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{{Coexpression_clusters
{
|full_id=C1308_CD14_CD4_Basophils_Peripheral_Neutrophils_Eosinophils_CD8
 

Latest revision as of 11:42, 17 September 2013


Full id: C1308_CD14_CD4_Basophils_Peripheral_Neutrophils_Eosinophils_CD8



Phase1 CAGE Peaks

Hg19::chr10:23727926..23727957,+p4@OTUD1
Hg19::chr10:23727989..23728040,+p2@OTUD1
Hg19::chr10:23728041..23728084,+p3@OTUD1
Hg19::chr15:63796779..63796863,+p1@USP3
Hg19::chr15:63796867..63796887,+p2@USP3
Hg19::chr15:63796904..63796916,+p4@USP3


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:0004221ubiquitin thiolesterase activity0.0316849169904627
GO:0004843ubiquitin-specific protease activity0.0316849169904627
GO:0019783small conjugating protein-specific protease activity0.0316849169904627
GO:0016790thiolester hydrolase activity0.0316849169904627
GO:0006511ubiquitin-dependent protein catabolic process0.0316849169904627
GO:0043632modification-dependent macromolecule catabolic process0.0316849169904627
GO:0019941modification-dependent protein catabolic process0.0316849169904627
GO:0051603proteolysis involved in cellular protein catabolic process0.0316849169904627
GO:0044257cellular protein catabolic process0.0316849169904627
GO:0008234cysteine-type peptidase activity0.0316849169904627
GO:0030163protein catabolic process0.0342956231334896
GO:0043285biopolymer catabolic process0.0400918403391028
GO:0044265cellular macromolecule catabolic process0.0415552303577736
GO:0006512ubiquitin cycle0.0415552303577736
GO:0009057macromolecule catabolic process0.0441540091840339



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
leukocyte5.29e-40136
hematopoietic lineage restricted progenitor cell3.15e-33120
nongranular leukocyte1.01e-32115
myeloid leukocyte1.95e-3172
defensive cell7.14e-2848
phagocyte7.14e-2848
granulocyte monocyte progenitor cell9.78e-2867
hematopoietic stem cell3.72e-27168
angioblastic mesenchymal cell3.72e-27168
classical monocyte1.98e-2642
CD14-positive, CD16-negative classical monocyte1.98e-2642
macrophage dendritic cell progenitor2.18e-2661
hematopoietic oligopotent progenitor cell9.92e-26161
hematopoietic multipotent progenitor cell9.92e-26161
myeloid lineage restricted progenitor cell1.57e-2566
monopoietic cell1.79e-2559
monocyte1.79e-2559
monoblast1.79e-2559
promonocyte1.79e-2559
hematopoietic cell3.01e-23177
myeloid cell8.37e-18108
common myeloid progenitor8.37e-18108
stuff accumulating cell1.60e-0987
mature alpha-beta T cell3.52e-0918
alpha-beta T cell3.52e-0918
immature T cell3.52e-0918
mature T cell3.52e-0918
immature alpha-beta T cell3.52e-0918
lymphoid lineage restricted progenitor cell3.25e-0852
lymphocyte1.02e-0753
common lymphoid progenitor1.02e-0753
nucleate cell2.09e-0755
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.94e-2698
blood island3.94e-2698
hemolymphoid system2.45e-24108
bone marrow1.05e-2176
immune system1.76e-2193
bone element3.93e-2082
skeletal element8.68e-1790
skeletal system1.56e-13100


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)
MA0003.15.21839
MA0004.13.45359
MA0006.10.391183
MA0007.11.33289
MA0009.11.03681
MA0014.15.69366
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.11.05129
MA0029.10.949428
MA0030.13.55198
MA0031.12.02362
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.11.45353
MA0050.11.34656
MA0051.10.661179
MA0052.10.959373
MA0055.11.71708
MA0056.10
MA0057.10.147053
MA0058.13.00536
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.51617
MA0074.10.660398
MA0076.11.19721
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.660742
MA0089.10
MA0090.13.14993
MA0091.12.36274
MA0092.10.522012
MA0093.15.90743
MA0095.10
MA0098.10
MA0100.11.62836
MA0101.10.397846
MA0103.10.993014
MA0105.10.134725
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.13.45912
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.107156
MA0146.17.58496
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.21.22729
MA0035.20.621793
MA0039.212.6407
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.21.35181
MA0047.20.695777
MA0112.21.12726
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.10.318517
MA0156.10.417278
MA0157.11.89858
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.17.2229
MA0163.10.113377
MA0164.10.738243
MA0080.20.394469
MA0018.21.69036
MA0099.20.629739
MA0079.27.0058
MA0102.21.58513
MA0258.10.289793
MA0259.10.336472
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#467311.23158726300440.001593459971184230.010038567132978
BCL11A#53335314.18472755180350.0008080831849424810.00616790175781684
BCLAF1#9774310.82632380506090.001772351046991060.0108871056932537
BHLHE40#8553322.43590677348870.0002103196104780280.00244605454328672
CCNT2#90566.336201576962631.54467812014647e-050.000362283041073383
CTCF#1066465.360256373075034.21437267579784e-050.000754706563593365
E2F4#1874612.66806031528442.41728555395527e-071.26736388538923e-05
E2F6#187665.017155731697396.26776799983417e-050.00102425195139208
EGR1#195864.988179094810146.48943962979974e-050.0010543724105424
ELF1#199764.258097958807540.0001677224776288830.00205066352623307
ELK4#200538.117840829234010.004056113134185760.019405240477381
FOSL2#235538.465100302280850.003598315634615090.0182181736747899
FOXA1#3169611.08141974938555.39600313513231e-072.50245635626147e-05
FOXA2#3170312.31523187633260.001219712440124520.0082041313540391
GTF2B#2959315.97191496716210.0005711653715892990.00486636810600545
GTF2F1#296236.369830438378830.008068208196303160.03191076254691
HDAC2#3066613.41562023662631.71355402088576e-079.4190457045941e-06
HEY1#2346264.040111043105710.0002298968555807510.00252872013691396
HMGN3#932468.178547723350593.33956428934731e-060.000111467163571474
HNF4A#3172311.56614518147680.001463487150085730.00937527660355786
HNF4G#3174314.37671126322340.0007769772937197380.00608889709452958
IRF1#365967.63716375356395.03701715640675e-060.000155455388533677
IRF4#3662310.95725634337210.001711753441810940.0106877394457639
JUN#372536.256414596168170.008486346850954870.0324048692467141
MAX#414966.452555509007121.3848964723355e-050.000334266703661307
MEF2A#420539.371615454822030.002687399947103910.0147969929921755
MEF2C#4208320.6556772463120.0002683563494060410.0028654400138654
MXI1#460169.96157162875931.02262624227062e-064.2978697028773e-05
MYC#460965.22228187160944.92821127172503e-050.00085313684237973
NR3C1#290837.486511665586520.00510866965984070.0237553139182593
POLR2A#543062.147453176558070.01019570676818780.0379821444324154
RFX5#599336.023955413597550.009437904036335060.0355997276672492
RXRA#6256310.03730856956660.002205419116789220.0127037541855578
SIN3A#2594265.408884726815143.99207083571449e-050.000741864565856202
SMC3#9126615.04493284493288.61317699636729e-085.12565009870999e-06
SRF#672236.89858913108390.00644245168930370.0279966384545911
STAT1#6772310.35329374859960.002016680459920930.0117199983614536
TAF1#687263.343046285745290.0007162474284635620.00572422445525758
TCF12#693835.317232451093210.013367345733860.0472364141802944
TCF7L2#6934610.77017656313736.40204410218762e-072.90832137446008e-05
USF1#739166.361499277207961.50818327938273e-050.000356849011136052
USF2#739236.49609869253480.007634319815300560.0314524941692377
ZEB1#693538.444216008771930.003623843810733590.0183332020804691
ZNF263#1012768.221841637010683.23542093046082e-060.000108615919818836



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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