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Coexpression cluster:C1035: Difference between revisions

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{{Coexpression_clusters
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|full_id=C1035_CD8_Eosinophils_Natural_Basophils_CD4_Peripheral_CD19
|id=C1035
}}

Latest revision as of 11:36, 17 September 2013


Full id: C1035_CD8_Eosinophils_Natural_Basophils_CD4_Peripheral_CD19



Phase1 CAGE Peaks

Hg19::chr14:64971438..64971450,+p2@ZBTB1
Hg19::chr14:64971461..64971542,+p1@ZBTB1
Hg19::chr16:85833774..85833799,-p@chr16:85833774..85833799
-
Hg19::chr21:38739399..38739420,+p6@DYRK1A
Hg19::chr2:109336045..109336054,+p6@RANBP2
Hg19::chr3:150126440..150126455,+p9@TSC22D2
Hg19::chr7:104654690..104654704,+p2@MLL5
Hg19::chr7:104654718..104654741,+p3@MLL5


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

No GOStat results

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
leukocyte4.65e-42136
hematopoietic stem cell1.19e-35168
angioblastic mesenchymal cell1.19e-35168
hematopoietic lineage restricted progenitor cell4.81e-33120
hematopoietic cell2.72e-32177
hematopoietic oligopotent progenitor cell9.59e-32161
hematopoietic multipotent progenitor cell9.59e-32161
nongranular leukocyte3.43e-30115
myeloid leukocyte1.87e-2472
classical monocyte1.63e-2342
CD14-positive, CD16-negative classical monocyte1.63e-2342
granulocyte monocyte progenitor cell2.57e-2167
myeloid lineage restricted progenitor cell4.96e-2066
defensive cell7.67e-2048
phagocyte7.67e-2048
myeloid cell1.29e-19108
common myeloid progenitor1.29e-19108
macrophage dendritic cell progenitor1.96e-1861
monopoietic cell2.59e-1759
monocyte2.59e-1759
monoblast2.59e-1759
promonocyte2.59e-1759
mesenchymal cell3.86e-12354
lymphoid lineage restricted progenitor cell8.67e-1252
nucleate cell9.38e-1255
lymphocyte2.48e-1153
common lymphoid progenitor2.48e-1153
connective tissue cell8.20e-11361
motile cell2.44e-09386
multi fate stem cell2.92e-09427
stem cell5.35e-09441
somatic stem cell9.04e-09433
mature alpha-beta T cell1.21e-0818
alpha-beta T cell1.21e-0818
immature T cell1.21e-0818
mature T cell1.21e-0818
immature alpha-beta T cell1.21e-0818
T cell1.26e-0725
pro-T cell1.26e-0725
Uber Anatomy
Ontology termp-valuen
hematopoietic system8.03e-2298
blood island8.03e-2298
hemolymphoid system1.74e-21108
immune system1.01e-1893
bone element2.76e-1882
bone marrow8.04e-1876
skeletal element3.42e-1590
skeletal system1.73e-13100
connective tissue4.05e-11371


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)
MA0003.10.576745
MA0004.10.455723
MA0006.10.812175
MA0007.10.437331
MA0009.10.918715
MA0014.11.78293
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.315574
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.11.12605
MA0043.10.919032
MA0046.10.90778
MA0048.10.316923
MA0050.10.443405
MA0051.11.36251
MA0052.10.842664
MA0055.13.84086
MA0056.10
MA0057.11.56323
MA0058.10.362328
MA0059.10.361075
MA0060.10.190336
MA0061.10.165998
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.823119
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.10.131075
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.948525
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.199853
MA0089.10
MA0090.10.391903
MA0091.10.458301
MA0092.10.421159
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.825856
MA0103.10.291333
MA0105.10.586268
MA0106.10.59853
MA0107.10.666147
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.10.231781
MA0115.11.1606
MA0116.10.239768
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.11.60834
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.155155
MA0140.10.516266
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.10.218541
MA0145.11.25866
MA0146.10.0399277
MA0147.10.681318
MA0148.12.09557
MA0149.10.506665
MA0062.20.485915
MA0035.20.515566
MA0039.20.00915579
MA0138.21.57302
MA0002.20.179788
MA0137.20.321796
MA0104.20.55506
MA0047.21.43258
MA0112.20.0572179
MA0065.20.490252
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.274121
MA0155.10.0535085
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.10.243637
MA0160.10.495355
MA0161.10
MA0162.18.59812
MA0163.11.83367
MA0164.10.627336
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.23.09265
MA0102.21.46209
MA0258.10.209744
MA0259.10.25092
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
CCNT2#90575.54417637984231.68072647241023e-050.00038706370904532
CEBPB#105143.985573812912410.01139163688734390.0417434884697838
E2F1#186984.907389214879322.97124777369457e-060.000101509370702286
E2F6#187663.762866798773040.001207680027997810.00818593551687848
ELF1#199773.72583571395660.0002503412725512720.0026987399013194
FOXA1#316945.540709874692730.003444272925946160.017521501223229
FOXA2#317039.236423907249470.003211939548395410.0168433297095234
GABPB1#255354.417302397613860.002182228654850360.012587527807573
GTF2F1#296246.369830438378830.002051908375195520.01191147011267
HEY1#2346273.53509716271750.0003566123056684080.00356745522909031
HMGN3#932455.111592327094120.001109515975889930.00770815798616164
JUND#372754.371664963669390.002289022009366710.0129897397107286
MYC#460963.916711403707050.0009649270569246440.00693906334078034
NFKB1#479064.116047568145380.0007299856589784310.00581532969016387
NR3C1#290835.614883749189890.01292443946090990.0464636512635701
PAX5#507965.002174148383370.0002416084515475770.00262929509963295
POLR2A#543082.147453176558070.002210725788971910.0127181883152163
POU2F2#545255.691327536089080.000670954773528490.00541528945846538
SIN3A#2594253.380552954259460.007342226961170280.0303640944641507
SIX5#14791236.407518258297120.008979882420728990.0340491555379943
SMARCB1#659836.844768417934030.007473690134633950.0308235487095145
SPI1#668844.102161754261360.01027800662400760.0381892960653455
TAF1#687272.925165500027130.001265325357915740.00849070387145734
TBP#690873.243424351209340.0006354223620492050.0052122899835106
TCF12#693856.646540563866510.0003223768920812840.0032995609792314
YY1#752853.069481718658660.0112591365358360.0413290088804365
ZNF263#1012766.166381227758017.27120729623729e-050.00114263860790209



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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