.528529,0.632849,0.892087,0.316693,0.728867,2.28567,0.806311,0.682839,1.09415,0.433165,0.911389,10.8485,0.0842336,3.15145,0.740899,0.463978,0.371755,0.493145,0.66492,0.539378,0.53106,0.648765,0.61613,0.822818,0.694903,0.173425,0.538016,0.90714,1.94963,0.699149,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,1.8276,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.692875,1.32819,0.336329,0.321165,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,0.353274,4.31432,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,1.28386,1.44917,1.14697,0.575476,0.717043,1.46636,0.489254,0.785429,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,1.58937,3.95711,0.234974,0.175846,1.24902,0.383416,0.824835,1.65997,2.11789,1.28873,0.632914,0.600782,1.44595,1.23002,1.07918,2.50192,0.997702,0.843324,0.423521,0.820225,3.65915|tfbs_overrepresentation_jaspar=MA0003.1;0.443649,MA0004.1;0.71247,MA0006.1;1.31813,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;1.86845,MA0017.1;0.577281,MA0019.1;0.873355,MA0024.1;1.09684,MA0025.1;1.34373,MA0027.1;2.83281,MA0028.1;0.550763,MA0029.1;1.11704,MA0030.1;1.10506,MA0031.1;1.03735,MA0038.1;0.824639,MA0040.1;1.12314,MA0041.1;0.732902,MA0042.1;0.697662,MA0043.1;1.20635,MA0046.1;1.19471,MA0048.1;0.25531,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.396851,MA0056.1;0,MA0057.1;1.98521,MA0058.1;0.605914,MA0059.1;0.604454,MA0060.1;2.70115,MA0061.1;1.68681,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;0.313194,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;3.33774,MA0074.1;0.819248,MA0076.1;0.623864,MA0077.1;1.16637,MA0078.1;0.926725,MA0081.1;0.604638,MA0083.1;1.21381,MA0084.1;1.72172,MA0087.1;1.17185,MA0088.1;1.62583,MA0089.1;0,MA0090.1;0.640115,MA0091.1;0.715356,MA0092.1;0.673508,MA0093.1;0.535768,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;2.29123,MA0103.1;0.521546,MA0105.1;1.22348,MA0106.1;0.869173,MA0107.1;1.1497,MA0108.2;1.03412,MA0109.1;0,MA0111.1;0.655276,MA0113.1;0.886811,MA0114.1;1.13665,MA0115.1;1.45393,MA0116.1;0.457606,MA0117.1;2.78257,MA0119.1;0.586221,MA0122.1;1.27173,MA0124.1;1.41151,MA0125.1;1.32534,MA0130.1;0,MA0131.1;0.94608,MA0132.1;0,MA0133.1;0,MA0135.1;1.23748,MA0136.1;0.832277,MA0139.1;1.63368,MA0140.1;0.779643,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;1.09982,MA0145.1;1.70272,MA0146.1;0.481,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;2.52211,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;1.37305,MA0104.2;0.392359,MA0047.2;0.856092,MA0112.2;1.05083,MA0065.2;3.22574,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.229241,MA0155.1;0.180766,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;5.0369,MA0163.1;2.49771,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;2.02192,MA0099.2;0.7872,MA0079.2;8.14977,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0}}
|full_id=C2309_hepatic_Fibroblast_Hepatic_Smooth_Urothelial_aorta_Olfactory
|id=C2309
}}

Latest revision as of 12:03, 17 September 2013


Full id: C2309_hepatic_Fibroblast_Hepatic_Smooth_Urothelial_aorta_Olfactory



Phase1 CAGE Peaks

Hg19::chr14:69445930..69445948,-p3@ACTN1
Hg19::chr14:69445968..69445984,-p2@ACTN1
Hg19::chr14:69445991..69446029,-p1@ACTN1
Hg19::chr14:69446034..69446048,-p4@ACTN1


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 tube1.22e-18117
vasculature4.67e-1878
vascular system4.67e-1878
cardiovascular system1.72e-15109
multi-cellular organism2.83e-15656
circulatory system6.96e-15112
organism subdivision9.28e-15264
epithelial tube open at both ends1.54e-1459
blood vessel1.54e-1459
blood vasculature1.54e-1459
vascular cord1.54e-1459
vessel3.44e-1468
trunk mesenchyme6.38e-14122
splanchnic layer of lateral plate mesoderm1.04e-1383
anatomical system1.08e-13624
mesenchyme1.79e-13160
entire embryonic mesenchyme1.79e-13160
anatomical group2.49e-13625
unilaminar epithelium4.24e-13148
trunk9.56e-13199
epithelial vesicle1.35e-1278
artery3.57e-1242
arterial blood vessel3.57e-1242
arterial system3.57e-1242
mesoderm2.64e-11315
mesoderm-derived structure2.64e-11315
presumptive mesoderm2.64e-11315
multilaminar epithelium4.48e-1183
somite2.94e-1071
presomitic mesoderm2.94e-1071
presumptive segmental plate2.94e-1071
dermomyotome2.94e-1071
trunk paraxial mesoderm2.94e-1071
cell layer3.28e-10309
dense mesenchyme tissue4.88e-1073
embryo5.68e-10592
paraxial mesoderm5.87e-1072
presumptive paraxial mesoderm5.87e-1072
epithelium6.92e-10306
muscle tissue7.75e-1064
musculature7.75e-1064
musculature of body7.75e-1064
skeletal muscle tissue1.02e-0962
striated muscle tissue1.02e-0962
myotome1.02e-0962
developing anatomical structure1.85e-09581
systemic artery1.98e-0933
systemic arterial system1.98e-0933
surface structure3.70e-0999
embryonic structure1.04e-08564
germ layer5.10e-08560
germ layer / neural crest5.10e-08560
embryonic tissue5.10e-08560
presumptive structure5.10e-08560
germ layer / neural crest derived structure5.10e-08560
epiblast (generic)5.10e-08560
anatomical conduit7.29e-07240
multi-tissue structure7.49e-07342
nephron epithelium8.85e-0715
renal tubule8.85e-0715
nephron tubule8.85e-0715
nephron8.85e-0715
uriniferous tubule8.85e-0715
nephrogenic mesenchyme8.85e-0715


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)
MA0003.10.443649
MA0004.10.71247
MA0006.11.31813
MA0007.10.6918
MA0009.11.20602
MA0014.11.86845
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.11.98521
MA0058.10.605914
MA0059.10.604454
MA0060.12.70115
MA0061.11.68681
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.13.33774
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.62583
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.12.29123
MA0103.10.521546
MA0105.11.22348
MA0106.10.869173
MA0107.11.1497
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.11.13665
MA0115.11.45393
MA0116.10.457606
MA0117.12.78257
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.11.63368
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.11.09982
MA0145.11.70272
MA0146.10.481
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.22.52211
MA0138.20.928035
MA0002.20.379056
MA0137.21.37305
MA0104.20.392359
MA0047.20.856092
MA0112.21.05083
MA0065.23.22574
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.15.0369
MA0163.12.49771
MA0164.10.90014
MA0080.20.535868
MA0018.22.02192
MA0099.20.7872
MA0079.28.14977
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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#90546.336201576962630.0006203100587215640.00511605166412552
CEBPB#105147.971147625824820.0002476385788090830.00267761937387326
CHD2#1106410.34402283411698.73193255208051e-050.00128989293324857
E2F1#186944.907389214879320.001724022357361790.0106352729462793
E2F6#187645.017155731697390.00157802193473060.00995933241729085
EGR1#195844.988179094810140.001615011500076050.010133993394403
ELF1#199744.258097958807540.003041525565781240.016070721874159
FOS#235348.99795530889440.0001525147711168630.00194653430046121
GABPB1#255347.067683836182170.0004006876864423170.00389967582558467
GATA1#2623413.56030814380042.95627390049268e-050.000613329936220808
GATA2#2624412.7449317335543.78864877853583e-050.00072073349686977
GATA3#2625427.2365163572061.81561517799785e-066.7601081488384e-05
HDAC2#3066413.41562023662633.0859005065161e-050.000625924185278763
HEY1#2346244.040111043105710.00375304636917980.0185747516704943
HMGN3#932448.178547723350590.0002234570284440470.00247850770960789
IRF1#365947.63716375356390.0002938853996185490.00307084514764999
IRF3#3661446.98195221148962.04940266214005e-071.10158293685664e-05
MYC#460945.22228187160940.001344309395272740.00886576969770708
NFYA#4800418.42558069983058.67100748407158e-060.00023424504672244
NFYB#4801416.75979325353651.26678572070404e-050.000311152008195224
PBX3#5090421.91451268674414.33289161192893e-060.000136179015064173
SMARCB1#6598418.25271578115749.00423392720929e-060.000240941118914633
SP1#666745.69838137814090.0009482606065333980.00683426882104351
SP2#6668426.15353049384462.13562021071447e-067.741827115127e-05
TAF1#687243.343046285745290.008005664898701650.0321664923770054
TAF7#6879411.43306940492395.85061525419808e-050.0009677421706259
TAL1#6886429.86861667744021.25525650806991e-065.03061145227602e-05
TBP#690843.706770687096390.005296377814784350.0243785104714968
USF1#739146.361499277207960.0006105011399140830.0050736157039458



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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