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Coexpression cluster:C2403: Difference between revisions

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{{Coexpression_clusters
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129351,0.141936,0.0786166,0.276997,0.205513,0.282389,0.251421,0.162089,0.000782065,0.0874139,0.233244,0.207281,0.327401,0.195748,0.27845,0.161712,0.237871,0.239139,0.095257,0.000767461,0.00080978,0.262022,0.274403,0.266687,0.0181825,0.248707,0.31749,0.0121139,0.287598,0.000621734,0.223773,0.036547,0.181895,0.000242325,0.30702,0.202977,0.170837,0.000748107,0.28543,0.222656,0.228479,0.127111,0.000269465,0.390754,0.355805,0.279739,0.108118,0.0371525,0.139723,0.00256967,0.0710478,0.196248,0.102645,0.0539258,1.15555e-06,0.401939,0.332746,0.271338,0.242121,0.298673,0.000205581,0.106889,0.128632,0.0036839,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.000901437,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.000282393,0.00137371,0.362662,0.0201006,6.10777e-05,0.334474,0.0600054,0.000258223,0.291176,0.000132638,0.322827,0.000156623,0.00114556,0.335984,0.000968095,4.76577e-06,0.265058,0.256405,0.00120337,0.302133,0.40806,0.151361,2.40814e-05,0.286696,0.150674,0.000231487,0.246177,0.35674,0.0737175,0.318525,0.213257,0.287217,0.122782,0.410951,0.000430266,0.266974,3.26592e-07,0.112897,0.398354,0.222091,4.49029e-06,5.4669e-06,0.0936726,0.343425,0.132374,0.285122,0.22741,0.203996,0.276721,0.000697427,0.00385437,0.450113|tfbs_overrepresentation_for_novel_motifs=0.590005,0.0888524,0.581696,0.741427,0.534346,1.75218,0.821651,0.395818,1.01802,0.151681,1.68405,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.635753,0.581762,0.505745,0.731221,0.528529,1.53003,4.87831,0.316693,0.728867,0.537869,0.806311,0.682839,1.09415,0.433165,0.911389,0.49475,0.285913,1.23038,1.75478,0.463978,0.371755,0.493145,0.66492,0.539378,0.53106,0.648765,1.49501,1.92371,0.694903,0.515703,1.33034,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,1.82985,0.297448,0.776148,1.13655,1.92893,1.0193,2.3411,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.692875,1.32819,0.336329,0.321165,1.49254,1.00941,1.08,0.62601,1.69485,1.02594,0.844168,0.399165,1.27559,0.353274,1.18341,2.2083,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,1.66879,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,2.81371,5.50441,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,3.22874,0.489254,0.785429,2.74919,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,2.52313,1.36323,2.02143,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,2.90835,2.68745,0.521611,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.359498|tfbs_overrepresentation_jaspar=MA0003.1;0.0214529,MA0004.1;0.71247,MA0006.1;2.26728,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;0.0695829,MA0017.1;1.41335,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;1.92746,MA0040.1;1.12314,MA0041.1;0.732902,MA0042.1;0.697662,MA0043.1;1.20635,MA0046.1;1.19471,MA0048.1;0.709734,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.125954,MA0056.1;0,MA0057.1;0.248209,MA0058.1;0.605914,MA0059.1;2.50216,MA0060.1;0.393285,MA0061.1;0.360128,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;1.93422,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;0.182167,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;0.539569,MA0103.1;0.521546,MA0105.1;0.232357,MA0106.1;0.869173,MA0107.1;0.453492,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;2.9994,MA0117.1;1.24497,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;0.344952,MA0140.1;0.779643,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;1.09982,MA0145.1;0.195821,MA0146.1;0.061409,MA0147.1;5.25242,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;0.483275,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;5.8901,MA0047.2;0.856092,MA0112.2;0.187982,MA0065.2;2.43626,MA0150.1;0.633493,MA0151.1;0,MA0152.1;1.84959,MA0153.1;1.30799,MA0154.1;2.64806,MA0155.1;0.180766,MA0156.1;1.37856,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;0.0928415,MA0163.1;0.0725493,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;0.0270533,MA0102.2;1.75932,MA0258.1;1.07498,MA0259.1;1.1888,MA0442.1;0}}
|full_id=C2403_skeletal_cervix_eye_cerebellum_dura_testicular_mature
|id=C2403
}}

Latest revision as of 12:05, 17 September 2013


Full id: C2403_skeletal_cervix_eye_cerebellum_dura_testicular_mature



Phase1 CAGE Peaks

Hg19::chr17:38256799..38256815,-p3@NR1D1
Hg19::chr17:38256822..38256851,-p1@NR1D1
Hg19::chr17:38256858..38256866,-p6@NR1D1
Hg19::chr17:38256877..38256900,-p2@NR1D1


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism4.47e-30114
neural tube1.67e-1656
neural rod1.67e-1656
future spinal cord1.67e-1656
neural keel1.67e-1656
regional part of nervous system1.51e-1553
regional part of brain1.51e-1553
regional part of forebrain6.35e-1441
forebrain6.35e-1441
anterior neural tube6.35e-1441
future forebrain6.35e-1441
brain3.10e-1368
future brain3.10e-1368
neural plate2.82e-1182
presumptive neural plate2.82e-1182
ecto-epithelium2.93e-11104
anatomical conduit4.17e-11240
central nervous system4.29e-1181
telencephalon5.84e-1134
neurectoderm8.41e-1186
ectoderm-derived structure1.61e-10171
ectoderm1.61e-10171
presumptive ectoderm1.61e-10171
nervous system1.70e-1089
brain grey matter2.37e-1034
gray matter2.37e-1034
cerebral hemisphere2.62e-1032
regional part of cerebral cortex3.86e-1022
regional part of telencephalon4.94e-1032
organ system subdivision1.28e-09223
organ1.43e-09503
neocortex2.30e-0920
pre-chordal neural plate1.48e-0861
structure with developmental contribution from neural crest2.01e-08132
anatomical group6.40e-08625
anatomical system7.90e-08624
tube8.68e-08192
anatomical cluster1.63e-07373
multi-cellular organism1.65e-07656
cerebral cortex2.99e-0725
pallium2.99e-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)
MA0003.10.0214529
MA0004.10.71247
MA0006.12.26728
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.11.41335
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.11.92746
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.709734
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.12.50216
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.11.93422
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.11.13665
MA0115.11.45393
MA0116.12.9994
MA0117.11.24497
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
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.11.09982
MA0145.10.195821
MA0146.10.061409
MA0147.15.25242
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.483275
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.25.8901
MA0047.20.856092
MA0112.20.187982
MA0065.22.43626
MA0150.10.633493
MA0151.10
MA0152.11.84959
MA0153.11.30799
MA0154.12.64806
MA0155.10.180766
MA0156.11.37856
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.0270533
MA0102.21.75932
MA0258.11.07498
MA0259.11.1888
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
ATF3#467422.46317452600873.92475754624726e-060.000127376554808116
BHLHE40#8553444.87181354697742.46312701995675e-071.28366528361908e-05
CCNT2#90546.336201576962630.0006203100587215640.00511928583349043
E2F1#186944.907389214879320.001724022357361790.0106459629267728
E2F4#1874412.66806031528443.88145892637771e-050.000726479729053695
E2F6#187645.017155731697390.00157802193473060.0099653545072759
EGR1#195844.988179094810140.001615011500076050.0101400857314202
ELF1#199744.258097958807540.003041525565781240.016081298464265
EP300#203346.77394172622320.0004748459821442640.00433917573971168
FOXA1#3169411.08141974938556.62943068949433e-050.00106979467209533
FOXA2#3170212.31523187633260.009361916285467240.0353411832190383
GTF2F1#2962412.73966087675773.79492332235515e-050.000717353840476833
HDAC2#3066310.06171517746970.00156372754474740.00992368846362482
HEY1#2346244.040111043105710.00375304636917980.0185906094550735
IRF1#365947.63716375356390.0002938853996185490.00307330502160425
MAFF#23764342.23651736745892.20786227449124e-050.000483816466818277
MAFK#7975213.5503665689150.00777202812098050.0319555468259943
MAX#414946.452555509007120.0005767613195645490.00485229381778652
MXI1#460149.96157162875930.0001015224754950450.00142301782555724
MYC#460945.22228187160940.001344309395272740.00887137172582392
NFKB1#479045.488063424193840.001102199566301980.00767622169278556
NR3C1#2908414.9730233311731.98868032687801e-050.00044275375113795
NRF1#4899412.21027944771094.49717228915276e-050.000793512716179803
SIN3A#2594245.408884726815140.001168172384885160.00795739340627582
SIX5#147912417.0867153554591.17257016123224e-050.000297382358108144
SPI1#668848.204323508522730.000220661881527680.00249412405247504
SREBF1#6720447.00584944048832.04523668136926e-071.10104367920373e-05
STAT3#6774410.51946499715428.16377768286615e-050.00123068241544581
TAF1#687243.343046285745290.008005664898701650.0321962199682507
TBP#690843.706770687096390.005296377814784350.0243989414934614
TCF7L2#6934410.77017656313737.42969445082454e-050.00115348574215797
USF1#739146.361499277207960.0006105011399140830.00507684756361867
USF2#7392412.99219738506963.50833029870167e-050.000681306262674049
ZNF143#7702413.50087655222793.00867915035614e-050.000620626983575044
ZNF263#1012748.221841637010680.0002187871180958320.00248692945437642



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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