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Coexpression cluster:C2815: Difference between revisions

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{{Coexpression_clusters
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.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.373453,0.362662,0.433518,0.184359,0.334474,0.325785,0.257476,0.291176,0.376537,0.322827,0.229571,0.359036,0.335984,0.171704,0.208256,0.265058,0.256405,0.362898,0.302133,0.40806,0.151361,0.279606,0.286696,0.150674,0.251128,0.246177,0.35674,0.35852,0.318525,0.213257,0.287217,0.122782,0.410951,0.289049,0.266974,0.125746,0.112897,0.398354,0.222091,0.205977,0.34423,0.0936726,0.343425,0.132374,0.285122,0.22741,0.203996,0.276721,0.321965,0.264707,0.450113|tfbs_overrepresentation_for_novel_motifs=0.590005,0.620826,1.42265,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,1.44778,0.706765,0.867962,0.341754,0.809319,0.532789,0.559384,2.39977,0.471262,0.356737,0.635753,0.581762,0.169357,0.731221,0.528529,1.53003,0.892087,0.316693,0.728867,0.537869,1.46495,0.682839,1.09415,1.10579,0.911389,1.23824,0.285913,0.491074,0.740899,0.463978,0.371755,0.493145,1.59701,0.183156,0.53106,0.0946706,2.53981,0.822818,0.694903,0.173425,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,1.34056,1.82985,0.297448,0.776148,1.13655,1.92893,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,1.5667,0.402607,0.692875,1.32819,0.336329,0.321165,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,1.17995,0.221873,1.44378,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.934671,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,1.88833,1.52945,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.393155,2.74919,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,3.02112,2.02143,1.24863,0.68598,1.37788,0.852645,1.52813,2.16698,0.676268,0.729481,3.26642,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.234974,0.521611,1.24902,0.383416,1.92786,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,1.96584,0.423521,1.91838,0.0401987|tfbs_overrepresentation_jaspar=MA0003.1;0.233555,MA0004.1;0.71247,MA0006.1;0.532262,MA0007.1;0.6918,MA0009.1;6.17107,MA0014.1;8.67501,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;4.37647,MA0046.1;1.19471,MA0048.1;2.02223,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.125954,MA0056.1;0,MA0057.1;1.28333,MA0058.1;0.605914,MA0059.1;1.47051,MA0060.1;0.393285,MA0061.1;0.360128,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;1.52107,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;0.0343867,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;0.447443,MA0115.1;1.45393,MA0116.1;0.457606,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;2.05538,MA0144.1;1.09982,MA0145.1;1.08195,MA0146.1;0.061409,MA0147.1;1.16748,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;8.68914,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;0.392359,MA0047.2;0.856092,MA0112.2;2.35508,MA0065.2;0.199162,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.649108,MA0155.1;0.533581,MA0156.1;1.37856,MA0157.1;0.97481,MA0158.1;0,MA0159.1;1.1691,MA0160.1;0.756582,MA0161.1;0,MA0162.1;8.56919,MA0163.1;0.918944,MA0164.1;0.90014,MA0080.2;1.32578,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;9.35212,MA0102.2;1.75932,MA0258.1;1.07498,MA0259.1;0.471671,MA0442.1;0}}
|full_id=C2815_Monocytederived_CD14_Mast_corpus_Macrophage_Dendritic_optic
|id=C2815
}}

Latest revision as of 12:13, 17 September 2013


Full id: C2815_Monocytederived_CD14_Mast_corpus_Macrophage_Dendritic_optic



Phase1 CAGE Peaks

Hg19::chr5:150632645..150632658,+p5@GM2A
Hg19::chr5:150632666..150632677,+p6@GM2A
Hg19::chr5:150632678..150632707,+p3@GM2A
Hg19::chr5:150632712..150632725,+p4@GM2A


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
organ2.99e-16503
neural tube2.73e-1556
neural rod2.73e-1556
future spinal cord2.73e-1556
neural keel2.73e-1556
anatomical group1.53e-14625
anatomical system2.71e-14624
neural plate5.74e-1482
presumptive neural plate5.74e-1482
regional part of nervous system1.08e-1353
regional part of brain1.08e-1353
adult organism1.42e-13114
ecto-epithelium1.57e-13104
multi-cellular organism3.70e-13656
central nervous system4.83e-1281
neurectoderm1.37e-1186
embryonic structure1.65e-11564
brain2.62e-1168
future brain2.62e-1168
germ layer3.06e-11560
germ layer / neural crest3.06e-11560
embryonic tissue3.06e-11560
presumptive structure3.06e-11560
germ layer / neural crest derived structure3.06e-11560
epiblast (generic)3.06e-11560
regional part of forebrain1.37e-1041
forebrain1.37e-1041
anterior neural tube1.37e-1041
future forebrain1.37e-1041
developing anatomical structure1.55e-10581
bone marrow2.80e-1076
pre-chordal neural plate6.78e-1061
bone element8.89e-1082
skeletal element9.58e-1090
embryo9.63e-10592
telencephalon1.02e-0934
brain grey matter1.38e-0934
gray matter1.38e-0934
nervous system1.41e-0989
immune system1.56e-0993
structure with developmental contribution from neural crest2.90e-09132
ectoderm-derived structure3.40e-09171
ectoderm3.40e-09171
presumptive ectoderm3.40e-09171
skeletal system5.03e-09100
regional part of telencephalon1.09e-0832
cerebral hemisphere1.21e-0832
tissue2.73e-07773


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)
MA0003.10.233555
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.16.17107
MA0014.18.67501
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
MA0043.14.37647
MA0046.11.19471
MA0048.12.02223
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.11.28333
MA0058.10.605914
MA0059.11.47051
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.11.52107
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.0343867
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
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
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
MA0143.12.05538
MA0144.11.09982
MA0145.11.08195
MA0146.10.061409
MA0147.11.16748
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.28.68914
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.22.35508
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.10.533581
MA0156.11.37856
MA0157.10.97481
MA0158.10
MA0159.11.1691
MA0160.10.756582
MA0161.10
MA0162.18.56919
MA0163.10.918944
MA0164.10.90014
MA0080.21.32578
MA0018.20.870662
MA0099.20.7872
MA0079.29.35212
MA0102.21.75932
MA0258.11.07498
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#90546.336201576962630.0006203100587215640.00513267011747912
CEBPB#105147.971147625824820.0002476385788090830.00268512515907826
CHD2#1106410.34402283411698.73193255208051e-050.00129300199036826
E2F6#187645.017155731697390.00157802193473060.00998648929536017
EGR1#195844.988179094810140.001615011500076050.0101614667182627
ELF1#199744.258097958807540.003041525565781240.0161212895130241
FOS#235348.99795530889440.0001525147711168630.00195321768003361
GABPB1#255347.067683836182170.0004006876864423170.00390768711218126
HEY1#2346244.040111043105710.00375304636917980.0186498743755422
HNF4G#3174214.37671126322340.006924169980439180.0293106918201641
IRF1#365947.63716375356390.0002938853996185490.00308009004021692
MAX#414946.452555509007120.0005767613195645490.00486130057735469
MXI1#460149.96157162875930.0001015224754950450.00142665578824367
MYC#460945.22228187160940.001344309395272740.00889328744744976
NFYA#4800418.42558069983058.67100748407158e-060.00023503538817258
NFYB#4801416.75979325353651.26678572070404e-050.00031181200538442
PAX5#507946.669565531177830.0005052774169483260.00444759107869079
POU2F2#545249.106124057742520.000145395665174930.00188656701145539
RFX5#5993412.04791082719514.74457429336527e-050.00082793415977406
RXRA#6256315.055962854350.0004758307997303580.00433982122897903
SIN3A#2594245.408884726815140.001168172384885160.00797716462044075
SP1#666745.69838137814090.0009482606065333980.00685460890682043
SP2#6668426.15353049384462.13562021071447e-067.7606833398333e-05
SPI1#668848.204323508522730.000220661881527680.00249763804539605
STAT3#6774410.51946499715428.16377768286615e-050.00123388824518214
TAF1#687243.343046285745290.008005664898701650.0323081895110129
TBP#690843.706770687096390.005296377814784350.0244875117357237
TCF7L2#6934410.77017656313737.42969445082454e-050.00115675292002037
THAP1#55145431.36914460285131.03171810326891e-064.32390076193025e-05
USF1#739146.361499277207960.0006105011399140830.00508778555310301
ZBTB7A#5134147.35190930787590.000342223540015990.00347173232595726
ZEB1#6935416.88843201754391.22862303393937e-050.0003050063252712



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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