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Coexpression cluster:C1207: Difference between revisions

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{{Coexpression_clusters
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polymerase II transcription factor activity!0.0164432371661441!3660;4261$GO:0043130!ubiquitin binding!0.0386029895776261!4261$GO:0032182!small conjugating protein binding!0.0386029895776261!4261|id=C1207|ontology_enrichment_celltype=CL:0000738!4.25e-57!136;CL:0002087!1.83e-56!115;CL:0000037!8.48e-50!168;CL:0000566!8.48e-50!168;CL:0002031!1.08e-49!120;CL:0000988!3.42e-49!177;CL:0002032!7.63e-46!161;CL:0000837!7.63e-46!161;CL:0002009!1.25e-38!61;CL:0002194!1.23e-36!59;CL:0000576!1.23e-36!59;CL:0000040!1.23e-36!59;CL:0000559!1.23e-36!59;CL:0000473!1.84e-36!48;CL:0000234!1.84e-36!48;CL:0000557!6.28e-35!67;CL:0000860!7.79e-34!42;CL:0002057!7.79e-34!42;CL:0000839!1.85e-30!66;CL:0000766!4.47e-30!72;CL:0000763!8.04e-27!108;CL:0000049!8.04e-27!108;CL:0000945!2.29e-20!24;CL:0000826!2.29e-20!24;CL:0000542!4.07e-17!53;CL:0000051!4.07e-17!53;CL:0000838!1.72e-16!52;CL:0002242!5.57e-16!55;CL:0000236!1.34e-13!14;CL:0000325!2.63e-13!87;CL:0000451!1.28e-11!10;CL:0000990!4.92e-10!8;CL:0002393!8.87e-08!9;CL:0002397!8.87e-08!9;CL:0000840!7.41e-07!5;CL:0001029!7.41e-07!5;CL:0000453!8.99e-07!5;CL:0000080!9.14e-07!6;CL:0000134!9.28e-07!354|ontology_enrichment_disease=DOID:0060058!3.42e-07!10|ontology_enrichment_uberon=UBERON:0002390!3.15e-46!98;UBERON:0003061!3.15e-46!98;UBERON:0002193!4.84e-42!108;UBERON:0002371!2.30e-31!76;UBERON:0002405!3.54e-31!93;UBERON:0001474!2.23e-27!82;UBERON:0007023!2.34e-25!114;UBERON:0004765!5.97e-23!90;UBERON:0001434!5.79e-20!100;UBERON:0003081!9.11e-13!203;UBERON:0000178!2.91e-12!15;UBERON:0000179!2.91e-12!15;UBERON:0000463!2.91e-12!15|pathway_enrichment=9.01000184573147e-06;0.00570333116834802;2;50;Type II interferon signaling (IFNG) (Wikipathways):WP619!6.25100917324437e-05;0.0197844440333184;2;131;IL-5 up reg. targets 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.455626,0.0086299,0.454846,0.350305,0.0875262,0.147486,0.117583,0.103076,0.518238,0.40865,0.634608,0.324846,0.25829,0.215261,0.235004,0.133496,0.433115,0.331422,0.440492,0.397558,0.266168,0.504119,0.0562494,0.371725,0.334024,0.500457,0.316975,0.435107,0.26559,0.378345,0.380153,0.160696,0.502341,0.507413,0.412407,0.42955,0.418893,0.300222,0.393729,0.487504,0.0342258,0.447581,0.482721,0.35808,0.406625,0.296254,0.0939442,0.135855,0.327684,0.279523,0.499937,0.444635,0.356463,0.364875,0.211724,0.409573,0.215534,0.536787,0.436872,0.181464,0.40945,0.231548,0.120636,0.121001,0.317719,0.172653,0.0924531,0.120918,0.593272,0.507382,0.425328,0.384398,0.462521,0.0873107,0.179489,0.214126,0.143317,0.261663,0.14273,0.227254,0.147968,0.168955,0.274981,0.236422,0.0999117,0.149301,0.196723,0.0836477,0.287028,0.413461,0.558766,0.545381,0.262234,0.299959,0.509613,0.498355,0.0966304,0.452427,0.56256,0.494497,0.366448,0.540845,0.161573,0.280842,0.335456,0.416632,0.404559,0.545676,0.467154,0.065788,0.249647,0.43669,0.446356,0.248584,0.397145,0.390152,0.537963,0.540199,0.00497189,0.342785,0.447064,0.20487,0.603936,0.449548,0.0179022,0.209566,0.189123,0.588995,0.355645,0.332105,0.0389799,0.158122,0.0387004,0.220023,0.444217,0.363335,0.329186,0.00274698,0.493369,0.416144,0.281368|tfbs_overrepresentation_for_novel_motifs=0.392069,0.100351,0.384703,0.529489,0.90845,0.52784,0.604235,0.226729,0.637583,0.200685,0.497563,0.647852,0.541517,0.592674,1.62257,0.365029,0.827563,0.28906,0.19568,0.0986842,0.384762,0.498384,0.520063,0.338096,1.09974,0.670692,0.49486,0.517892,0.346214,0.459534,0.475674,0.864517,0.714156,0.186138,0.309012,0.71891,0.825031,0.529001,0.282922,0.207499,0.307642,1.16235,0.254304,1.61728,0.0257952,1.06715,0.60533,0.486696,0.0670664,0.346342,0.684981,1.49721,0.373994,0.941629,1.09491,0.595623,0.924875,0.562713,0.897759,0.561701,0.905643,0.60771,0.638689,0.799729,0.625758,1.80489,1.18348,1.55228,0.854088,1.38987,0.4462,1.22295,0.744055,1.0929,0.179863,0.503161,1.47572,0.782748,0.850825,0.424224,0.200147,0.798651,0.625403,0.229431,1.04131,0.0324537,0.662518,0.146388,0.711163,1.65172,1.27705,1.01423,0.881388,0.26423,0.343884,0.277058,0.566252,0.924148,0.715799,0.132387,0.776034,0.875714,0.918549,0.831244,0.753567,0.493026,0.815341,0.589207,1.09919,0.327379,0.395884,0.915771,0.379203,0.507004,1.22894,0.304323,0.155979,0.474472,0.762789,0.26701,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,0.597853,0.886402,1.12733,0.76179,1.01492,5.36988,1.14174,0.633392,1.28996,0.854586,0.469685,0.518459,1.24743,2.10682,1.70417,2.71195,0.59959,0.920609,0.755332,0.554217,0.738579,1.94751,0.456039,0.26104,0.345641,0.0685123,1.0153,0.216774,0.607223,1.42052,0.694887,0.329354,0.430431,0.401655,1.2088,0.996724,3.27972,0.404861,0.7715,0.624608,0.24928,0.602897,0.212606|tfbs_overrepresentation_jaspar=MA0003.1;0.110456,MA0004.1;0.502801,MA0006.1;0.341337,MA0007.1;0.483857,MA0009.1;0.973289,MA0014.1;0.0723474,MA0017.1;0.380797,MA0019.1;0.652951,MA0024.1;0.867125,MA0025.1;1.10816,MA0027.1;2.59001,MA0028.1;0.35747,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;0.120314,MA0050.1;1.22833,MA0051.1;0.602745,MA0052.1;0.896548,MA0055.1;1.01052,MA0056.1;0,MA0057.1;0.115382,MA0058.1;0.406232,MA0059.1;0.404929,MA0060.1;0.224688,MA0061.1;1.09187,MA0063.1;0,MA0066.1;0.607474,MA0067.1;1.29359,MA0068.1;0.488375,MA0069.1;0.958358,MA0070.1;0.947018,MA0071.1;0.567661,MA0072.1;0.942461,MA0073.1;0.215865,MA0074.1;0.60198,MA0076.1;0.422297,MA0077.1;0.934645,MA0078.1;1.67751,MA0081.1;0.405093,MA0083.1;2.24713,MA0084.1;1.48179,MA0087.1;0.939982,MA0088.1;0.0723293,MA0089.1;0,MA0090.1;0.436918,MA0091.1;0.505453,MA0092.1;1.17914,MA0093.1;0.344385,MA0095.1;0,MA0098.1;0,MA0100.1;0.621149,MA0101.1;0.918548,MA0103.1;0.332048,MA0105.1;0.695228,MA0106.1;0.648997,MA0107.1;1.3795,MA0108.2;0.806528,MA0109.1;0,MA0111.1;0.45062,MA0113.1;0.665691,MA0114.1;0.269076,MA0115.1;1.21667,MA0116.1;0.760835,MA0117.1;1.01134,MA0119.1;2.6796,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;1.491,MA0139.1;0.547495,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;0.0127148,MA0147.1;0.281049,MA0148.1;2.2535,MA0149.1;0.555119,MA0062.2;0.193221,MA0035.2;0.564239,MA0039.2;0.128723,MA0138.2;0.704862,MA0002.2;0.213296,MA0137.2;0.36398,MA0104.2;0.223944,MA0047.2;2.60575,MA0112.2;0.0758925,MA0065.2;0.0828768,MA0150.1;0.430951,MA0151.1;0,MA0152.1;0.571637,MA0153.1;1.07307,MA0154.1;0.335384,MA0155.1;0.071478,MA0156.1;0.36627,MA0157.1;0.749547,MA0158.1;0,MA0159.1;0.281681,MA0160.1;0.543522,MA0161.1;0,MA0162.1;0.0249953,MA0163.1;0.19677,MA0164.1;1.62495,MA0080.2;0.911393,MA0018.2;0.650405,MA0099.2;0.572,MA0079.2;0.478894,MA0102.2;1.51913,MA0258.1;0.245543,MA0259.1;0.289405,MA0442.1;0}}
|full_id=C1207_migratory_granulocyte_CD19_CD14_immature_adult_Dendritic
|id=C1207
}}

Latest revision as of 11:40, 17 September 2013


Full id: C1207_migratory_granulocyte_CD19_CD14_immature_adult_Dendritic



Phase1 CAGE Peaks

Hg19::chr15:45028225..45028238,+p13@TRIM69
Hg19::chr16:10971037..10971076,+p1@CIITA
Hg19::chr16:10971077..10971090,+p2@CIITA
Hg19::chr16:10971094..10971117,+p3@CIITA
Hg19::chr16:10971144..10971153,+p4@CIITA
Hg19::chr16:11004975..11004985,+p@chr16:11004975..11004985
+
Hg19::chr4:185395590..185395627,-p3@IRF2


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

p.valueFDRnGenesnPathwayName
9.01000184573147e-060.00570333116834802250Type II interferon signaling (IFNG) (Wikipathways):WP619
6.25100917324437e-050.01978444403331842131IL-5 up reg. targets (Netpath):NetPath_17



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:0003702RNA polymerase II transcription factor activity0.0164432371661441
GO:0043130ubiquitin binding0.0386029895776261
GO:0032182small conjugating protein binding0.0386029895776261



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
leukocyte4.25e-57136
nongranular leukocyte1.83e-56115
hematopoietic stem cell8.48e-50168
angioblastic mesenchymal cell8.48e-50168
hematopoietic lineage restricted progenitor cell1.08e-49120
hematopoietic cell3.42e-49177
hematopoietic oligopotent progenitor cell7.63e-46161
hematopoietic multipotent progenitor cell7.63e-46161
macrophage dendritic cell progenitor1.25e-3861
monopoietic cell1.23e-3659
monocyte1.23e-3659
monoblast1.23e-3659
promonocyte1.23e-3659
defensive cell1.84e-3648
phagocyte1.84e-3648
granulocyte monocyte progenitor cell6.28e-3567
classical monocyte7.79e-3442
CD14-positive, CD16-negative classical monocyte7.79e-3442
myeloid lineage restricted progenitor cell1.85e-3066
myeloid leukocyte4.47e-3072
myeloid cell8.04e-27108
common myeloid progenitor8.04e-27108
lymphocyte of B lineage2.29e-2024
pro-B cell2.29e-2024
lymphocyte4.07e-1753
common lymphoid progenitor4.07e-1753
lymphoid lineage restricted progenitor cell1.72e-1652
nucleate cell5.57e-1655
B cell1.34e-1314
stuff accumulating cell2.63e-1387
dendritic cell1.28e-1110
conventional dendritic cell4.92e-108
intermediate monocyte8.87e-089
CD14-positive, CD16-positive monocyte8.87e-089
immature conventional dendritic cell7.41e-075
common dendritic progenitor7.41e-075
Langerhans cell8.99e-075
circulating cell9.14e-076
mesenchymal cell9.28e-07354
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.15e-4698
blood island3.15e-4698
hemolymphoid system4.84e-42108
bone marrow2.30e-3176
immune system3.54e-3193
bone element2.23e-2782
adult organism2.34e-25114
skeletal element5.97e-2390
skeletal system5.79e-20100
lateral plate mesoderm9.11e-13203
blood2.91e-1215
haemolymphatic fluid2.91e-1215
organism substance2.91e-1215
Disease
Ontology termp-valuen
lymphoma3.42e-0710


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)
MA0003.10.110456
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.10.0723474
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
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
MA0048.10.120314
MA0050.11.22833
MA0051.10.602745
MA0052.10.896548
MA0055.11.01052
MA0056.10
MA0057.10.115382
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.11.09187
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.488375
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.215865
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.11.67751
MA0081.10.405093
MA0083.12.24713
MA0084.11.48179
MA0087.10.939982
MA0088.10.0723293
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.11.17914
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.918548
MA0103.10.332048
MA0105.10.695228
MA0106.10.648997
MA0107.11.3795
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.10.760835
MA0117.11.01134
MA0119.12.6796
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.11.491
MA0139.10.547495
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.276317
MA0146.10.0127148
MA0147.10.281049
MA0148.12.2535
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.20.128723
MA0138.20.704862
MA0002.20.213296
MA0137.20.36398
MA0104.20.223944
MA0047.22.60575
MA0112.20.0758925
MA0065.20.0828768
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.335384
MA0155.10.071478
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.10.0249953
MA0163.10.19677
MA0164.11.62495
MA0080.20.911393
MA0018.20.650405
MA0099.20.572
MA0079.20.478894
MA0102.21.51913
MA0258.10.245543
MA0259.10.289405
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
BATF#10538517.39842985164552.2818035468994e-068.14454137507269e-05
BCL11A#53335416.21111720206124.9553880252627e-050.00084897600060763
E2F1#186953.505278010628090.005090553587915050.0236890044186722
EBF1#187945.089409626610860.004198233162502420.0199944946535907
FAM48A#555784660.0964285714291.88892317757448e-112.27540078134604e-09
IRF3#3661426.84682983513696.81330236493166e-060.000198154966775577
IRF4#3662412.52257867813950.0001356731131035550.00177652510775103
MEF2A#4205513.38802207831728.2817757531295e-060.000229001953370689
NFKB1#479053.92004530299560.003036581424484610.0161188069830621
PAX5#507954.763975379412740.001218821047007470.00820024810464555
POU2F2#545256.504374326958950.0002767851340330550.00294820628386316
REST#597845.514302123501730.003115641375761960.0163769927849013
RXRA#6256411.47120979379040.0001906958571785010.00230510238748443
SMC3#912648.597104482818770.0005798466280161370.00486688113665333
SP1#666754.070272412957780.002549206128991580.0141097323072633
SPI1#668867.032277293019482.05436318006376e-050.000455145600684511
TCF12#693857.596046358704590.0001311126373938080.00172437636780908
TCF7L2#693457.692983259383820.0001233198850154260.00165928954794203
YY1#752853.507979107038470.005072570672808980.0236147904295934
ZNF143#770247.714786601273090.0008771969606613480.00654149042302824



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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