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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.582496492444005,0.

Latest revision as of 11:34, 17 September 2013


Full id: C936_CD4_CD14_granulocyte_CD14CD16_CD8_Dendritic_Hair



Phase1 CAGE Peaks

Hg19::chr20:35580040..35580066,-p3@SAMHD1
Hg19::chr20:35580068..35580094,-p1@SAMHD1
Hg19::chr20:35580104..35580133,-p2@SAMHD1
Hg19::chr20:35580152..35580163,-p5@SAMHD1
Hg19::chr20:35580173..35580200,-p4@SAMHD1
Hg19::chr20:35580214..35580223,-p7@SAMHD1
Hg19::chr20:35580240..35580251,-p6@SAMHD1
Hg19::chr7:142960556..142960600,+p1@GSTK1
Hg19::chr9:4985246..4985329,+p1@JAK2


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:0030288outer membrane-bounded periplasmic space0.0115035799203901
GO:0030313cell envelope0.0115035799203901
GO:0044462external encapsulating structure part0.0115035799203901
GO:0007262STAT protein nuclear translocation0.0115035799203901
GO:0004718Janus kinase activity0.0115035799203901
GO:0042597periplasmic space0.0115035799203901
GO:0030312external encapsulating structure0.0115035799203901
GO:0004716receptor signaling protein tyrosine kinase activity0.0196075728125403
GO:0004602glutathione peroxidase activity0.0196075728125403
GO:0015035protein disulfide oxidoreductase activity0.0196075728125403
GO:0042169SH2 domain binding0.0196075728125403
GO:0007260tyrosine phosphorylation of STAT protein0.0196075728125403
GO:0006749glutathione metabolic process0.0196075728125403
GO:0015036disulfide oxidoreductase activity0.0196746334083543
GO:0000060protein import into nucleus, translocation0.0196746334083543
GO:0007259JAK-STAT cascade0.0280287321429359
GO:0004715non-membrane spanning protein tyrosine kinase activity0.0280287321429359
GO:0018108peptidyl-tyrosine phosphorylation0.0280287321429359
GO:0018212peptidyl-tyrosine modification0.0280287321429359
GO:0004364glutathione transferase activity0.0280287321429359
GO:0007498mesoderm development0.0280287321429359
GO:0045121lipid raft0.0280287321429359
GO:0002376immune system process0.0320820002381753
GO:0004601peroxidase activity0.0359033090866457
GO:0016684oxidoreductase activity, acting on peroxide as acceptor0.0359033090866457
GO:0030099myeloid cell differentiation0.0396633258639042
GO:0016765transferase activity, transferring alkyl or aryl (other than methyl) groups0.0411241581148477
GO:0006790sulfur metabolic process0.0411241581148477
GO:0006606protein import into nucleus0.0418241842302334
GO:0051170nuclear import0.0418241842302334
GO:0042579microbody0.0418241842302334
GO:0005777peroxisome0.0418241842302334
GO:0018193peptidyl-amino acid modification0.0479928798143188
GO:0017038protein import0.0479928798143188
GO:0019904protein domain specific binding0.0485252268225351



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
leukocyte2.27e-31136
nongranular leukocyte1.43e-30115
macrophage dendritic cell progenitor8.81e-2961
myeloid leukocyte1.74e-2872
monopoietic cell1.99e-2859
monocyte1.99e-2859
monoblast1.99e-2859
promonocyte1.99e-2859
granulocyte monocyte progenitor cell5.76e-2867
hematopoietic lineage restricted progenitor cell4.00e-27120
hematopoietic stem cell3.92e-25168
angioblastic mesenchymal cell3.92e-25168
defensive cell5.33e-2548
phagocyte5.33e-2548
myeloid lineage restricted progenitor cell2.70e-2466
hematopoietic oligopotent progenitor cell5.02e-23161
hematopoietic multipotent progenitor cell5.02e-23161
hematopoietic cell3.75e-22177
classical monocyte1.23e-2142
CD14-positive, CD16-negative classical monocyte1.23e-2142
myeloid cell1.85e-18108
common myeloid progenitor1.85e-18108
stuff accumulating cell1.09e-1687
mature alpha-beta T cell1.87e-0918
alpha-beta T cell1.87e-0918
immature T cell1.87e-0918
mature T cell1.87e-0918
immature alpha-beta T cell1.87e-0918
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.43e-3098
blood island2.43e-3098
hemolymphoid system3.85e-30108
immune system1.69e-2593
bone marrow6.38e-2476
adult organism3.58e-22114
bone element2.78e-1982
skeletal element2.37e-1890
skeletal system1.13e-16100
lateral plate mesoderm1.24e-09203
musculoskeletal system2.52e-07167


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)
MA0003.11.64541
MA0004.10.415381
MA0006.10.265592
MA0007.10.397529
MA0009.10.870971
MA0014.12.77991
MA0017.10.301634
MA0019.10.558663
MA0024.10.766783
MA0025.11.00397
MA0027.12.48103
MA0028.11.40203
MA0029.10.785955
MA0030.10.774581
MA0031.10.710608
MA0038.10.514558
MA0040.10.791764
MA0041.10.433167
MA0042.10.402577
MA0043.10.871285
MA0046.10.860127
MA0048.10.264106
MA0050.10.403421
MA0051.10.510444
MA0052.10.795605
MA0055.10.088427
MA0056.10
MA0057.10.0725989
MA0058.10.325084
MA0059.10.323879
MA0060.10.9464
MA0061.10.139804
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.11.73295
MA0069.10.856287
MA0070.10.845142
MA0071.10.47692
MA0072.10.840664
MA0073.10.0176541
MA0074.10.509711
MA0076.10.339975
MA0077.10.832987
MA0078.10.607575
MA0081.10.324031
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.10.0408613
MA0089.10
MA0090.10.353576
MA0091.10.417885
MA0092.10.381858
MA0093.10.26836
MA0095.10
MA0098.10
MA0100.13.31755
MA0101.10.271368
MA0103.10.714036
MA0105.10.0643619
MA0106.10.554855
MA0107.10.205358
MA0108.20.707575
MA0109.10
MA0111.10.366362
MA0113.10.57094
MA0114.10.582067
MA0115.11.11137
MA0116.10.208403
MA0117.10.908433
MA0119.10.308914
MA0122.10.934245
MA0124.11.06995
MA0125.12.25779
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.11.31371
MA0140.10.474342
MA0141.10.322254
MA0142.10.679161
MA0143.10.571113
MA0144.10.552298
MA0145.10.177438
MA0146.10.0794051
MA0147.10.211483
MA0148.10.439278
MA0149.10.464973
MA0062.20.421263
MA0035.20.473658
MA0039.20.679176
MA0138.20.608783
MA0002.20.152495
MA0137.20.28622
MA0104.20.161609
MA0047.20.542971
MA0112.20.166662
MA0065.20.0483532
MA0150.10.34802
MA0151.10
MA0152.10.480711
MA0153.10.969315
MA0154.10.225151
MA0155.10.156896
MA0156.10.288314
MA0157.10.652111
MA0158.10
MA0159.11.14546
MA0160.10.453945
MA0161.10
MA0162.10.0107891
MA0163.10.384654
MA0164.10.583138
MA0080.20.268439
MA0018.20.556211
MA0099.20.481058
MA0079.23.47892e-06
MA0102.21.41188
MA0258.10.180288
MA0259.11.82941
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#467717.47135796467351.14940906869096e-088.6237883423143e-07
CTCF#1066484.764672331622251.10088565904027e-050.000285015858563477
CTCFL#140690817.55242165242163.70770685210878e-103.6914127352468e-08
E2F1#186984.36212374655942.18983367577486e-050.000481279543906252
E2F4#187479.852935800776795.95188909661047e-072.73716136222326e-05
E2F6#187695.017155731697394.96068808485209e-072.32431270925916e-05
HEY1#2346294.040111043105713.4850025352467e-060.000115987947666868
HMGN3#932487.269820198533864.00320733604597e-071.93560634708012e-05
JUN#372579.732200482928266.47658215823223e-072.93834823641883e-05
MXI1#460177.747889044590563.07469224127045e-060.000103720214142779
NANOG#79923722.74593881856541.84595149658852e-091.59991143860754e-07
NRF1#4899912.21027944771091.65394511709215e-101.73604396064308e-08
PAX5#507953.705314183987680.005616557077719420.0253945021273621
PBX3#5090717.04462097857881.36394115359822e-081.00315950803271e-06
POLR2A#543092.147453176558070.001029412892608020.00728887139600606
RFX5#599379.370597310040638.3937256470655e-073.65111333966628e-05
SIN3A#2594284.807897534946791.02597602607548e-050.000268080836095314
TAF1#687293.343046285745291.91655056102793e-050.000433533948544935
TBP#690893.706770687096397.56501052505806e-060.000215928432420481
TCF7L2#693478.376803993551271.80610965338292e-066.77300847718704e-05
TFAP2A#7020814.68323055381771.5325776526732e-091.35415293965767e-07
TFAP2C#702289.608203208764644.42575919806395e-082.89794272656176e-06
THAP1#55145724.39822357999551.13434844000145e-091.04195441271162e-07
ZEB1#693535.629477339181290.01330488236341950.0470379678803415



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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