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{{Coexpression_clusters
{
|full_id=C168_Mast_CD14_immature_Basophils_Eosinophils_CD34_Peripheral
 

Latest revision as of 10:47, 17 September 2013


Full id: C168_Mast_CD14_immature_Basophils_Eosinophils_CD34_Peripheral



Phase1 CAGE Peaks

Hg19::chr10:126847337..126847340,+p@chr10:126847337..126847340
+
Hg19::chr10:127751126..127751139,-p@chr10:127751126..127751139
-
Hg19::chr10:17270214..17270247,+p5@VIM
Hg19::chr10:17270313..17270321,+p17@VIM
Hg19::chr10:17278167..17278185,+p12@VIM
Hg19::chr10:3846319..3846333,+p@chr10:3846319..3846333
+
Hg19::chr10:63805867..63805883,-p@chr10:63805867..63805883
-
Hg19::chr11:72470335..72470363,+p@chr11:72470335..72470363
+
Hg19::chr11:72470426..72470435,+p@chr11:72470426..72470435
+
Hg19::chr11:75051987..75052000,+p@chr11:75051987..75052000
+
Hg19::chr12:51787972..51787981,-p@chr12:51787972..51787981
-
Hg19::chr12:52432402..52432424,-p@chr12:52432402..52432424
-
Hg19::chr12:52444929..52444945,-p@chr12:52444929..52444945
-
Hg19::chr14:102553761..102553785,+p@chr14:102553761..102553785
+
Hg19::chr14:105143676..105143707,+p@chr14:105143676..105143707
+
Hg19::chr16:2560210..2560219,+p@chr16:2560210..2560219
+
Hg19::chr16:29302386..29302409,-p@chr16:29302386..29302409
-
Hg19::chr16:87887433..87887438,+p@chr16:87887433..87887438
+
Hg19::chr16:87887504..87887535,-p@chr16:87887504..87887535
-
Hg19::chr17:38476709..38476744,+p@chr17:38476709..38476744
+
Hg19::chr17:40168540..40168552,+p16@NKIRAS2
Hg19::chr17:41437738..41437747,-p3@AK023939
Hg19::chr17:41437922..41437939,+p@chr17:41437922..41437939
+
Hg19::chr17:72270457..72270470,+p3@DNAI2
Hg19::chr17:80250634..80250653,-p1@ENST00000499745
p1@uc002kek.1
Hg19::chr18:2848716..2848718,+p@chr18:2848716..2848718
+
Hg19::chr18:74206012..74206020,+p@chr18:74206012..74206020
+
Hg19::chr19:10527253..10527264,-p@chr19:10527253..10527264
-
Hg19::chr19:10542701..10542730,-p@chr19:10542701..10542730
-
Hg19::chr19:12902103..12902116,-p@chr19:12902103..12902116
-
Hg19::chr19:13951943..13951963,-p@chr19:13951943..13951963
-
Hg19::chr19:2168550..2168572,+p@chr19:2168550..2168572
+
Hg19::chr19:2476825..2476847,+p12@GADD45B
Hg19::chr19:2477163..2477216,+p2@GADD45B
Hg19::chr19:2477661..2477696,+p5@GADD45B
Hg19::chr19:2495478..2495481,-p@chr19:2495478..2495481
-
Hg19::chr19:2546698..2546709,-p@chr19:2546698..2546709
-
Hg19::chr19:2546728..2546743,-p@chr19:2546728..2546743
-
Hg19::chr19:2547016..2547029,+p@chr19:2547016..2547029
+
Hg19::chr19:45947743..45947780,+p@chr19:45947743..45947780
+
Hg19::chr19:45959758..45959769,+p@chr19:45959758..45959769
+
Hg19::chr19:49377218..49377242,+p@chr19:49377218..49377242
+
Hg19::chr19:49377471..49377488,+p@chr19:49377471..49377488
+
Hg19::chr19:49378119..49378134,+p@chr19:49378119..49378134
+
Hg19::chr19:49379626..49379630,-p@chr19:49379626..49379630
-
Hg19::chr19:54692317..54692331,+p@chr19:54692317..54692331
+
Hg19::chr1:1136756..1136767,-p@chr1:1136756..1136767
-
Hg19::chr1:1136782..1136795,-p@chr1:1136782..1136795
-
Hg19::chr1:161469716..161469730,+p@chr1:161469716..161469730
+
Hg19::chr1:168148677..168148693,+p@chr1:168148677..168148693
+
Hg19::chr1:224522323..224522330,+p@chr1:224522323..224522330
+
Hg19::chr1:226850887..226850894,+p@chr1:226850887..226850894
+
Hg19::chr1:235111193..235111206,+p@chr1:235111193..235111206
+
Hg19::chr22:22171149..22171186,+p@chr22:22171149..22171186
+
Hg19::chr22:44423030..44423043,+p@chr22:44423030..44423043
+
Hg19::chr22:50364701..50364715,+p@chr22:50364701..50364715
+
Hg19::chr2:145271497..145271510,+p@chr2:145271497..145271510
+
Hg19::chr2:157190984..157191018,-p@chr2:157190984..157191018
-
Hg19::chr2:157191084..157191095,-p@chr2:157191084..157191095
-
Hg19::chr2:157191294..157191331,+p@chr2:157191294..157191331
+
Hg19::chr2:157199008..157199023,-p3@NR4A2
Hg19::chr2:208394431..208394446,+p9@CREB1
Hg19::chr2:218767650..218767673,+p@chr2:218767650..218767673
+
Hg19::chr2:232476619..232476634,-p@chr2:232476619..232476634
-
Hg19::chr2:28114069..28114081,-p3@LOC100302650
Hg19::chr3:15837528..15837578,-p@chr3:15837528..15837578
-
Hg19::chr3:15839395..15839435,-p2@ANKRD28
Hg19::chr3:20227970..20227982,+p@chr3:20227970..20227982
+
Hg19::chr3:5020551..5020568,-p@chr3:5020551..5020568
-
Hg19::chr3:5048638..5048647,+p@chr3:5048638..5048647
+
Hg19::chr3:71150221..71150222,-p@chr3:71150221..71150222
-
Hg19::chr3:72532128..72532133,-p@chr3:72532128..72532133
-
Hg19::chr4:170581182..170581201,-p@chr4:170581182..170581201
-
Hg19::chr4:48533348..48533351,+p@chr4:48533348..48533351
+
Hg19::chr5:172185174..172185217,-p@chr5:172185174..172185217
-
Hg19::chr5:179245946..179245962,-p@chr5:179245946..179245962
-
Hg19::chr5:179245976..179245995,-p@chr5:179245976..179245995
-
Hg19::chr5:95297924..95297956,+p@chr5:95297924..95297956
+
Hg19::chr5:96038250..96038274,-p@chr5:96038250..96038274
-
Hg19::chr6:130005395..130005398,+p@chr6:130005395..130005398
+
Hg19::chr6:134610234..134610241,+p@chr6:134610234..134610241
+
Hg19::chr6:134617297..134617322,+p@chr6:134617297..134617322
+
Hg19::chr6:138187511..138187525,+p@chr6:138187511..138187525
+
Hg19::chr6:138200216..138200227,+p@chr6:138200216..138200227
+
Hg19::chr6:14711644..14711656,+p@chr6:14711644..14711656
+
Hg19::chr6:14712257..14712276,-p@chr6:14712257..14712276
-
Hg19::chr6:14712846..14712851,+p@chr6:14712846..14712851
+
Hg19::chr7:37726701..37726704,-p@chr7:37726701..37726704
-
Hg19::chr7:38409431..38409457,-p@chr7:38409431..38409457
-
Hg19::chr7:643862..643881,-p@chr7:643862..643881
-
Hg19::chr7:963120..963124,-p14@ADAP1
Hg19::chr8:103819280..103819302,+p2@ENST00000405813
p2@ENST00000517910
p2@uc003ykw.1
Hg19::chr8:12624204..12624207,-p@chr8:12624204..12624207
-
Hg19::chr8:2075387..2075430,-p@chr8:2075387..2075430
-
Hg19::chr8:29260411..29260429,+p@chr8:29260411..29260429
+
Hg19::chr8:38627853..38627874,-p@chr8:38627853..38627874
-
Hg19::chr8:81397624..81397636,-p@chr8:81397624..81397636
-
Hg19::chr9:102581773..102581785,-p@chr9:102581773..102581785
-
Hg19::chr9:107814448..107814480,+p@chr9:107814448..107814480
+
Hg19::chr9:108061944..108061969,+p@chr9:108061944..108061969
+
Hg19::chr9:127048403..127048433,+p9@NEK6
Hg19::chr9:132245474..132245496,-p@chr9:132245474..132245496
-
Hg19::chr9:33165989..33166005,+p@chr9:33165989..33166005
+


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:0007243protein kinase cascade0.0148895998999346
GO:0007249I-kappaB kinase/NF-kappaB cascade0.0346361068868663
GO:0042069regulation of catecholamine metabolic process0.0346361068868663
GO:0035085cilium axoneme0.0346361068868663
GO:0042053regulation of dopamine metabolic process0.0346361068868663
GO:0042384cilium biogenesis0.0346361068868663
GO:0000185activation of MAPKKK activity0.0346361068868663
GO:0044441cilium part0.0424204890790849
GO:0048468cell development0.0427417232591816
GO:0030071regulation of mitotic metaphase/anaphase transition0.0427417232591816
GO:0042417dopamine metabolic process0.0427417232591816
GO:0000186activation of MAPKK activity0.0427417232591816
GO:0007091mitotic metaphase/anaphase transition0.0427417232591816
GO:0007165signal transduction0.0427417232591816
GO:0005858axonemal dynein complex0.0427417232591816
GO:0045103intermediate filament-based process0.0427417232591816
GO:0044447axoneme part0.0427417232591816
GO:0007154cell communication0.048522230700641
GO:0005930axoneme0.0489452501682876
GO:0032502developmental process0.0489452501682876



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
classical monocyte4.74e-11942
CD14-positive, CD16-negative classical monocyte4.74e-11942
defensive cell5.99e-10348
phagocyte5.99e-10348
granulocyte monocyte progenitor cell1.89e-9567
myeloid leukocyte1.48e-9272
myeloid lineage restricted progenitor cell3.55e-8866
macrophage dendritic cell progenitor4.12e-8661
monopoietic cell2.10e-8059
monocyte2.10e-8059
monoblast2.10e-8059
promonocyte2.10e-8059
leukocyte8.36e-72136
hematopoietic lineage restricted progenitor cell1.42e-64120
myeloid cell3.39e-64108
common myeloid progenitor3.39e-64108
nongranular leukocyte1.14e-58115
hematopoietic stem cell5.13e-56168
angioblastic mesenchymal cell5.13e-56168
hematopoietic cell1.35e-52177
stuff accumulating cell2.04e-5287
hematopoietic oligopotent progenitor cell5.51e-52161
hematopoietic multipotent progenitor cell5.51e-52161
mesenchymal cell1.68e-20354
connective tissue cell7.13e-20361
motile cell1.15e-17386
stem cell5.33e-15441
multi fate stem cell5.83e-15427
somatic stem cell1.38e-14433
intermediate monocyte2.88e-139
CD14-positive, CD16-positive monocyte2.88e-139
histamine secreting cell5.08e-125
biogenic amine secreting cell5.08e-125
granulocytopoietic cell5.08e-125
mast cell5.08e-125
mast cell progenitor5.08e-125
basophil mast progenitor cell5.08e-125
basophil5.82e-113
natural killer cell1.01e-103
pro-NK cell1.01e-103
single nucleate cell1.28e-103
mononuclear cell1.28e-103
CD1a-positive Langerhans cell1.08e-072
immature CD1a-positive Langerhans cell1.08e-072
somatic cell1.82e-07588
Uber Anatomy
Ontology termp-valuen
bone marrow4.75e-8376
bone element2.82e-7682
hematopoietic system1.28e-7198
blood island1.28e-7198
skeletal element1.24e-6890
immune system4.21e-6693
hemolymphoid system4.85e-64108
skeletal system8.83e-61100
musculoskeletal system2.81e-32167
lateral plate mesoderm4.52e-29203
connective tissue5.11e-19371
mesoderm7.50e-15315
mesoderm-derived structure7.50e-15315
presumptive mesoderm7.50e-15315


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)
MA0003.10.700933
MA0004.10.958978
MA0006.10.39153
MA0007.10.626928
MA0009.10.0921642
MA0014.10.577565
MA0017.10.402482
MA0019.10.504641
MA0024.10.198986
MA0025.10.923504
MA0027.11.42991
MA0028.10.210899
MA0029.10.0601147
MA0030.10.453645
MA0031.10.974905
MA0038.10.0359403
MA0040.10.223045
MA0041.10.218259
MA0042.10.00930795
MA0043.10.307993
MA0046.10.295342
MA0048.10.161668
MA0050.10.451309
MA0051.10.381857
MA0052.12.96432
MA0055.10.443248
MA0056.10
MA0057.11.52054
MA0058.11.15615
MA0059.10.899343
MA0060.10.00930125
MA0061.16.92534
MA0063.10
MA0066.13.39227
MA0067.11.36704
MA0068.10.559506
MA0069.10.086095
MA0070.10.987203
MA0071.10.305567
MA0072.10.273833
MA0073.11.572
MA0074.10.214065
MA0076.10.156064
MA0077.10.0769176
MA0078.10.39005
MA0081.10.683036
MA0083.11.08534
MA0084.10.409533
MA0087.10.271192
MA0088.10.244357
MA0089.10
MA0090.10.181103
MA0091.10.501238
MA0092.10.239454
MA0093.11.17269
MA0095.10
MA0098.10
MA0100.10.660407
MA0101.12.73593
MA0103.10.0902359
MA0105.17.3946
MA0106.10.494419
MA0107.15.20566
MA0108.20.616283
MA0109.10
MA0111.10.4976
MA0113.10.158907
MA0114.10.944847
MA0115.10.220284
MA0116.10.177999
MA0117.12.33979
MA0119.11.88232
MA0122.10.383492
MA0124.10.567147
MA0125.10.450579
MA0130.10
MA0131.10.427326
MA0132.10
MA0133.10
MA0135.10.698856
MA0136.10.637491
MA0139.10.317558
MA0140.10.716044
MA0141.10.33669
MA0142.10.298046
MA0143.10.538664
MA0144.11.4431
MA0145.10.0627909
MA0146.10.500399
MA0147.10.387377
MA0148.10.120048
MA0149.10.0666029
MA0062.20.266483
MA0035.20.482582
MA0039.20.755864
MA0138.20.96134
MA0002.20.49005
MA0137.20.659786
MA0104.20.715033
MA0047.20.268265
MA0112.21.77209
MA0065.22.04963
MA0150.14.03264
MA0151.10
MA0152.10.3138
MA0153.10.138305
MA0154.10.648737
MA0155.10.533937
MA0156.10.672397
MA0157.10.485583
MA0158.10
MA0159.10.681517
MA0160.10.137225
MA0161.10
MA0162.10.506222
MA0163.12.72681
MA0164.10.172403
MA0080.20.735795
MA0018.21.43857
MA0099.25.16974
MA0079.25.42527
MA0102.20.439224
MA0258.10.332955
MA0259.10.211125
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#467132.83515794988460.0006727927181139720.0054297039399664
BATF#10538214.966153763479381.16077477380197e-091.06435607200267e-07
BCL11A#53335267.161221676638681.92719180107166e-153.53732837455401e-13
BCL3#60282.68327012067870.01027586921989930.0381867885517032
BHLHE40#855393.920838076920360.0005145406138027210.00445885389685881
BRCA1#672112.155597447334580.01324098343438840.0468437745640084
CCNT2#905332.030045165434633.15721512839807e-050.000634230411222863
CEBPB#1051262.012134352149950.0003341858312318010.00340208929018599
CHD2#1106191.908120716973010.004429718625851930.0209716855650657
E2F6#1876311.510017744491450.009137929446383090.0345668518762289
EBF1#1879302.594116557253116.32812689574944e-072.88730120080898e-05
EGR1#1958401.937156930023358.91683125747582e-060.000240326436051488
ELF1#1997381.570948761501810.001543646797760670.00981175387446455
EP300#2033432.827956254636873.26974537581366e-113.76503789751492e-09
FOS#2353403.494351576269673.01982620722442e-134.486310515737e-11
FOSL1#8061259.639218377760448.42341747685346e-181.82517281714751e-15
FOSL2#2355193.123046713462848.93730378292971e-060.000240753951453546
FOXA1#3169171.828972191646140.01072690529354330.0395938244195925
GATA1#2623263.422990405231182.14782927650375e-081.52285907541599e-06
GATA2#2624232.845955629822744.0275252107329e-060.000130024947599299
GATA3#262592.379889778784990.01370978107303590.0482814885853386
HDAC2#3066263.386467244196922.66652060204438e-081.83578605904359e-06
HDAC8#55869215.0793016235620.007962358263699860.0321943761015311
HEY1#23462411.608199541430430.0005350770464764240.0046241548743857
HMGN3#9324241.905681022916640.001293556034646570.00866900017341201
HNF4A#3172112.470438776626120.005040227491175830.0234799196641649
HNF4G#317492.512434978039040.009899330589638530.0371390253413053
IRF4#3662112.340384850040640.007457311471562180.0307608575685644
JUN#3725374.494899806955771.54574387035481e-152.86233943397139e-13
JUNB#3726236.83538399199892.73705844172212e-134.09535310308047e-11
JUND#3727442.988011780993452.53603723070725e-123.42197922917099e-10
MAFK#7975133.420480881473680.000111739712223130.00154467025875201
MAX#4149251.566154249759010.01334919526105080.0471866446851987
MEF2A#4205254.54932789069031.39234497305929e-101.48231515434596e-08
MEF2C#4208135.214054450525371.35547938097667e-065.33000418184571e-05
MXI1#4601181.740857177841430.01392549597686770.0488944318146946
NFE2#477864.497335571939560.002307536895626990.013090540241303
NFKB1#4790392.078004597510292.17673777088325e-067.83108219267226e-05
NR3C1#2908243.488859805321875.98045133211694e-083.71781164687477e-06
PAX5#5079291.877838838875310.0004432087831974670.00412809079714263
POLR2A#5430821.709622917259825.99081800988995e-127.73393129956609e-10
PRDM1#63956.399560960070910.001181748512050720.00801745049045505
RFX5#5993171.988490136527350.004790930152026120.0225123708335938
RXRA#6256173.313286323934621.3365721109624e-050.000326145454899071
SIRT6#5154845.966539960777670.004743562571040140.0223430718151293
SMARCB1#6598152.658162492401570.0004974201267148670.00439658603706618
SMARCC1#6599114.663077208892682.59187428613474e-050.000560092610324076
SMC3#9126172.483144255959790.0004448036491960320.00414072986169751
SP1#6667351.936343186746914.47669723279248e-050.00079325039412218
SPI1#6688231.832033404815750.002782336895330850.0152409778145106
SRF#6722152.009297805170070.007375773761196420.0304835154667824
STAT1#6772112.211383130768850.01111016394843030.0408611618343525
STAT3#6774262.655398931320492.90859979083336e-069.9826241720291e-05
TAL1#6886123.479838836206630.0001782095646655080.00216192690487873
TBP#6908481.727427116316761.5821530720177e-050.000370157895807474
TCF12#6938262.684428033561622.3806799689872e-068.42833339935777e-05
TCF7L2#6934222.300426062029340.0001700029165921630.00207684344437583
TFAP2A#7020182.886751638007864.48589510610971e-050.00079420647395659
TFAP2C#7022232.41371124297855.63626269724667e-050.000944856564747585
USF1#7391362.223436640577541.34941661350107e-065.31216440623589e-05
USF2#7392192.396618935109920.0003070670771912570.00316457257497312
YY1#7528321.525800621313820.006788290413490210.0287880075727658
ZBTB7A#51341322.284088328660473.84483790774418e-060.000125563172685083



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

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