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Coexpression cluster:C875: Difference between revisions

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{{Coexpression_clusters
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5538,0.0320214,0.488946,0.0329877,0.65774,0.223643,0.495864,0.724355,0.425327,0.39901,0.366863,0.796642,0.261599,0.106224,0.0445596,0.415361,0.186313,0.319052,0.633308,0.450888,0.02821,0.451482,0.262422,0.47592,0.781285,0.466904,0.886979,0.325329,0.829098,0.0377034,0.940822,0.431922,0.891199,0.714915,0.900971,0.529155,0.22098,0.0245221,0.0411894,0.758804,0.732314,0.497193,0.539178,0.361435,0.432419,0.421792,0.483823,0.229876,0.680622,0.584585,0.000332826,0.703152,0.409234,0.651399,0.467644,0.158036,0.899287,0.774,0.741759,0.0485226,0.00527166,0.248843,0.75678,0.529689,0.726725,0.251805,0.362565,0.665579,0.562983,0.164776,0.666697,0.295828,0.152906,0.769132,0.627588,0.215433,0.0163198,0.840679,0.352485,0.172039,0.0655848,0.141382,0.471539,0.845795,0.299839,0.301565,0.842298,0.632112,0.452975,0.572271,0.198802,0.248665,0.747678,0.0739987,0.76693,0.857722,0.73691,0.71215,0.483774,0.154027,0.0617526,0.342384,0.658486,0.656834,0.0344425,0.498323,0.0213911,0.21597,0.621861,0.498105,0.0977699,0.467889,0.59289,0.465133,0.200614,0.23601,0.412715,0.470602,0.413744,0.524403,0.155677,0.0332709,0.259678,0.420165,0.217215,0.759777,0.222104,0.502321,0.263547,0.447445,0.0278516,0.527097,0.53086,0.714696,0.306869,0.521806,0.485334,0.462243,0.326222,0.486977,0.00462527,0.0355835,0.327893,0.120241,0.181152,0.0766925,0.235347,0.344033,0.503902,0.574041,0.529704,0.188703,0.504091,0.605432,0.302353,0.37651,0.54245,0.411826,0.184047,0.425621,0.111096,0.18548,0.148563,0.130525,0.241802,0.49107,0.725948,0.0917383,0.318983,0.267772,0.291371,0.168254,0.51798,0.40407,0.52603,0.478764,0.0609888,0.594172,0.668525,0.449854,0.40705,0.590314,0.387463,0.16781,0.327588,0.457295,0.459324,0.201671,0.5923,0.231323,0.495225,0.51408,0.502377,0.368078,0.474502,0.576606,0.309128,0.533737,0.208377,0.434445,0.145807,0.363467,0.482434,0.561852,0.0933934,0.343945,0.589766,0.530537,0.111066,0.44213,0.263525,0.0314561,0.672069,0.628217,0.169229,0.226979,0.491955,0.287253,0.152349,0.152802,0.38832,0.216263,0.117262,0.152699,0.685459,0.0139744,0.50945,0.129789,0.549887,0.467691,0.22458,0.266409,0.180355,0.322962,0.179632,0.282128,0.186072,0.211757,0.338622,0.29306,0.126579,0.187708,0.245457,0.106235,0.352719,0.150936,0.650742,0.637062,0.721601,0.367773,0.599943,0.0607278,0.488202,0.538989,0.28742,0.0123582,0.443905,0.0804409,0.601983,0.345488,0.408688,0.499886,0.486539,0.637365,0.554869,0.692656,0.308763,0.521884,0.532407,0.307503,0.478305,0.470512,0.629431,0.631734,0.578048,0.41706,0.533176,0.255282,0.696023,0.53587,0.502814,0.260932,0.236266,0.108433,0.110542,0.404852,0.613018,0.198522,0.611947,0.273479,0.530083,0.44039,0.0154193,0.517565,0.0586842,0.499348,0.739615|tfbs_overrepresentation_for_novel_motifs=0.312007,0.479568,0.823567,1.12193,0.267236,0.439064,0.511871,0.164003,0.161941,1.65033,0.410439,0.553754,0.799936,0.500805,0.734361,0.287179,0.728104,0.218596,0.137566,0.473089,0.305279,0.33045,1.9325,0.262652,0.347482,0.575764,0.36063,0.429643,0.270022,0.329945,0.389837,0.764231,0.190489,0.807612,0.23642,0.452714,0.233607,1.9611,0.611187,0.884996,0.235191,0.97787,0.366128,0.731232,0.513344,0.333541,0.51292,1.0341,0.615516,0.270138,0.589559,0.524278,0.257164,0.839846,0.99088,0.503626,0.273964,0.472204,0.329728,0.47124,0.804523,1.28186,0.162346,0.700946,3.33727,0.667267,1.07848,1.44489,0.754027,1.28328,0.362234,0.168734,0.253077,0.988898,0.784625,0.741954,0.105027,0.684401,0.750836,0.341765,0.436045,0.699894,0.532172,0.166331,0.937974,0.89521,0.468577,0.320664,0.614883,1.54397,1.17124,0.911274,0.78075,0.571859,0.267904,0.598862,0.136404,0.82268,0.619373,0.290348,0.613956,0.775192,0.817185,0.731699,0.656016,0.406162,0.716172,0.49749,1.64174,0.252953,0.846745,3.1686,0.300169,1.89062,1.12352,0.232218,0.0867932,0.388709,0.664981,0.199081,0.980696,0.612519,0.436445,0.543065,1.23356,0.685145,0.50576,0.785662,1.02292,0.208774,0.911957,2.6976,1.03718,0.539846,1.18405,0.307751,0.384215,0.430179,1.14186,1.99816,1.59626,1.10478,0.507423,0.819206,0.657732,0.464114,0.641461,1.83907,0.37143,0.193834,0.50389,0.347165,0.912334,0.155464,0.514733,1.31376,0.599133,0.254737,0.347536,0.320853,1.10357,0.894035,0.750062,0.323817,0.673453,0.531409,0.183544,0.510589,0.333592|tfbs_overrepresentation_jaspar=MA0003.1;0.426041,MA0004.1;0.415381,MA0006.1;0.265592,MA0007.1;0.397529,MA0009.1;0.870971,MA0014.1;0.367355,MA0017.1;0.301634,MA0019.1;0.558663,MA0024.1;0.766783,MA0025.1;1.00397,MA0027.1;2.48103,MA0028.1;0.767002,MA0029.1;0.785955,MA0030.1;0.774581,MA0031.1;0.710608,MA0038.1;0.514558,MA0040.1;0.791764,MA0041.1;0.433167,MA0042.1;0.402577,MA0043.1;2.02319,MA0046.1;0.860127,MA0048.1;0.0764047,MA0050.1;0.403421,MA0051.1;0.510444,MA0052.1;0.795605,MA0055.1;0.0199484,MA0056.1;0,MA0057.1;0.919325,MA0058.1;0.325084,MA0059.1;0.323879,MA0060.1;0.9464,MA0061.1;0.851955,MA0063.1;0,MA0066.1;0.514973,MA0067.1;1.18766,MA0068.1;0.354973,MA0069.1;0.856287,MA0070.1;0.845142,MA0071.1;1.20007,MA0072.1;0.840664,MA0073.1;0.447621,MA0074.1;0.509711,MA0076.1;1.61616,MA0077.1;0.832987,MA0078.1;0.607575,MA0081.1;0.865814,MA0083.1;0.878452,MA0084.1;1.37471,MA0087.1;0.838229,MA0088.1;0.363555,MA0089.1;0,MA0090.1;0.353576,MA0091.1;0.417885,MA0092.1;0.381858,MA0093.1;0.26836,MA0095.1;0,MA0098.1;0,MA0100.1;1.30927,MA0101.1;0.746654,MA0103.1;0.257174,MA0105.1;2.36395,MA0106.1;0.554855,MA0107.1;1.11943,MA0108.2;0.707575,MA0109.1;0,MA0111.1;0.366362,MA0113.1;0.57094,MA0114.1;0.200901,MA0115.1;1.11137,MA0116.1;0.208403,MA0117.1;0.908433,MA0119.1;0.308914,MA0122.1;0.934245,MA0124.1;1.06995,MA0125.1;0.986127,MA0130.1;0,MA0131.1;0.625452,MA0132.1;0,MA0133.1;0,MA0135.1;0.90122,MA0136.1;0.521435,MA0139.1;1.90392,MA0140.1;1.19454,MA0141.1;1.55341,MA0142.1;0.679161,MA0143.1;0.571113,MA0144.1;0.552298,MA0145.1;0.177438,MA0146.1;0.75319,MA0147.1;0.211483,MA0148.1;1.11902,MA0149.1;0.464973,MA0062.2;1.95022,MA0035.2;0.473658,MA0039.2;0.199243,MA0138.2;0.608783,MA0002.2;0.46405,MA0137.2;0.780538,MA0104.2;0.161609,MA0047.2;0.542971,MA0112.2;0.674448,MA0065.2;0.408099,MA0150.1;0.34802,MA0151.1;0,MA0152.1;0.480711,MA0153.1;0.969315,MA0154.1;0.062786,MA0155.1;0.359913,MA0156.1;0.785298,MA0157.1;0.652111,MA0158.1;0,MA0159.1;0.212043,MA0160.1;1.15068,MA0161.1;0,MA0162.1;1.08366,MA0163.1;0.034916,MA0164.1;0.583138,MA0080.2;0.739941,MA0018.2;0.556211,MA0099.2;0.481058,MA0079.2;1.24237,MA0102.2;1.41188,MA0258.1;1.01999,MA0259.1;0.218904,MA0442.1;0}}
|full_id=C875_Eosinophils_Neutrophils_Mast_CD19_CD14_Basophils_Peripheral
|id=C875
}}

Latest revision as of 11:32, 17 September 2013


Full id: C875_Eosinophils_Neutrophils_Mast_CD19_CD14_Basophils_Peripheral



Phase1 CAGE Peaks

Hg19::chr10:70660801..70660814,-p@chr10:70660801..70660814
-
Hg19::chr11:102187888..102187900,-p@chr11:102187888..102187900
-
Hg19::chr19:2270812..2270826,-p@chr19:2270812..2270826
-
Hg19::chr1:225655463..225655481,-p@chr1:225655463..225655481
-
Hg19::chr1:66801524..66801541,-p@chr1:66801524..66801541
-
Hg19::chr20:34330506..34330528,+p@chr20:34330506..34330528
+
Hg19::chr20:34330534..34330580,+p@chr20:34330534..34330580
+
Hg19::chr2:208031542..208031595,-p2@KLF7
Hg19::chr5:130971280..130971333,+p@chr5:130971280..130971333
+


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>

Cell Type
Ontology termp-valuen
leukocyte9.62e-59136
hematopoietic cell4.39e-50177
hematopoietic stem cell6.33e-50168
angioblastic mesenchymal cell6.33e-50168
hematopoietic lineage restricted progenitor cell1.44e-46120
hematopoietic oligopotent progenitor cell4.34e-46161
hematopoietic multipotent progenitor cell4.34e-46161
nongranular leukocyte7.03e-45115
classical monocyte7.63e-3142
CD14-positive, CD16-negative classical monocyte7.63e-3142
myeloid leukocyte2.30e-3072
defensive cell3.77e-2548
phagocyte3.77e-2548
granulocyte monocyte progenitor cell1.02e-2467
myeloid cell4.57e-24108
common myeloid progenitor4.57e-24108
myeloid lineage restricted progenitor cell3.45e-2366
macrophage dendritic cell progenitor2.06e-2261
monopoietic cell2.31e-2159
monocyte2.31e-2159
monoblast2.31e-2159
promonocyte2.31e-2159
lymphoid lineage restricted progenitor cell3.94e-2152
lymphocyte1.30e-2053
common lymphoid progenitor1.30e-2053
nucleate cell1.23e-1955
mesenchymal cell1.95e-19354
connective tissue cell3.01e-19361
motile cell9.32e-17386
stem cell4.01e-16441
multi fate stem cell4.28e-16427
somatic stem cell2.62e-15433
stuff accumulating cell1.43e-1287
mature alpha-beta T cell9.24e-1118
alpha-beta T cell9.24e-1118
immature T cell9.24e-1118
mature T cell9.24e-1118
immature alpha-beta T cell9.24e-1118
lymphocyte of B lineage1.32e-1024
pro-B cell1.32e-1024
T cell1.03e-0925
pro-T cell1.03e-0925
B cell3.39e-0914
native cell8.40e-09722
CD8-positive, alpha-beta T cell2.02e-0811
granulocyte4.01e-088
intermediate monocyte9.59e-089
CD14-positive, CD16-positive monocyte9.59e-089
blood cell6.63e-0711
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.33e-3198
blood island1.33e-3198
hemolymphoid system6.72e-30108
bone marrow1.09e-2276
immune system4.88e-2293
bone element8.82e-2282
skeletal element2.97e-1990
connective tissue7.06e-18371
skeletal system5.46e-16100
lateral plate mesoderm3.23e-14203
blood1.82e-0915
haemolymphatic fluid1.82e-0915
organism substance1.82e-0915
musculoskeletal system8.14e-08167


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)
MA0003.10.426041
MA0004.10.415381
MA0006.10.265592
MA0007.10.397529
MA0009.10.870971
MA0014.10.367355
MA0017.10.301634
MA0019.10.558663
MA0024.10.766783
MA0025.11.00397
MA0027.12.48103
MA0028.10.767002
MA0029.10.785955
MA0030.10.774581
MA0031.10.710608
MA0038.10.514558
MA0040.10.791764
MA0041.10.433167
MA0042.10.402577
MA0043.12.02319
MA0046.10.860127
MA0048.10.0764047
MA0050.10.403421
MA0051.10.510444
MA0052.10.795605
MA0055.10.0199484
MA0056.10
MA0057.10.919325
MA0058.10.325084
MA0059.10.323879
MA0060.10.9464
MA0061.10.851955
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.10.354973
MA0069.10.856287
MA0070.10.845142
MA0071.11.20007
MA0072.10.840664
MA0073.10.447621
MA0074.10.509711
MA0076.11.61616
MA0077.10.832987
MA0078.10.607575
MA0081.10.865814
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.10.363555
MA0089.10
MA0090.10.353576
MA0091.10.417885
MA0092.10.381858
MA0093.10.26836
MA0095.10
MA0098.10
MA0100.11.30927
MA0101.10.746654
MA0103.10.257174
MA0105.12.36395
MA0106.10.554855
MA0107.11.11943
MA0108.20.707575
MA0109.10
MA0111.10.366362
MA0113.10.57094
MA0114.10.200901
MA0115.11.11137
MA0116.10.208403
MA0117.10.908433
MA0119.10.308914
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.11.90392
MA0140.11.19454
MA0141.11.55341
MA0142.10.679161
MA0143.10.571113
MA0144.10.552298
MA0145.10.177438
MA0146.10.75319
MA0147.10.211483
MA0148.11.11902
MA0149.10.464973
MA0062.21.95022
MA0035.20.473658
MA0039.20.199243
MA0138.20.608783
MA0002.20.46405
MA0137.20.780538
MA0104.20.161609
MA0047.20.542971
MA0112.20.674448
MA0065.20.408099
MA0150.10.34802
MA0151.10
MA0152.10.480711
MA0153.10.969315
MA0154.10.062786
MA0155.10.359913
MA0156.10.785298
MA0157.10.652111
MA0158.10
MA0159.10.212043
MA0160.11.15068
MA0161.10
MA0162.11.08366
MA0163.10.034916
MA0164.10.583138
MA0080.20.739941
MA0018.20.556211
MA0099.20.481058
MA0079.21.24237
MA0102.21.41188
MA0258.11.01999
MA0259.10.218904
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
BCL3#602311.51570093457940.001785915017827760.0109549617377489
BRCA1#67248.970769174766120.0006202690356731910.00514006806448245
CHD2#110666.896015222744575.28898897155739e-050.00089758972895756
CTCF#1066463.573504248716680.002103883629372150.0121645076879809
E2F4#187445.630249029015310.003536571815964610.017945584680183
E2F6#187663.344770487798260.003009555364094890.0159842835979814
EBF1#187965.937644564379340.0001242436507924170.00165593193531256
EGR1#195863.325452729873420.003104936414383980.016325653435123
ELF1#199794.258097958807542.17161853202127e-067.82074716778515e-05
FOS#235354.998864060496890.001450289921505040.00929757713535482
FOSL2#235535.643400201520560.01321558041905920.0467570718312314
FOXA1#316944.925075444171310.005758150542003090.0259280626220687
FOXA2#317038.210154584221750.00467281236756890.0220515950863734
GABPB1#255353.926491020101210.004337976092287310.0205830668803051
GATA1#262346.026803619466860.002753144894242950.0151000787527486
GTF2F1#296245.662071500781180.00346420020706550.0176022966539707
HEY1#2346273.142308589082220.001258763462843770.0084564516464647
IRF3#3661315.66065073716320.0007351478720625020.00579282545724579
IRF4#3662512.17472927041342.1331797509613e-050.000470015105507695
MAFF#23764212.51452366443230.01044482063014860.0386975991270384
MAX#414975.018654284783325.77474544696214e-050.000962202679858454
MXI1#460155.534206460421830.000906612702046980.00660152854975141
MYC#460963.48152124773960.002423669811459260.0136544207271007
NFKB1#479063.658708949462560.001850649648602720.0109333634263163
NFYA#480036.141860233276840.01048163163058090.0388147050266368
NFYB#480135.586597751178820.01358500277111940.047947149620254
NRF1#489956.783488582061620.0003500419849025880.00352400567391955
PAX5#507985.928502694380291.99061202941177e-067.30233683666089e-05
POLR2A#543092.147453176558070.001029412892608020.00728393313625267
POU2F2#545277.082540933799745.66141070992737e-060.000170444529586078
REST#597855.361127064515570.001050372213652920.00742368705567415
RFX5#599345.354627034308930.004249445027674740.0202199548610562
RXRA#625636.691539046377760.008273246622947750.0325958051929244
SIN3A#2594263.605923151210090.002003057991334320.0116453670428059
SP1#666763.79892091876060.001506997871138380.00962390550714326
SP2#666838.71784349794820.003945531750578630.0189430143198033
SPI1#668887.292732007575763.90517100687164e-071.89786949644796e-05
SRF#672246.132079227630140.002582573603250730.0142860913426856
STAT1#677236.902195832399730.007591561082166650.0312862066080184
TAF1#687293.343046285745291.91655056102793e-050.000433440069387606
TBP#690883.294907277419010.0001918853220272470.00231492562633749
TCF12#693867.089643268124284.5123563262149e-050.000793777972635268
TCF7L2#693455.983431423965190.0006305154397321440.00518384649375623
TFAP2A#702035.506211457681650.01413162662770550.0495848464092368
TFAP2C#702244.804101604382320.006299303434747120.0277849882347138
TRIM28#1015548.262455575672230.0008469285971791930.00638368762707836
USF2#739245.774309948919820.003223241005374920.0166996759281849
YY1#752873.819799472108550.0003529672812141940.00353573277217813
ZBTB33#10009310.55490834332710.002291721628821160.0130036463757716



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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