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Coexpression cluster:C1171: Difference between revisions

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{{Coexpression_clusters
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helicase activity!0.0126628131237378!10856;22907$GO:0017111!nucleoside-triphosphatase activity!0.0126628131237378!10856;55210;22907$GO:0016462!pyrophosphatase activity!0.0126628131237378!10856;55210;22907$GO:0016818!hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides!0.0126628131237378!10856;55210;22907$GO:0016817!hydrolase activity, acting on acid anhydrides!0.0126628131237378!10856;55210;22907$GO:0005524!ATP binding!0.0126628131237378!10856;55210;7407;22907$GO:0032559!adenyl ribonucleotide binding!0.0126628131237378!10856;55210;7407;22907$GO:0030554!adenyl nucleotide binding!0.0130157929178116!10856;55210;7407;22907$GO:0004386!helicase activity!0.015254011509818!10856;22907$GO:0035267!NuA4 histone acetyltransferase complex!0.015254011509818!10856$GO:0043189!H4/H2A histone acetyltransferase complex!0.0159176240429507!10856$GO:0032553!ribonucleotide binding!0.0159176240429507!10856;55210;7407;22907$GO:0032555!purine ribonucleotide binding!0.0159176240429507!10856;55210;7407;22907$GO:0017076!purine nucleotide binding!0.0170004643870686!10856;55210;7407;22907$GO:0000123!histone acetyltransferase complex!0.0194313746840619!10856$GO:0004832!valine-tRNA ligase activity!0.0194313746840619!7407$GO:0006438!valyl-tRNA aminoacylation!0.0194313746840619!7407$GO:0000166!nucleotide binding!0.0240891554983028!10856;55210;7407;22907$GO:0042623!ATPase activity, coupled!0.0262980976105518!10856;22907$GO:0016887!ATPase activity!0.0348302374230744!10856;22907$GO:0046822!regulation of nucleocytoplasmic transport!0.0348302374230744!8086$GO:0043231!intracellular membrane-bound organelle!0.0348302374230744!10856;26155;7407;8086;22907$GO:0043227!membrane-bound organelle!0.0348302374230744!10856;26155;7407;8086;22907$GO:0004003!ATP-dependent DNA helicase activity!0.0369966852587803!10856$GO:0016363!nuclear matrix!0.0459929166824502!10856$GO:0003678!DNA helicase activity!0.0459929166824502!10856$GO:0003684!damaged DNA binding!0.0459929166824502!10856$GO:0003725!double-stranded RNA 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,0.600528,0.249647,0.43669,0.446356,0.248584,0.397145,0.390152,0.537963,0.540199,0.488863,0.342785,0.447064,0.20487,0.603936,0.449548,0.41929,0.209566,0.189123,0.588995,0.355645,0.332105,0.522124,0.158122,0.521096,0.220023,0.444217,0.363335,0.329186,0.432735,0.493369,0.416144,0.648861|tfbs_overrepresentation_for_novel_motifs=1.01633,0.465735,0.384703,0.529489,0.343148,0.52784,0.604235,0.226729,0.637583,0.443077,0.497563,0.647852,1.03506,0.592674,0.341795,0.365029,0.827563,0.28906,0.569568,0.0986842,0.384762,0.23059,1.29221,0.338096,0.430372,0.670692,0.164928,0.517892,0.346214,0.150685,0.475674,0.864517,0.257226,0.546594,0.8321,0.0934825,0.825031,0.529001,0.282922,0.597792,0.307642,0.459366,0.0729319,0.340293,0.265117,0.415364,1.47235,1.22101,0.0670664,0.346342,0.684981,0.617179,0.373994,0.941629,1.09491,0.595623,0.350547,0.562713,0.150585,0.561701,0.905643,0.60771,0.224801,0.799729,0.625758,0.76514,1.18348,1.55228,0.854088,1.38987,0.4462,0.232216,1.2198,1.0929,2.29516,0.971313,0.156354,1.84122,0.850825,0.424224,0.200147,0.798651,0.625403,0.229431,1.04131,2.24329,0.662518,0.448771,0.711163,1.65172,1.27705,1.01423,0.881388,0.26423,0.910085,0.277058,0.566252,0.924148,0.715799,0.132387,0.28424,0.875714,0.918549,0.831244,0.753567,1.23455,1.90834,1.43846,0.43012,0.873303,0.395884,0.915771,0.379203,0.507004,1.22894,0.304323,1.90797,0.474472,0.762789,0.26701,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,0.597853,0.886402,1.12733,0.27799,1.01492,0.47854,1.14174,0.633392,1.28996,0.140417,0.469685,0.518459,1.24743,2.10682,1.70417,1.21002,0.59959,0.920609,0.755332,0.554217,0.738579,1.94751,0.456039,0.722945,0.703388,1.85412,1.0153,0.619774,0.607223,1.42052,0.694887,0.329354,0.430431,0.401655,1.2088,0.996724,0.850033,1.04428,0.7715,0.624608,0.24928,0.602897,0.594713|tfbs_overrepresentation_jaspar=MA0003.1;5.48657,MA0004.1;0.502801,MA0006.1;0.904424,MA0007.1;0.483857,MA0009.1;0.973289,MA0014.1;0.912418,MA0017.1;0.380797,MA0019.1;0.652951,MA0024.1;0.867125,MA0025.1;1.10816,MA0027.1;2.59001,MA0028.1;1.67753,MA0029.1;0.886702,MA0030.1;0.875089,MA0031.1;0.809638,MA0038.1;0.60704,MA0040.1;0.892629,MA0041.1;0.521615,MA0042.1;0.48922,MA0043.1;0.973609,MA0046.1;0.962263,MA0048.1;1.8235,MA0050.1;0.490116,MA0051.1;0.602745,MA0052.1;0.896548,MA0055.1;0.362619,MA0056.1;0,MA0057.1;0.369442,MA0058.1;1.04727,MA0059.1;0.404929,MA0060.1;0.638423,MA0061.1;0.575931,MA0063.1;0,MA0066.1;0.607474,MA0067.1;1.29359,MA0068.1;0.162298,MA0069.1;0.958358,MA0070.1;0.947018,MA0071.1;0.567661,MA0072.1;0.942461,MA0073.1;0.065183,MA0074.1;0.60198,MA0076.1;1.90063,MA0077.1;0.934645,MA0078.1;0.703614,MA0081.1;0.405093,MA0083.1;0.980893,MA0084.1;1.48179,MA0087.1;0.939982,MA0088.1;0.538456,MA0089.1;0,MA0090.1;0.436918,MA0091.1;0.505453,MA0092.1;0.467172,MA0093.1;0.344385,MA0095.1;0,MA0098.1;0,MA0100.1;0.621149,MA0101.1;0.347695,MA0103.1;0.332048,MA0105.1;0.340955,MA0106.1;0.648997,MA0107.1;0.274127,MA0108.2;0.806528,MA0109.1;0,MA0111.1;1.14351,MA0113.1;0.665691,MA0114.1;0.269076,MA0115.1;1.21667,MA0116.1;0.760835,MA0117.1;1.01134,MA0119.1;0.388712,MA0122.1;1.03753,MA0124.1;1.17486,MA0125.1;1.0901,MA0130.1;0,MA0131.1;0.722072,MA0132.1;0,MA0133.1;0,MA0135.1;1.00402,MA0136.1;0.614215,MA0139.1;1.65047,MA0140.1;0.564957,MA0141.1;0.403171,MA0142.1;0.777365,MA0143.1;0.66587,MA0144.1;0.254954,MA0145.1;0.276317,MA0146.1;0.547931,MA0147.1;1.40486,MA0148.1;0.528066,MA0149.1;0.555119,MA0062.2;2.39331,MA0035.2;0.564239,MA0039.2;0.403603,MA0138.2;0.704862,MA0002.2;0.213296,MA0137.2;0.36398,MA0104.2;2.61139,MA0047.2;0.636643,MA0112.2;1.95102,MA0065.2;0.0828768,MA0150.1;0.430951,MA0151.1;0,MA0152.1;0.571637,MA0153.1;1.07307,MA0154.1;0.685508,MA0155.1;0.250175,MA0156.1;0.36627,MA0157.1;0.749547,MA0158.1;0,MA0159.1;0.281681,MA0160.1;0.543522,MA0161.1;0,MA0162.1;1.13878,MA0163.1;1.30651,MA0164.1;0.678332,MA0080.2;0.344472,MA0018.2;1.56673,MA0099.2;0.572,MA0079.2;0.263996,MA0102.2;1.51913,MA0258.1;0.687127,MA0259.1;0.787775,MA0442.1;0}}
|full_id=C1171_Alveolar_Renal_Bronchial_Mesenchymal_Smooth_Keratinocyte_embryonic
|id=C1171
}}

Latest revision as of 11:39, 17 September 2013


Full id: C1171_Alveolar_Renal_Bronchial_Mesenchymal_Smooth_Keratinocyte_embryonic



Phase1 CAGE Peaks

Hg19::chr12:53715328..53715411,-p1@AAAS
Hg19::chr19:49497121..49497164,+p1@RUVBL2
Hg19::chr1:1447517..1447556,+p1@ATAD3A
Hg19::chr1:894620..894659,-p1@NOC2L
Hg19::chr3:47866490..47866534,+p1@DHX30
Hg19::chr6:31763408..31763545,-p1@VARS
Hg19::chr7:1177874..1177936,-p2@C7orf50


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:0008026ATP-dependent helicase activity0.0126628131237378
GO:0017111nucleoside-triphosphatase activity0.0126628131237378
GO:0016462pyrophosphatase activity0.0126628131237378
GO:0016818hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides0.0126628131237378
GO:0016817hydrolase activity, acting on acid anhydrides0.0126628131237378
GO:0005524ATP binding0.0126628131237378
GO:0032559adenyl ribonucleotide binding0.0126628131237378
GO:0030554adenyl nucleotide binding0.0130157929178116
GO:0004386helicase activity0.015254011509818
GO:0035267NuA4 histone acetyltransferase complex0.015254011509818
GO:0043189H4/H2A histone acetyltransferase complex0.0159176240429507
GO:0032553ribonucleotide binding0.0159176240429507
GO:0032555purine ribonucleotide binding0.0159176240429507
GO:0017076purine nucleotide binding0.0170004643870686
GO:0000123histone acetyltransferase complex0.0194313746840619
GO:0004832valine-tRNA ligase activity0.0194313746840619
GO:0006438valyl-tRNA aminoacylation0.0194313746840619
GO:0000166nucleotide binding0.0240891554983028
GO:0042623ATPase activity, coupled0.0262980976105518
GO:0016887ATPase activity0.0348302374230744
GO:0046822regulation of nucleocytoplasmic transport0.0348302374230744
GO:0043231intracellular membrane-bound organelle0.0348302374230744
GO:0043227membrane-bound organelle0.0348302374230744
GO:0004003ATP-dependent DNA helicase activity0.0369966852587803
GO:0016363nuclear matrix0.0459929166824502
GO:0003678DNA helicase activity0.0459929166824502
GO:0003684damaged DNA binding0.0459929166824502
GO:0003725double-stranded RNA binding0.0479566301137395



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>

Cell Type
Ontology termp-valuen
epithelial cell1.54e-23253
animal cell1.36e-22679
eukaryotic cell1.36e-22679
embryonic cell1.39e-22250
mesodermal cell2.76e-14121
non-terminally differentiated cell1.39e-10106
native cell2.72e-10722
contractile cell1.45e-0959
electrically responsive cell6.13e-0961
electrically active cell6.13e-0961
epithelial cell of nephron2.00e-0815
somatic cell2.66e-08588
muscle cell5.88e-0855
muscle precursor cell1.24e-0758
myoblast1.24e-0758
multi-potent skeletal muscle stem cell1.24e-0758
kidney cortical cell1.51e-0712
renal cortical epithelial cell1.51e-0712
kidney cell2.49e-0717
kidney epithelial cell2.49e-0717
meso-epithelial cell2.97e-0745
squamous epithelial cell3.62e-0763
endothelial cell5.17e-0736
smooth muscle cell6.68e-0743
smooth muscle myoblast6.68e-0743
lining cell6.75e-0758
barrier cell6.75e-0758
Uber Anatomy
Ontology termp-valuen
epithelial tube1.13e-14117
unilaminar epithelium2.41e-13148
epithelial vesicle6.52e-1378
trunk9.58e-13199
vasculature4.82e-1178
vascular system4.82e-1178
organism subdivision4.95e-11264
cell layer8.13e-11309
epithelial tube open at both ends8.13e-1159
blood vessel8.13e-1159
blood vasculature8.13e-1159
vascular cord8.13e-1159
vessel8.27e-1168
epithelium3.50e-10306
mesenchyme3.58e-10160
entire embryonic mesenchyme3.58e-10160
multilaminar epithelium4.16e-1083
artery6.16e-1042
arterial blood vessel6.16e-1042
arterial system6.16e-1042
trunk mesenchyme8.16e-10122
somite8.43e-1071
presomitic mesoderm8.43e-1071
presumptive segmental plate8.43e-1071
dermomyotome8.43e-1071
trunk paraxial mesoderm8.43e-1071
paraxial mesoderm1.78e-0972
presumptive paraxial mesoderm1.78e-0972
splanchnic layer of lateral plate mesoderm1.80e-0983
dense mesenchyme tissue2.90e-0973
nephron epithelium2.00e-0815
renal tubule2.00e-0815
nephron tubule2.00e-0815
nephron2.00e-0815
uriniferous tubule2.00e-0815
nephrogenic mesenchyme2.00e-0815
parenchyma5.71e-0815
cortex of kidney1.51e-0712
renal parenchyma1.51e-0712
trunk region element1.94e-07101
excretory tube1.95e-0716
kidney epithelium1.95e-0716
simple squamous epithelium2.25e-0722
skeletal muscle tissue2.69e-0762
striated muscle tissue2.69e-0762
myotome2.69e-0762
primordium5.58e-07160
cortex6.36e-0715
Disease
Ontology termp-valuen
cancer4.05e-17235
disease of cellular proliferation5.97e-17239
hematologic cancer3.67e-1051
immune system cancer3.67e-1051
organ system cancer3.24e-09137
leukemia3.69e-0939
myeloid leukemia4.60e-0831
cell type cancer5.10e-08143
carcinoma5.68e-07106


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)
MA0003.15.48657
MA0004.10.502801
MA0006.10.904424
MA0007.10.483857
MA0009.10.973289
MA0014.10.912418
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.11.67753
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.11.8235
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.362619
MA0056.10
MA0057.10.369442
MA0058.11.04727
MA0059.10.404929
MA0060.10.638423
MA0061.10.575931
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.065183
MA0074.10.60198
MA0076.11.90063
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.538456
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.332048
MA0105.10.340955
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.11.14351
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.10.760835
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.11.65047
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.276317
MA0146.10.547931
MA0147.11.40486
MA0148.10.528066
MA0149.10.555119
MA0062.22.39331
MA0035.20.564239
MA0039.20.403603
MA0138.20.704862
MA0002.20.213296
MA0137.20.36398
MA0104.22.61139
MA0047.20.636643
MA0112.21.95102
MA0065.20.0828768
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.685508
MA0155.10.250175
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.11.13878
MA0163.11.30651
MA0164.10.678332
MA0080.20.344472
MA0018.21.56673
MA0099.20.572
MA0079.20.263996
MA0102.21.51913
MA0258.10.687127
MA0259.10.787775
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
BCLAF1#977439.279706118623640.00299499233575710.0159207005931764
CCNT2#90565.431029923110839.35028339706757e-050.00135818393283218
CHD2#110657.38858773865490.0001498689600820670.00193212743142958
CTCF#1066453.828754552196450.003387371192681340.0172926806135715
CTCFL#140690411.28369963369960.0002032736265059930.00241356233272617
E2F1#186953.505278010628090.005090553587915050.0236879489470798
E2F4#1874610.85833741310091.57765285246789e-066.00249494567919e-05
EGR1#195864.275582081265830.0003762130619866450.00373633662807372
ELF1#199774.258097958807543.93848941900192e-050.000735046276681812
ELK4#200549.277532376267440.0004328178589665770.00404212325606817
ETS1#211379.728760922202341.21106237796078e-076.97640064488944e-06
FOSL1#8061211.34673706182090.01223664790675720.0443636362944358
GABPB1#255377.067683836182171.13438576906404e-064.65700138896537e-05
GTF2F1#296235.459854661467560.0132988216841570.0470245001987972
HDAC2#306647.666068706643580.0008986373447057820.00668609999599111
HEY1#2346263.462952322662040.001267890095872120.00850572801405375
HMGN3#932455.841819802393280.0004629187191299590.00426338343097123
IRF1#365944.364093573465090.00739345582427820.0305505492712875
IRF3#3661213.42341491756850.00885816023056540.0336144682915493
MAX#414954.608968220719370.001424337014033610.00917909005360088
MXI1#460157.115408306256640.0001797256225248230.00217905320302647
MYC#460975.22228187160949.4355989882785e-060.000250940800289487
NFKB1#479075.488063424193846.66568321176054e-060.000194620433031328
NFYB#480137.182768537229910.00619473990889960.0273746484448492
PAX5#507954.763975379412740.001218821047007470.00819919171197507
POLR2A#543072.147453176558070.004747636447610280.0223310395852986
REST#597845.514302123501730.003115641375761960.0163761685779166
SIN3A#2594275.408884726815147.3795239773719e-060.000211501126419523
SIX5#14791249.763837345976570.0003555371351068720.00355908586728904
SMARCC1#6599212.47524551989470.01020047316571840.0379890602629699
SMC3#912636.447828362114080.008384311283437850.0329451479036444
SP1#666764.884326895549340.0001736361122290910.00211307176941202
SP2#6668414.94487456791126.81071539656055e-050.00108795396956468
SRF#672247.884101864095890.0008074788728092760.0061659929807215
STAT1#677238.874251784513940.003402369532693760.0173590655410358
TAF1#687273.343046285745290.0002142336319622450.0024649494644161
TAF7#687946.533182517099380.00164849410947510.0103118756767771
TBP#690873.706770687096390.0001039672097505110.00145066552025834
TFAP2A#702037.079414731304980.006452554472180970.0280288789468913
TFAP2C#702257.720877578471590.0001211811995604330.00164193607951376
THAP1#55145313.44391911550770.001029040833692380.00728920209102
TRIM28#1015537.967367876541080.004622341263156460.0218321589717256
USF1#739154.543928055148540.001522788355968760.00970397785764972
YY1#752874.911170749853861.45048003565243e-050.000345308147808306
ZBTB7A#5134166.301636549607913.91424956694869e-050.000731306458895446
ZNF143#7702611.57217990190961.08146108094101e-064.4980770144324e-05
ZNF263#1012744.698195221148960.00564122953609810.0254839902902612



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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