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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:28, 17 September 2013


Full id: C686_CD14_immature_CD19_Eosinophils_migratory_Mast_Basophils



Phase1 CAGE Peaks

Hg19::chr11:62572901..62572919,-p1@NXF1
Hg19::chr11:65153902..65153912,-p@chr11:65153902..65153912
-
Hg19::chr11:9482656..9482660,+p@chr11:9482656..9482660
+
Hg19::chr12:111020479..111020516,-p@chr12:111020479..111020516
-
Hg19::chr12:111020600..111020632,+p@chr12:111020600..111020632
+
Hg19::chr13:41635806..41635828,-p14@ELF1
Hg19::chr1:200638744..200638765,+p1@ENST00000422640
Hg19::chr1:6845035..6845053,-p1@ENST00000442889
Hg19::chr4:106394656..106394684,+p@chr4:106394656..106394684
+
Hg19::chr6:112126045..112126050,+p@chr6:112126045..112126050
+
Hg19::chr6:14117995..14118012,+p1@CD83
Hg19::chr7:151047008..151047012,-p@chr7:151047008..151047012
-


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:0016973poly(A)+ mRNA export from nucleus0.00794725374557758
GO:0050858negative regulation of antigen receptor-mediated signaling pathway0.00794725374557758
GO:0050860negative regulation of T cell receptor signaling pathway0.00794725374557758
GO:0042405nuclear inclusion body0.00794725374557758
GO:0016234inclusion body0.0105950906474368
GO:0050856regulation of T cell receptor signaling pathway0.0105950906474368
GO:0005487nucleocytoplasmic transporter activity0.0105950906474368
GO:0050854regulation of antigen receptor-mediated signaling pathway0.0132426936896461
GO:0050852T cell receptor signaling pathway0.0200070579879434
GO:0006406mRNA export from nucleus0.0211733427389052
GO:0050851antigen receptor-mediated signaling pathway0.0211733427389052
GO:0002429immune response-activating cell surface receptor signaling pathway0.0211733427389052
GO:0006405RNA export from nucleus0.0211733427389052
GO:0002768immune response-regulating cell surface receptor signaling pathway0.0211733427389052
GO:0002757immune response-activating signal transduction0.0211733427389052
GO:0002764immune response-regulating signal transduction0.0211733427389052
GO:0003729mRNA binding0.0211733427389052
GO:0006955immune response0.0228402138005044
GO:0001817regulation of cytokine production0.0228402138005044
GO:0051168nuclear export0.0232838193519774
GO:0002376immune system process0.027740075393911
GO:0002253activation of immune response0.0308132798303632
GO:0006959humoral immune response0.0308132798303632
GO:0051028mRNA transport0.0308132798303632
GO:0050778positive regulation of immune response0.0308132798303632
GO:0002684positive regulation of immune system process0.0308132798303632
GO:0005643nuclear pore0.0308132798303632
GO:0050658RNA transport0.0308132798303632
GO:0051236establishment of RNA localization0.0308132798303632
GO:0050657nucleic acid transport0.0308132798303632
GO:0006403RNA localization0.0308132798303632
GO:0046930pore complex0.0308132798303632
GO:0050776regulation of immune response0.0308132798303632
GO:0002682regulation of immune system process0.0308132798303632
GO:0015931nucleobase, nucleoside, nucleotide and nucleic acid transport0.0308132798303632
GO:0051240positive regulation of multicellular organismal process0.0308132798303632
GO:0044453nuclear membrane part0.0314082394328219
GO:0001816cytokine production0.0314082394328219
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.0376154392284251
GO:0031965nuclear membrane0.0391808275779859
GO:0006913nucleocytoplasmic transport0.0391808275779859
GO:0051169nuclear transport0.0391808275779859
GO:0005635nuclear envelope0.0475384409643424



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
leukocyte2.04e-62136
hematopoietic cell4.84e-54177
hematopoietic stem cell5.09e-54168
angioblastic mesenchymal cell5.09e-54168
hematopoietic lineage restricted progenitor cell3.08e-50120
hematopoietic oligopotent progenitor cell1.25e-49161
hematopoietic multipotent progenitor cell1.25e-49161
nongranular leukocyte9.26e-49115
classical monocyte2.91e-3942
CD14-positive, CD16-negative classical monocyte2.91e-3942
myeloid leukocyte3.09e-3672
granulocyte monocyte progenitor cell1.46e-3367
defensive cell8.41e-3348
phagocyte8.41e-3348
macrophage dendritic cell progenitor1.57e-3061
myeloid cell3.35e-30108
common myeloid progenitor3.35e-30108
myeloid lineage restricted progenitor cell1.33e-2966
monopoietic cell1.20e-2859
monocyte1.20e-2859
monoblast1.20e-2859
promonocyte1.20e-2859
lymphoid lineage restricted progenitor cell1.20e-1752
lymphocyte3.84e-1753
common lymphoid progenitor3.84e-1753
mesenchymal cell1.96e-16354
nucleate cell3.46e-1655
connective tissue cell1.31e-15361
stuff accumulating cell1.87e-1487
motile cell8.71e-13386
intermediate monocyte2.28e-099
CD14-positive, CD16-positive monocyte2.28e-099
lymphocyte of B lineage3.82e-0924
pro-B cell3.82e-0924
multi fate stem cell8.60e-08427
stem cell1.30e-07441
T cell1.67e-0725
pro-T cell1.67e-0725
dendritic cell1.71e-0710
somatic stem cell3.91e-07433
mature alpha-beta T cell5.28e-0718
alpha-beta T cell5.28e-0718
immature T cell5.28e-0718
mature T cell5.28e-0718
immature alpha-beta T cell5.28e-0718
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.26e-3398
blood island4.26e-3398
hemolymphoid system2.46e-29108
bone marrow3.41e-2976
immune system1.89e-2793
bone element5.15e-2682
skeletal element1.87e-2290
skeletal system2.85e-18100
connective tissue1.69e-14371
lateral plate mesoderm4.20e-10203


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)
MA0003.12.92196
MA0004.10.32225
MA0006.11.66321
MA0007.11.4951
MA0009.10.756202
MA0014.11.48847
MA0017.10.220105
MA0019.10.45566
MA0024.10.654931
MA0025.10.886436
MA0027.12.35633
MA0028.10.583404
MA0029.10.673506
MA0030.10.662482
MA0031.10.600685
MA0038.11.06455
MA0040.10.67914
MA0041.10.338572
MA0042.10.835565
MA0043.10.756508
MA0046.10.745626
MA0048.10.357781
MA0050.10.837296
MA0051.11.85986
MA0052.10.682867
MA0055.10.400018
MA0056.10
MA0057.10.3421
MA0058.10.240796
MA0059.10.239727
MA0060.11.13897
MA0061.19.28097
MA0063.10
MA0066.10.414559
MA0067.11.06751
MA0068.11.78302
MA0069.11.75682
MA0070.11.73434
MA0071.10.379038
MA0072.10.726666
MA0073.10.0284577
MA0074.11.05467
MA0076.10.706813
MA0077.10.719193
MA0078.10.502027
MA0081.10.67392
MA0083.10.763502
MA0084.11.25286
MA0087.10.724294
MA0088.10.397386
MA0089.10
MA0090.10.266215
MA0091.10.324543
MA0092.10.291716
MA0093.10.191154
MA0095.10
MA0098.10
MA0100.10.426863
MA0101.14.0219
MA0103.10.181541
MA0105.110.1515
MA0106.11.14663
MA0107.15.9266
MA0108.21.45646
MA0109.10
MA0111.10.277713
MA0113.10.467266
MA0114.10.134281
MA0115.10.992167
MA0116.10.140463
MA0117.10.792789
MA0119.11.87032
MA0122.10.818044
MA0124.10.951337
MA0125.10.868909
MA0130.10
MA0131.11.29006
MA0132.10
MA0133.10
MA0135.10.785738
MA0136.10.420617
MA0139.10.567946
MA0140.10.376643
MA0141.10.238287
MA0142.10.570448
MA0143.10.467429
MA0144.10.39221
MA0145.10.441471
MA0146.12.01134
MA0147.12.01107
MA0148.10.344198
MA0149.10.367947
MA0062.20.992751
MA0035.20.376007
MA0039.22.09733
MA0138.20.503176
MA0002.20.0954816
MA0137.20.595725
MA0104.22.93885
MA0047.20.440861
MA0112.20.216805
MA0065.20.0221687
MA0150.10.261236
MA0151.10
MA0152.10.382565
MA0153.10.852412
MA0154.10.5526
MA0155.10.64751
MA0156.10.208455
MA0157.10.544523
MA0158.10
MA0159.10.441451
MA0160.10.940794
MA0161.10
MA0162.11.52545
MA0163.11.22194
MA0164.11.20414
MA0080.20.191221
MA0018.22.00546
MA0099.20.996203
MA0079.20.496387
MA0102.21.28978
MA0258.10.117513
MA0259.12.0602
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#602411.51570093457940.0002880249986307050.00306168374880328
CCNT2#90573.696117586561540.0009222264038614660.00670446912104188
CHD2#110665.172011417058430.0004497895363246330.00418378779695478
E2F1#186993.680541911159497.26432475498673e-050.00114172883835374
E2F4#187455.278358464701850.00151155031186490.00965179769019675
E2F6#187693.762866798773046.04050132232551e-050.000991612570893357
EBF1#187964.45323342328450.001011881476986250.0071798280844464
EGR1#195883.325452729873420.0005908801842285490.00494637187885904
ELF1#1997113.903256462240241.12752972864617e-064.6361447767747e-05
ESRRA#2101280.6400523560210.0002773648879577920.00295377908977504
FAM48A#55578196.26406250.01033908141615570.0384011993321912
GABPB1#255363.533841918091090.003432770268573880.0174680907269337
GATA1#262344.520102714600150.00904025655514040.0342209262182787
GTF2B#295937.985957483581060.005455491186982880.024717628045521
HDAC2#306644.471873412208750.009386758586501720.0354208794311397
HEY1#2346272.356731441811660.01346982061264720.0475792131418222
HMGN3#932453.407728218062750.01028040559075030.0381954919776723
IRF1#365974.455012189578940.0002850277586319370.00303136599630966
MAX#414963.226277754503560.00548348112691290.024833670934203
MYC#460983.48152124773960.0004253796270131130.00397514520988032
NFKB1#4790125.488063424193841.33744036073436e-091.20414598133393e-07
PAX5#507995.002174148383375.4522949797447e-060.000165340370322171
PBX3#509047.304837562248040.001595779184409490.0100525714603138
POLR2A#5430122.147453176558070.0001039292038462010.00145265820670415
RFX5#599344.01597027573170.01363878775694360.0481207173591243
SIN3A#2594262.704442363407570.01325491342780750.0468851149321542
SP1#666773.324055803915520.001772697031948130.0108885905616439
SPI1#668874.785855379971590.0001804037199722320.0021870207905026
STAT1#677258.627744790499670.0001560891708225230.00196857830111502
TAF1#6872102.785871904787740.000200797123383880.00239368231584169
TAL1#688637.467154169360050.00657536370072610.0280972304545695
TBP#6908113.397873129838354.97194305024537e-060.000153537776530034
TCF12#693865.317232451093210.0003865425927634440.00378280751926737
TCF7L2#693465.385088281568670.0003605763085939490.00360503820536506
TFAP2C#702276.30538335575183.01291531004594e-050.00061990910572476
ZBTB7A#5134174.288613762927610.0003629129921758860.00362423694682132
ZNF274#107821118.4788461538460.008407999695537070.0330369857111436



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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