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Coexpression cluster:C1210: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.392069,0.247072,0.384703,0.529489,0.343148,0.52784,0.604235,0.226729,0.224331,1.65644,0.497563,0.647852,0.541517,0.592674,0.341795,0.365029,0.827563,0.28906,0.569568,0.32524,0.384762,0.498384,0.520063,0.338096,0.430372,1.60904,0.164928,0.517892,0.915262,0.459534,0.475674,0.864517,0.257226,1.04347,1.50609,0.232776,0.305874,0.529001,0.282922,0.597792,0.307642,0.459366,0.541549,0.902101,0.794027,1.87706,0.60533,0.486696,0.511111,0.346342,1.63878,0.617179,0.117127,0.941629,1.09491,0.595623,0.350547,0.562713,0.150585,0.561701,0.905643,0.60771,0.638689,0.799729,1.51519,0.76514,1.18348,1.55228,0.854088,1.38987,1.13397,0.232216,0.744055,1.0929,0.531388,0.503161,0.156354,0.782748,0.850825,0.424224,0.200147,0.798651,0.625403,0.229431,1.04131,1.28944,0.322252,0.448771,0.711163,1.65172,1.27705,1.01423,0.881388,0.26423,0.910085,0.277058,1.07593,0.924148,0.715799,0.413337,0.28424,0.875714,0.918549,0.831244,0.753567,0.493026,0.815341,0.589207,0.43012,1.57162,0.395884,0.915771,0.988112,1.2644,1.22894,0.304323,0.358137,0.474472,0.762789,0.26701,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,0.597853,0.886402,1.12733,1.39367,1.01492,0.47854,1.14174,0.633392,1.28996,0.140417,0.469685,0.518459,1.24743,2.10682,1.70417,1.21002,0.59959,0.920609,0.755332,1.36465,0.738579,1.94751,0.456039,1.33119,0.345641,0.887646,1.0153,0.619774,0.607223,1.42052,0.694887,0.329354,0.430431,1.83026,1.2088,0.996724,0.850033,0.404861,0.7715,0.624608,0.695791,0.602897,0.594713
|tfbs_overrepresentation_jaspar=MA0003.1;1.35295,MA0004.1;1.25543,MA0006.1;0.341337,MA0007.1;1.21493,MA0009.1;0.973289,MA0014.1;2.12603,MA0017.1;0.991615,MA0019.1;0.652951,MA0024.1;0.867125,MA0025.1;1.10816,MA0027.1;2.59001,MA0028.1;1.67753,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;0.0407081,MA0056.1;0,MA0057.1;0.744639,MA0058.1;1.84591,MA0059.1;0.404929,MA0060.1;0.638423,MA0061.1;0.198335,MA0063.1;0,MA0066.1;0.607474,MA0067.1;1.29359,MA0068.1;0.162298,MA0069.1;0.958358,MA0070.1;0.947018,MA0071.1;0.567661,MA0072.1;0.942461,MA0073.1;0.336328,MA0074.1;0.60198,MA0076.1;0.422297,MA0077.1;0.934645,MA0078.1;0.703614,MA0081.1;0.405093,MA0083.1;0.980893,MA0084.1;1.48179,MA0087.1;0.939982,MA0088.1;0.538456,MA0089.1;0,MA0090.1;0.436918,MA0091.1;0.505453,MA0092.1;0.467172,MA0093.1;1.63168,MA0095.1;0,MA0098.1;0,MA0100.1;0.621149,MA0101.1;0.918548,MA0103.1;0.332048,MA0105.1;0.340955,MA0106.1;0.648997,MA0107.1;0.752965,MA0108.2;0.806528,MA0109.1;0,MA0111.1;0.45062,MA0113.1;0.665691,MA0114.1;2.09327,MA0115.1;1.21667,MA0116.1;0.277571,MA0117.1;1.01134,MA0119.1;0.388712,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;0.614215,MA0139.1;0.186511,MA0140.1;0.564957,MA0141.1;0.403171,MA0142.1;0.777365,MA0143.1;0.66587,MA0144.1;0.254954,MA0145.1;0.581146,MA0146.1;0.162729,MA0147.1;1.40486,MA0148.1;0.528066,MA0149.1;0.555119,MA0062.2;0.563664,MA0035.2;0.564239,MA0039.2;2.22341,MA0138.2;0.704862,MA0002.2;0.213296,MA0137.2;0.36398,MA0104.2;1.85658,MA0047.2;0.636643,MA0112.2;0.262665,MA0065.2;2.03906,MA0150.1;0.430951,MA0151.1;0,MA0152.1;0.571637,MA0153.1;1.07307,MA0154.1;0.335384,MA0155.1;0.534073,MA0156.1;0.36627,MA0157.1;0.749547,MA0158.1;0,MA0159.1;0.281681,MA0160.1;0.543522,MA0161.1;0,MA0162.1;2.01861,MA0163.1;0.382702,MA0164.1;0.678332,MA0080.2;0.344472,MA0018.2;1.56673,MA0099.2;0.572,MA0079.2;2.37344,MA0102.2;1.51913,MA0258.1;0.245543,MA0259.1;0.787775,MA0442.1;0
}}
}}

Revision as of 19:46, 22 January 2013


Full id: C1210_CD14_Mast_immature_Eosinophils_Basophils_Neutrophils_CD34



Phase1 CAGE Peaks

Hg19::chr15:52311403..52311461,+p1@MAPK6
Hg19::chr17:30677160..30677200,+p1@ZNF207
Hg19::chr1:94344686..94344748,-p1@DNTTIP2
Hg19::chr1:94344754..94344768,-p2@DNTTIP2
Hg19::chr2:178129358..178129403,-p5@NFE2L2
Hg19::chr5:131132637..131132648,-p2@FNIP1
Hg19::chr5:133561752..133561791,-p1@PPP2CA
p2@SKP1


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

GO IDGO nameFDR corrected p-value
GO:0050732negative regulation of peptidyl-tyrosine phosphorylation0.0370566280032591
GO:0042518negative regulation of tyrosine phosphorylation of Stat3 protein0.0370566280032591
GO:0042532negative regulation of tyrosine phosphorylation of STAT protein0.0370566280032591
GO:0046426negative regulation of JAK-STAT cascade0.0370566280032591
GO:0033239negative regulation of amine metabolic process0.0370566280032591
GO:0001933negative regulation of protein amino acid phosphorylation0.0370566280032591
GO:0045763negative regulation of amino acid metabolic process0.0370566280032591
GO:0042516regulation of tyrosine phosphorylation of Stat3 protein0.0370566280032591
GO:0046983protein dimerization activity0.0370566280032591
GO:0042503tyrosine phosphorylation of Stat3 protein0.0370566280032591
GO:0042326negative regulation of phosphorylation0.0370566280032591
GO:0042509regulation of tyrosine phosphorylation of STAT protein0.0370566280032591
GO:0045936negative regulation of phosphate metabolic process0.0370566280032591
GO:0046425regulation of JAK-STAT cascade0.039697686838835
GO:0007260tyrosine phosphorylation of STAT protein0.0416733700027195
GO:0000188inactivation of MAPK activity0.0416733700027195



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
leukocyte1.12e-34136
hematopoietic stem cell6.73e-31168
angioblastic mesenchymal cell6.73e-31168
myeloid leukocyte1.12e-2972
hematopoietic cell4.33e-28177
hematopoietic oligopotent progenitor cell4.51e-28161
hematopoietic multipotent progenitor cell4.51e-28161
hematopoietic lineage restricted progenitor cell5.79e-28120
granulocyte monocyte progenitor cell2.29e-2667
classical monocyte5.19e-2642
CD14-positive, CD16-negative classical monocyte5.19e-2642
myeloid lineage restricted progenitor cell1.36e-2566
nongranular leukocyte1.70e-25115
myeloid cell2.85e-24108
common myeloid progenitor2.85e-24108
macrophage dendritic cell progenitor1.10e-2361
defensive cell2.79e-2348
phagocyte2.79e-2348
monopoietic cell1.14e-2259
monocyte1.14e-2259
monoblast1.14e-2259
promonocyte1.14e-2259
stuff accumulating cell1.60e-1287
mesenchymal cell8.39e-10354
motile cell1.30e-09386
connective tissue cell9.79e-09361
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.12e-2298
blood island3.12e-2298
bone marrow1.03e-2176
bone element6.08e-2182
skeletal element6.96e-2090
skeletal system1.16e-16100
hemolymphoid system2.17e-16108
immune system7.55e-1593
connective tissue1.80e-08371
Disease
Ontology termp-valuen
carcinoma7.60e-08106
cancer9.09e-07235


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)
MA0003.11.35295
MA0004.11.25543
MA0006.10.341337
MA0007.11.21493
MA0009.10.973289
MA0014.12.12603
MA0017.10.991615
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.11.67753
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
MA0055.10.0407081
MA0056.10
MA0057.10.744639
MA0058.11.84591
MA0059.10.404929
MA0060.10.638423
MA0061.10.198335
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.336328
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.538456
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.11.63168
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.918548
MA0103.10.332048
MA0105.10.340955
MA0106.10.648997
MA0107.10.752965
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.12.09327
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.10.186511
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.581146
MA0146.10.162729
MA0147.11.40486
MA0148.10.528066
MA0149.10.555119
MA0062.20.563664
MA0035.20.564239
MA0039.22.22341
MA0138.20.704862
MA0002.20.213296
MA0137.20.36398
MA0104.21.85658
MA0047.20.636643
MA0112.20.262665
MA0065.22.03906
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.335384
MA0155.10.534073
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.12.01861
MA0163.10.382702
MA0164.10.678332
MA0080.20.344472
MA0018.21.56673
MA0099.20.572
MA0079.22.37344
MA0102.21.51913
MA0258.10.245543
MA0259.10.787775
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#467516.04512466143483.40064550879441e-060.000113469653767725
BHLHE40#8553212.82051815627930.009678410183733830.0364201009288383
BRCA1#672411.53384608184210.0001867121495693760.00225956317368205
CCNT2#90565.431029923110839.35028339706757e-050.00135837285812539
CHD2#110657.38858773865490.0001498689600820670.00193236596568037
E2F1#186964.206333612753710.0004135232017007640.00393763217199363
E2F4#187447.238891608733970.001117741430524870.00766586533113914
E2F6#187653.583682665498130.004598101897827240.0217255322162133
EGR1#195853.562985067721530.004722351211058930.0222592245399551
ELF1#199763.649798250406460.0009377479782620690.00679036685167525
ETS1#211345.559291955544190.003022564475303460.0160501124281177
GTF2B#2959313.69021282899610.0009761963170245720.00701575606618011
GTF2F1#296235.459854661467560.0132988216841570.0470260923606458
HEY1#2346274.040111043105715.68979821988558e-050.000950170828728223
HMGN3#932444.673455841914620.005751881099938870.0259087686619734
IRF1#365977.63716375356396.59398174986938e-072.98771739685296e-05
JUND#372754.996188529907880.0009734308600070920.00699684415611017
MAX#414954.608968220719370.001424337014033610.0091796564892722
MEF2A#420538.032813246990310.004516397834675020.0213539804181097
MXI1#460157.115408306256640.0001797256225248230.00217930619887031
MYC#460953.730201336863860.003821944222306690.0188701381663825
NFKB1#479064.704054363594720.000216115061401970.00247731762679841
NR3C1#290836.417009999074160.008497228015651550.0324321893332833
NRF1#489946.977302541549090.00128531428862220.00861929748230472
POLR2A#543072.147453176558070.004747636447610280.022340094748906
REST#597868.271453185252597.89289295030691e-060.000222790769415433
SIN3A#2594264.636186908698690.0002351678146357830.00256562116293184
SIX5#14791237.322878009482430.00586667625269160.0263315914373139
SP1#666754.070272412957780.002549206128991580.0141104801200844
SRF#672235.913076398071920.01066868130167450.0393928374214455
TAF1#687273.343046285745290.0002142336319622450.00246603618301609
TAF7#687969.799773775649072.89681485118392e-069.9487157593817e-05
TBP#690873.706770687096390.0001039672097505110.00145105324323582
TCF7L2#693446.154386607507050.002064676148138040.0119716140481561
USF2#739235.568084593601250.01259853435761050.0455554592588888
YY1#752864.209574928446160.000411683378865750.00392261658656692
ZBTB7A#5134144.201091033071940.00849410661287350.0324285714483804
ZEB1#693537.237899436090220.00606280792035710.0268325110769631



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C1210&oldid=2569721"