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Coexpression cluster:C838: Difference between revisions

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{{Coexpression_clusters
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|full_id=C838_Eosinophils_CD4_Neutrophils_CD8_CD14_Natural_CD19
|id=C838
|ontology_enrichment_celltype=CL:0000738!7.20e-43!140;CL:0002087!1.05e-34!119;CL:0002031!3.05e-33!124;CL:0000037!7.71e-28!172;CL:0000566!7.71e-28!172;CL:0002032!4.28e-25!165;CL:0000837!4.28e-25!165;CL:0000766!8.16e-25!76;CL:0000988!1.88e-24!182;CL:0002057!1.34e-23!42;CL:0000557!2.54e-21!71;CL:0002009!2.78e-20!65;CL:0000860!1.53e-19!45;CL:0002194!2.07e-19!63;CL:0000576!2.07e-19!63;CL:0000040!2.07e-19!63;CL:0000559!2.07e-19!63;CL:0000839!4.14e-18!70;CL:0000838!7.13e-14!52;CL:0000542!2.53e-13!53;CL:0000051!2.53e-13!53;CL:0000763!2.72e-12!112;CL:0000049!2.72e-12!112;CL:0000791!2.78e-11!18;CL:0000789!2.78e-11!18;CL:0002420!2.78e-11!18;CL:0002419!2.78e-11!18;CL:0000790!2.78e-11!18;CL:0000084!6.50e-10!25;CL:0000827!6.50e-10!25;CL:0000625!2.60e-07!11
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!3.60e-26!115;UBERON:0002390!2.83e-25!102;UBERON:0003061!2.83e-25!102;UBERON:0002193!1.58e-23!112;UBERON:0002371!7.72e-18!80;UBERON:0001474!5.82e-16!86;UBERON:0002405!4.89e-14!115;UBERON:0004765!1.94e-12!101;UBERON:0001434!1.94e-12!101;UBERON:0001049!1.96e-10!57;UBERON:0005068!1.96e-10!57;UBERON:0006241!1.96e-10!57;UBERON:0007135!1.96e-10!57;UBERON:0003080!1.12e-09!42;UBERON:0002780!2.38e-09!41;UBERON:0001890!2.38e-09!41;UBERON:0006240!2.38e-09!41;UBERON:0002616!1.33e-08!59;UBERON:0002020!6.65e-08!34;UBERON:0003528!6.65e-08!34;UBERON:0001893!9.03e-08!34;UBERON:0002791!1.44e-07!33;UBERON:0001869!3.16e-07!32
}}

Latest revision as of 11:32, 17 September 2013


Full id: C838_Eosinophils_CD4_Neutrophils_CD8_CD14_Natural_CD19



Phase1 CAGE Peaks

Hg19::chr15:93443871..93443879,+p5@CHD2
Hg19::chr16:4466565..4466605,-p1@CORO7
Hg19::chr16:50776021..50776045,+p2@CYLD
Hg19::chr17:76778320..76778331,-p6@CYTH1
Hg19::chr3:156877232..156877257,-p7@CCNL1
Hg19::chr3:71774516..71774587,-p1@EIF4E3
Hg19::chr6:139456226..139456300,+p1@HECA
Hg19::chr6:139499652..139499656,+p@chr6:139499652..139499656
+
Hg19::chr6:143266297..143266356,-p1@HIVEP2
Hg19::chr6:33378780..33378838,+p1@PHF1


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
leukocyte8.86e-48136
nongranular leukocyte7.22e-40115
hematopoietic lineage restricted progenitor cell4.31e-38120
hematopoietic stem cell2.62e-33168
angioblastic mesenchymal cell2.62e-33168
hematopoietic oligopotent progenitor cell4.76e-30161
hematopoietic multipotent progenitor cell4.76e-30161
hematopoietic cell4.08e-29177
myeloid leukocyte1.32e-2772
defensive cell2.49e-2448
phagocyte2.49e-2448
granulocyte monocyte progenitor cell5.73e-2467
macrophage dendritic cell progenitor2.37e-2361
classical monocyte3.56e-2342
CD14-positive, CD16-negative classical monocyte3.56e-2342
monopoietic cell1.61e-2259
monocyte1.61e-2259
monoblast1.61e-2259
promonocyte1.61e-2259
myeloid lineage restricted progenitor cell2.63e-2166
lymphoid lineage restricted progenitor cell2.47e-1552
lymphocyte4.13e-1553
common lymphoid progenitor4.13e-1553
myeloid cell5.46e-15108
common myeloid progenitor5.46e-15108
nucleate cell6.83e-1455
mature alpha-beta T cell2.23e-1118
alpha-beta T cell2.23e-1118
immature T cell2.23e-1118
mature T cell2.23e-1118
immature alpha-beta T cell2.23e-1118
T cell1.33e-0925
pro-T cell1.33e-0925
stuff accumulating cell1.87e-0887
CD8-positive, alpha-beta T cell2.16e-0711
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.32e-2898
blood island5.32e-2898
hemolymphoid system1.95e-25108
adult organism5.46e-24114
bone marrow1.14e-2076
immune system2.69e-2093
bone element6.39e-1982
skeletal element6.53e-1790
skeletal system1.50e-14100
regional part of forebrain5.64e-0941
forebrain5.64e-0941
anterior neural tube5.64e-0941
future forebrain5.64e-0941
neural tube5.85e-0956
neural rod5.85e-0956
future spinal cord5.85e-0956
neural keel5.85e-0956
regional part of nervous system1.23e-0853
regional part of brain1.23e-0853
brain grey matter4.61e-0834
gray matter4.61e-0834
telencephalon6.81e-0834
regional part of telencephalon1.77e-0732
cerebral hemisphere1.92e-0732
regional part of cerebral cortex3.50e-0722


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)
MA0003.16.34255
MA0004.10.990587
MA0006.10.665232
MA0007.10.363007
MA0009.10.828613
MA0014.14.95045
MA0017.10.270554
MA0019.10.520264
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.10.25013
MA0029.10.744375
MA0030.10.733118
MA0031.10.669876
MA0038.10.477043
MA0040.10.750125
MA0041.10.397617
MA0042.10.367902
MA0043.10.828925
MA0046.10.817858
MA0048.11.25863
MA0050.10.368721
MA0051.10.473017
MA0052.10.753928
MA0055.10.577037
MA0056.10
MA0057.12.25468
MA0058.10.293055
MA0059.10.291897
MA0060.10.848451
MA0061.11.80643
MA0063.10
MA0066.10.477449
MA0067.12.57737
MA0068.10.304755
MA0069.10.814052
MA0070.10.803003
MA0071.10.440254
MA0072.10.798564
MA0073.16.11061
MA0074.10.4723
MA0076.10.307383
MA0077.10.790956
MA0078.10.568317
MA0081.10.292043
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.11.25978
MA0089.10
MA0090.10.857892
MA0091.10.382762
MA0092.10.347826
MA0093.10.671378
MA0095.10
MA0098.10
MA0100.10.49029
MA0101.11.25862
MA0103.10.646502
MA0105.13.32465
MA0106.11.28468
MA0107.11.60878
MA0108.20.666881
MA0109.10
MA0111.10.33284
MA0113.11.31824
MA0114.10.174997
MA0115.11.06753
MA0116.10.182037
MA0117.10.865782
MA0119.10.277531
MA0122.10.891407
MA0124.11.0263
MA0125.10.942948
MA0130.10
MA0131.10.585907
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.10.483775
MA0139.10.353333
MA0140.10.437738
MA0141.10.290336
MA0142.10.638837
MA0143.10.532484
MA0144.10.163394
MA0145.10.602634
MA0146.15.19153
MA0147.10.543675
MA0148.10.403564
MA0149.10.428597
MA0062.20.366815
MA0035.20.437071
MA0039.25.63897
MA0138.20.569505
MA0002.20.129981
MA0137.20.255808
MA0104.21.97382
MA0047.20.504873
MA0112.20.904106
MA0065.21.37627
MA0150.10.845871
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.10.414714
MA0155.11.25014
MA0156.10.257809
MA0157.10.612166
MA0158.10
MA0159.11.04074
MA0160.10.417847
MA0161.10
MA0162.15.77676
MA0163.17.56381
MA0164.10.544294
MA0080.20.238846
MA0018.22.21993
MA0099.20.444294
MA0079.223.8956
MA0102.21.36707
MA0258.11.47203
MA0259.11.68088
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
E2F1#186973.435172450415530.0009731854789143080.00699652496952788
EGR1#195862.992907456886080.006446587185075730.0280134442465725
HEY1#2346272.8280777301740.003295391007019310.0170489592996527
IRF1#365953.818581876781950.005465628575453730.0247581880114422
SIN3A#2594263.245330836089080.004223840630485730.0201036180835482
TAF1#687272.34013240002170.01040839844348330.0386394172338161
USF1#739163.816899566324770.001780928663791640.0109288682482952
YY1#752862.946702449912310.006987247873951880.0295405894307437



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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