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Difference between revisions of "Coexpression cluster:C411"

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|tf_chipseq_enrich=BRCA1#672;5:4.03684612864475:0.00689254689097077:0.0291874753576652!CCNT2#905;14:3.54827288309908:4.62126213135399e-06:0.00014368561945117!EBF1#1879;10:3.5625867386276:0.000209250484315379:0.00243687682107648!EGR1#1958;13:2.59385312930127:0.00037778572640151:0.00374661128854309!EP300#2033;9:2.43861902144035:0.00717124881905474:0.0297784603162204!GATA3#2625;6:6.53676392572944:0.000236828365665375:0.00257942618434937!GTF2B#2959;6:7.66651918423782:9.94934489292016e-05:0.00140040381573004!GTF2F1#2962;7:3.56710504549214:0.00248487859809469:0.0139555945314267!HMGN3#9324;12:3.92570290720828:1.23148160281096e-05:0.000304197509735037!HSF1#3297;11:72.2878933333333:1.66913017282451e-18:3.78961491564389e-16!IRF1#3659;12:3.66583860171067:2.49394930213504e-05:0.000539936921985244!MXI1#4601;9:3.58616578635335:0.000470323889250828:0.00431825553138173!NFKB1#4790;12:2.63427044361304:0.000648461623178439:0.00531340683062396!POLR2A#5430;21:1.80386066830878:0.000129903105445809:0.00171062292644747!PPARGC1A#10891;8:112.016363636364:4.35959567622917e-15:7.71714936999488e-13!PRDM1#639;3:15.8197146932953:0.000884249246251442:0.0065926689769599!RDBP#7936;4:24.582144638404:2.02574085028561e-05:0.000449471741370254!SIN3A#25942;10:2.16355389072605:0.0100430877544989:0.0376540078256789!SRF#6722;6:3.31132278292027:0.0077135267669906:0.0317512621006515!STAT1#6772;5:4.14131749943984:0.00619545137151441:0.027376634050755!STAT2#6773;4:10.4422033898305:0.000537967092450348:0.00464797693319176!STAT3#6774;10:4.2077859988617:5.1112914742446e-05:0.000870403016922602!TAF1#6872;16:2.13954962287699:0.000436887104077226:0.00407247878103547!TAF7#6879;8:3.65858220957565:0.00094706251346002:0.00685258846080443!TBP#6908;13:1.92752075729012:0.00683471173406966:0.0289825189327419!TCF12#6938;7:2.9776501726122:0.00680129072796867:0.0288419685860939!TFAP2C#7022;8:3.45895315515527:0.00136807008625109:0.0090014409209335!ZBTB33#10009;4:5.06635600479698:0.00739199014156867:0.0305457014479422
 
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2,0.443156,0.460683,0.55775,0.341477,0.217236,0.192768,0.244418,0.0711387,0.611504,0.285078,0.401003,0.473357,0.663367,0.249737,0.621412,0.717883,0.21481,0.0187233,0.002241,0.281212,0.0421994,0.0123304,0.371887,0.699845,0.150028,0.101822,0.326847,0.129683,0.0786054,0.00254187,0.483051,0.210919,0.159945,0.237836,0.660348,0.735996,0.136273,0.782456,0.717165,0.539939,0.199599,0.535355,0.332237,0.564273,0.225414,0.333106,0.489143,0.618473,0.68234,0.328116,0.179906,0.553071,0.358267,0.582073,0.348035,0.412488,0.480191,0.559317,0.371913,0.250566,0.47392,0.752053,0.0210496,0.876537,0.870153,0.3183,0.652799,0.264434,0.485702,0.0734334,0.389894,0.333916,0.402364,0.407464,0.47711,0.949177,0.460226,0.879005,0.546402,0.260611,0.673241,0.798919,2.4648e-07,0.00140042,0.573885,0.871422,0.247693,0.115695,0.249309,0.344423,0.0532934,0.853313,0.480513,0.322542,0.0754266,0.455142,0.36027,0.404158,0.273973,0.694451,0.318682,0.369884,0.636121,0.0095883,0.793433,0.603049,0.617317,0.387716,0.891898,0.482397,0.311924,0.74782,0.0369149,0.0574723,0.061692,0.640758,0.794588,0.674403,0.159299,0.416886,0.528103,0.387407,0.530448,0.756244,0.462976,0.552172,0.0956284,0.372704,0.743469,0.574207,0.167419,0.460645,0.833653,0.707694,0.635069,0.0365005,0.157304,0.0909037,0.166344,0.247559,0.632347,0.630636,0.248461,0.216857,0.564129,0.254301,0.908076,0.359665,0.218722,0.106457,0.231921,0.632083,0.194051,0.452757,0.00877528,0.855759,0.196784,0.519729,0.158398,0.243884,0.413655,0.378411,0.0416484,0.398064,0.684454,0.226351,0.152309,0.0244209,0.44087,0.0360262,0.263811,0.284802,0.326863,0.309455,0.697365,0.0876441,0.190486,0.378317,0.633512,0.375601,0.335749,0.528332,0.739256,0.492238,0.872263,0.840125,0.249352,0.320121,0.437455,0.051017,0.994079,0.627413,0.197323,0.123212,0.779527,0.0276105,0.519347,0.955306,0.580753,0.000132251,0.00155756,0.632261,0.408451,0.1131,0.580339,0.306114,0.370562,0.503191,0.0518165,0.540774,0.18982,0.264049,0.156908,0.419666,0.18077,0.258747,0.277689,0.453408,0.957146,0.674677,0.000568042,0.235898,0.150516,0.488485,0.431683,0.00412657,0.162154,0.506751,6.25879e-05,0.546282,7.00813e-05,0.17919,0.0366128,0.0252333,0.00205623,0.0436947,0.28675,0.571306,0.94912,0.448614,0.0972826,0.289658,0.571977,0.756924,0.719066,0.284213,0.206527,0.956975,0.706265,0.188898,0.373081,0.656104,0.766657,0.0484167,0.821604,0.811405,0.52193,0.000635911,0.40527,0.275803,0.263773,0.406599,0.00474111,0.968422,0.101631,0.773668,0.0496673,5.19932e-06,0.461342,0.876597,0.938448,0.938211,0.415037,0.317093,0.726251,0.298941,0.737609,0.712325,0.229873,0.781666,0.840699,0.515949,0.824912,0.793706,0.217964,0.65516,0.900615,0.738263,0.0770997,0.977423,0.98745,0.591727,0.324531,0.893898,0.00340643,0.0536865,0.103227,0.0636582,0.972773,0.931701,0.738974,0.807132,0.899681,0.979121,0.364406,0.0855972,0.820766,0.385221,0.540039,0.0361603,0.76594,0.252926,0.835391,0.874189,0.542797,0.113263,0.528669,0.890688,0.243953,0.953115,0.147373,0.765099,0.53675,0.170844,0.255208,0.744013,0.73514,0.747851,0.575387,0.906329,0.314528,0.137042,0.114676,0.0288311,0.773273,0.654807,0.0266682,0.948745,0.96739,0.57081,0.801537,0.491279,0.932887,0.852644,0.248582,0.256698,0.711945,0.824157,0.463118,0.11759,0.434939,0.829106,0.773119,0.873106,0.856787,0.544605,0.203911,0.779955,0.911225,0.208903,0.704157,0.577046,0.548815,0.490365,0.535119,0.875092,0.620995,0.140264,0.954966,0.871172,0.116063,0.0966892,0.666068,0.283875,0.241285,0.557937,0.100333,0.491902,0.882841,0.934305,0.171719,0.326953,0.133472,0.6851,0.876996,0.440601,0.309314,0.260354,0.264284,0.377523,0.638517,0.433521,0.885449,0.201306,0.00457444,0.434406,0.360297,0.321937,0.734201,0.121263,0.155284,0.40917,0.28892,0.579256,0.0725169,0.400551,0.60129,0.000726226,0.156455,0.836325,0.668878,0.713741,0.0908473,0.494205,0.76585,0.450735,0.0494807,0.334071,0.667946,0.242183,0.509282,0.465088,0.454206,0.718576,0.565968,0.865306,0.306722,0.720561,0.533358,0.426987,0.0207031,0.625363,0.418278,0.469621,0.286579,0.71486,0.839506,0.0828436,0.757791,0.689901,0.0403769,0.0621721,0.792827,0.0817615,0.572443,0.0426195,0.814891,0.144387,0.152174,0.510875,0.291172,0.60962,0.368167,0.369103,0.744723,0.491808,0.292816,0.368891,0.830473,0.463515,0.31748,0.823193,0.891106,0.52257,0.506646,0.577077,0.424465,0.66156,0.423054,0.235112,0.435547,0.483649,0.682862,0.250765,0.313355,0.438694,0.542667,0.268004,0.701284,0.851239,0.788906,0.771521,0.284397,0.720186,0.721785,0.000247544,0.554958,0.883624,0.793707,0.912527,0.80408,0.765474,0.116851,0.691923,0.767643,0.854091,0.843017,0.940255,0.390206,0.838603,0.641475,0.87123,0.878949,0.271855,0.835924,0.829025,0.936552,0.0629393,0.0954735,0.776666,0.354719,0.197963,0.00223153,0.881424,0.577814,0.568247,0.00105667,0.958228,0.791885,0.0585179,0.928436,0.459206,0.126779,0.588303,0.877271,0.80062,0.759718,0.14737,0.437713,0.302165,0.00169993
 +
|tfbs_overrepresentation_for_novel_motifs=0.928021,2.21776,0.528759,0.880383,0.196868,0.446495,0.193858,0.654186,0.390585,0.82522,0.127781,0.223608,0.136369,0.546792,0.195296,0.835818,0.359143,0.32265,1.49865,0.463347,0.528893,0.986392,0.856439,0.745682,0.635488,0.673629,0.405008,0.431583,0.442629,0.812047,1.22178,0.389116,0.260815,0.284748,1.92581,0.688768,0.15531,0.448243,0.310421,0.864002,0.0403609,0.106777,0.453553,0.193557,0.488146,0.599921,0.566947,0.38574,0.15986,0.442908,0.69748,0.202536,1.10569,1.14968,0.587358,0.188158,0.0561267,0.965707,0.350885,0.166299,0.423157,1.08335,0.646102,0.336984,0.599837,0.309988,0.667509,1.01514,0.380596,0.859886,1.1169,0.215242,0.0499727,0.585564,0.268256,1.26368,0.372449,0.323653,0.37794,1.54046,0.0604183,0.336133,0.208117,0.665547,0.539768,0.332833,0.0847843,0.534985,0.741627,1.11136,0.753896,0.516018,0.402998,0.113524,0.197724,0.29887,0.520617,0.438691,0.272612,0.284931,0.0328569,0.398316,0.433978,0.362101,0.814251,0.394926,0.349366,0.18395,0.306554,0.710341,0.075464,0.431643,0.240351,0.415422,0.70928,0.635439,1.78273,0.742462,0.308176,0.116148,0.578146,0.267369,0.143829,0.215895,1.90282,0.324249,0.189628,0.407146,0.616494,0.126749,0.516623,0.752499,0.629526,0.213587,0.765929,0.0774004,0.112299,0.432429,0.726382,1.55835,1.16239,0.691851,0.557784,1.11129,0.302448,0.486671,0.78843,1.40098,0.342157,0.26801,0.334285,0.165687,0.516957,0.368962,0.569975,0.888975,0.257209,0.0480206,0.0919218,4.70407,0.690731,0.500787,0.377296,0.079602,0.314905,0.597974,0.464037,0.192969,2.99624
 
}}
 
}}

Revision as of 05:11, 26 November 2012


Full id: C411_vagina_Mast_breast_heart_CD14_aorta_liver



Phase1 CAGE Peaks

  Short description
Hg19::chr11:133904003..133904027,- p@chr11:133904003..133904027
-
Hg19::chr11:133907166..133907180,+ p2@ENST00000531938
Hg19::chr11:133907234..133907249,+ p3@ENST00000531938
Hg19::chr11:133907376..133907387,+ p5@ENST00000531938
Hg19::chr11:65374430..65374474,- p5@MAP3K11
Hg19::chr12:2903742..2903763,- p3@CBX3P4
Hg19::chr12:2903775..2903794,- p2@CBX3P4
Hg19::chr12:57082286..57082368,+ p@chr12:57082286..57082368
+
Hg19::chr13:31736027..31736053,- p1@HSPH1
Hg19::chr14:70195360..70195363,- p@chr14:70195360..70195363
-
Hg19::chr14:77924458..77924475,+ p2@AHSA1
Hg19::chr16:87378830..87378846,- p@chr16:87378830..87378846
-
Hg19::chr16:89930250..89930272,- p1@AK098674
Hg19::chr16:89930279..89930301,- p2@AK098674
Hg19::chr18:19284854..19284899,+ p2@MIB1
Hg19::chr19:14629195..14629216,- p1@DNAJB1
Hg19::chr1:245026181..245026208,- p19@HNRNPU
Hg19::chr22:43041411..43041417,+ p@chr22:43041411..43041417
+
Hg19::chr4:88343933..88343946,+ p6@NUDT9
Hg19::chr6:31783311..31783328,+ p1@HSPA1A
p1@HSPA1B
Hg19::chr6:31789738..31789757,- p@chr6:31789738..31789757
-
Hg19::chr6:31795506..31795525,+ p2@HSPA1A
p2@HSPA1B
Hg19::chr7:75923952..75923971,- p@chr7:75923952..75923971
-
Hg19::chr7:75924283..75924306,+ p@chr7:75924283..75924306
+
Hg19::chr7:75931755..75931775,- p@chr7:75931755..75931775
-


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


p.valueFDRnGenesnPathwayName
2.54761513593594e-050.0161264038104745232{HSPA8,34} (Static Module):NA



Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


GO IDGO nameFDR corrected p-value
GO:0051789response to protein stimulus5.16481965377491e-05
GO:0006986response to unfolded protein5.16481965377491e-05
GO:0009607response to biotic stimulus0.00408991908245404
GO:0006950response to stress0.0113033427993079
GO:0030189chaperone activator activity0.0131932179441893
GO:0042221response to chemical stimulus0.0167213722932249
GO:0019144ADP-sugar diphosphatase activity0.0183373558696005
GO:0005737cytoplasm0.0183373558696005
GO:0047631ADP-ribose diphosphatase activity0.0197851668314843
GO:0004706JUN kinase kinase kinase activity0.0197851668314843
GO:0051082unfolded protein binding0.0273491196999661
GO:0001671ATPase activator activity0.0274729278152382
GO:0005739mitochondrion0.0320692916310955
GO:0001947heart looping0.0320692916310955
GO:0044424intracellular part0.0320692916310955
GO:0045665negative regulation of neuron differentiation0.0320692916310955
GO:0051085chaperone cofactor-dependent protein folding0.0320692916310955
GO:0016071mRNA metabolic process0.0320692916310955
GO:0044444cytoplasmic part0.0320692916310955
GO:0006457protein folding0.0320692916310955
GO:0005524ATP binding0.0320692916310955
GO:0032559adenyl ribonucleotide binding0.0320692916310955
GO:0003007heart morphogenesis0.0320692916310955
GO:0051084'de novo' posttranslational protein folding0.0320692916310955
GO:0001839neural plate morphogenesis0.0320692916310955
GO:0051087chaperone binding0.0320692916310955
GO:0001841neural tube formation0.0320692916310955
GO:0006458'de novo' protein folding0.0320692916310955
GO:0001840neural plate development0.0320692916310955
GO:0000080G1 phase of mitotic cell cycle0.0320692916310955
GO:0001838embryonic epithelial tube formation0.0320692916310955
GO:0045807positive regulation of endocytosis0.0320692916310955
GO:0030530heterogeneous nuclear ribonucleoprotein complex0.0320692916310955
GO:0004709MAP kinase kinase kinase activity0.0320692916310955
GO:0001756somitogenesis0.0320692916310955
GO:0030554adenyl nucleotide binding0.0320692916310955
GO:0046328regulation of JNK cascade0.0320692916310955
GO:0051318G1 phase0.0320692916310955
GO:0021915neural tube development0.0320692916310955
GO:0007257activation of JNK activity0.0343930784770196
GO:0016331morphogenesis of embryonic epithelium0.0343930784770196
GO:0043229intracellular organelle0.0343930784770196
GO:0043226organelle0.0343930784770196
GO:0043507positive regulation of JNK activity0.0343930784770196
GO:0043506regulation of JNK activity0.0365444265241635
GO:0045664regulation of neuron differentiation0.0371756059842438
GO:0035282segmentation0.037779597917854
GO:0006402mRNA catabolic process0.0397233584196399
GO:0005227calcium activated cation channel activity0.0446830244551175
GO:0030100regulation of endocytosis0.0446830244551175
GO:0032553ribonucleotide binding0.0447701239990005
GO:0032555purine ribonucleotide binding0.0447701239990005
GO:0051050positive regulation of transport0.047090896044346
GO:0017076purine nucleotide binding0.0491008753794253



Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data


Cell Type
Ontology termp-valuen
classical monocyte7.51e-0742
CD14-positive, CD16-negative classical monocyte7.51e-0742
Uber Anatomy
Ontology termp-valuen
adult organism1.99e-41114
neural tube2.64e-2656
neural rod2.64e-2656
future spinal cord2.64e-2656
neural keel2.64e-2656
regional part of nervous system7.07e-2453
regional part of brain7.07e-2453
neurectoderm3.22e-2086
neural plate5.62e-2082
presumptive neural plate5.62e-2082
brain1.05e-1668
future brain1.05e-1668
regional part of forebrain1.49e-1641
forebrain1.49e-1641
anterior neural tube1.49e-1641
future forebrain1.49e-1641
central nervous system1.53e-1581
nervous system2.03e-1489
brainstem4.30e-146
ecto-epithelium5.60e-14104
brain grey matter7.78e-1334
gray matter7.78e-1334
telencephalon1.09e-1234
posterior neural tube2.17e-1115
chordal neural plate2.17e-1115
structure with developmental contribution from neural crest5.12e-11132
pre-chordal neural plate1.14e-1061
regional part of telencephalon2.53e-1032
cerebral hemisphere4.45e-1032
neural nucleus5.51e-099
nucleus of brain5.51e-099
segmental subdivision of hindbrain6.56e-0912
hindbrain6.56e-0912
presumptive hindbrain6.56e-0912
medulla oblongata2.15e-083
myelencephalon2.15e-083
future myelencephalon2.15e-083
segmental subdivision of nervous system3.89e-0813
regional part of cerebral cortex6.99e-0822
organ system subdivision9.09e-08223
pons2.18e-073
organ3.45e-07503
ectoderm-derived structure3.71e-07171
ectoderm3.71e-07171
presumptive ectoderm3.71e-07171
neocortex5.08e-0720
tube7.55e-07192
cerebral cortex9.50e-0725
pallium9.50e-0725


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
BRCA1#67254.036846128644750.006892546890970770.0291874753576652
CCNT2#905143.548272883099084.62126213135399e-060.00014368561945117
EBF1#1879103.56258673862760.0002092504843153790.00243687682107648
EGR1#1958132.593853129301270.000377785726401510.00374661128854309
EP300#203392.438619021440350.007171248819054740.0297784603162204
GATA3#262566.536763925729440.0002368283656653750.00257942618434937
GTF2B#295967.666519184237829.94934489292016e-050.00140040381573004
GTF2F1#296273.567105045492140.002484878598094690.0139555945314267
HMGN3#9324123.925702907208281.23148160281096e-050.000304197509735037
HSF1#32971172.28789333333331.66913017282451e-183.78961491564389e-16
IRF1#3659123.665838601710672.49394930213504e-050.000539936921985244
MXI1#460193.586165786353350.0004703238892508280.00431825553138173
NFKB1#4790122.634270443613040.0006484616231784390.00531340683062396
POLR2A#5430211.803860668308780.0001299031054458090.00171062292644747
PPARGC1A#108918112.0163636363644.35959567622917e-157.71714936999488e-13
PRDM1#639315.81971469329530.0008842492462514420.0065926689769599
RDBP#7936424.5821446384042.02574085028561e-050.000449471741370254
SIN3A#25942102.163553890726050.01004308775449890.0376540078256789
SRF#672263.311322782920270.00771352676699060.0317512621006515
STAT1#677254.141317499439840.006195451371514410.027376634050755
STAT2#6773410.44220338983050.0005379670924503480.00464797693319176
STAT3#6774104.20778599886175.1112914742446e-050.000870403016922602
TAF1#6872162.139549622876990.0004368871040772260.00407247878103547
TAF7#687983.658582209575650.000947062513460020.00685258846080443
TBP#6908131.927520757290120.006834711734069660.0289825189327419
TCF12#693872.97765017261220.006801290727968670.0288419685860939
TFAP2C#702283.458953155155270.001368070086251090.0090014409209335
ZBTB33#1000945.066356004796980.007391990141568670.0305457014479422



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.