KOGMWU-package: Functional summary and meta-analysis of gene expression data
In KOGMWU: Functional Summary and Meta-Analysis of Gene Expression Data
Description
Details
Author(s)
References
Examples
Description
Rank-based tests for enrichment of KOG (euKaryotic Orthologous Groups) classes with up- or down-regulated genes based on a continuous measure. The meta-analysis is based on correlation of KOG delta-ranks across datasets (delta-rank is the difference between mean rank of genes belonging to a KOG class and mean rank of all other genes). With binary measure (1 or 0 to indicate significant and non-significant genes), one-tailed Fisher's exact test for over-representation of each KOG class among significant genes will be performed.
Details
Package: KOGMWU
Type: Package
Version: 1.2
Date: 2019-02-19
License: GPL-3
The most important function is kog.mwu, which performs a series of Mann-Whitney U tests when given two data tables: one, containing measures of interest for each gene (for example, log fold-change), and another, listing the association of each gene with a KOG class. The KOG class annotations for a collection of genes can be obtained using eggNOG-mapper: http://eggnogdb.embl.de/#/app/emapper. To extract KOG annotations understood by this package out of the eggNOG-mapper output, see here: https://github.com/z0on/emapper_to_GOMWU_KOGMWU
Author(s)
Mikhail V. Matz
Maintainer: Mikhail V. Matz <matz@utexas.edu>
References
Dixon, G. B., Davies, S. W., Aglyamova, G. V., Meyer, E., Bay, L. K. and Matz, M. V. Genomic determinants of coral heat tolerance across latitudes. Science 2015, 348:1460-1462.
eggNOG-mapper to obtain KOG annotations: http://eggnogdb.embl.de/#/app/emapper
To extract KOG annotations from eggNOG-mapper output: https://github.com/z0on/emapper_to_GOMWU_KOGMWU
Examples
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## Not run:
data(adults.3dHeat.logFoldChange)
data(larvae.longTerm)
data(larvae.shortTerm)
data(gene2kog)
# Analyzing adult coral response to 3-day heat stress:
alfc.lth=kog.mwu(adults.3dHeat.logFoldChange,gene2kog)
alfc.lth
# coral larvae response to 5-day heat stress:
l.lth=kog.mwu(larvae.longTerm,gene2kog)
l.lth
# coral larvae response to 4-hour heat stress
l.sth=kog.mwu(larvae.shortTerm,gene2kog)
l.sth
# compiling a table of delta-ranks to compare these results:
ktable=makeDeltaRanksTable(list("adults.long"=alfc.lth,"larvae.long"=l.lth,"larvae.short"=l.sth))
# Making a heatmap with hierarchical clustering trees:
pheatmap(as.matrix(ktable),clustering_distance_cols="correlation")
# exploring correlations between datasets
pairs(ktable, lower.panel = panel.smooth, upper.panel = panel.cor)
# p-values of these correlations in the upper panel:
pairs(ktable, lower.panel = panel.smooth, upper.panel = panel.cor.pval)
# plotting individual delta-rank correlations:
corrPlot(x="adults.long",y="larvae.long",ktable)
corrPlot(x="larvae.short",y="larvae.long",ktable)
## End(Not run)
Example output
Loading required package: pheatmap
[1] "Continuous measure of interest: will perform MWU test"
term nseqs
6 Signal transduction mechanisms 4723
8 Translation, ribosomal structure and biogenesis 431
11 Inorganic ion transport and metabolism 387
1 Energy production and conversion 350
17 Cell wall/membrane/envelope biogenesis 235
13 Intracellular trafficking, secretion, and vesicular transport 713
3 Cell cycle control, cell division, chromosome partitioning 456
12 Transcription 926
22 Carbohydrate transport and metabolism 514
15 Cytoskeleton 808
10 Nucleotide transport and metabolism 124
9 Chromatin structure and dynamics 314
4 Posttranslational modification, protein turnover, chaperones 1663
5 Cell motility 66
23 Coenzyme transport and metabolism 99
2 Replication, recombination and repair 510
18 Nuclear structure 106
20 Secondary metabolites biosynthesis, transport and catabolism 246
7 Defense mechanisms 602
19 Lipid transport and metabolism 483
21 Extracellular structures 382
16 Amino acid transport and metabolism 551
14 RNA processing and modification 599
delta.rank pval padj
6 503 1.975290e-12 4.543167e-11
8 -1348 5.045068e-12 5.801828e-11
11 977 2.039699e-06 1.563769e-05
1 -916 2.208820e-05 1.270072e-04
17 1100 2.796245e-05 1.286273e-04
13 -609 7.164623e-05 2.746439e-04
3 743 9.132167e-05 3.000569e-04
12 -452 8.573269e-04 2.464815e-03
22 -496 5.664578e-03 1.447614e-02
15 327 2.391698e-02 5.388752e-02
10 -802 2.577229e-02 5.388752e-02
9 -463 4.185822e-02 7.699672e-02
4 -211 4.351989e-02 7.699672e-02
5 -899 6.794914e-02 1.116307e-01
23 -702 8.095447e-02 1.241302e-01
2 297 9.908850e-02 1.424397e-01
18 560 1.501987e-01 2.032100e-01
20 360 1.607049e-01 2.053451e-01
7 -214 1.971382e-01 2.386410e-01
19 204 2.689993e-01 3.007196e-01
21 226 2.745700e-01 3.007196e-01
16 -69 6.921105e-01 7.235701e-01
14 15 9.275128e-01 9.275128e-01
[1] "Continuous measure of interest: will perform MWU test"
term nseqs
5 Signal transduction mechanisms 3527
7 Translation, ribosomal structure and biogenesis 372
1 Energy production and conversion 312
13 Cell wall/membrane/envelope biogenesis 188
10 Intracellular trafficking, secretion, and vesicular transport 624
17 Cytoskeleton 661
18 Lipid transport and metabolism 411
12 Amino acid transport and metabolism 449
3 Posttranslational modification, protein turnover, chaperones 1336
16 Extracellular structures 296
19 Inorganic ion transport and metabolism 293
6 Defense mechanisms 475
4 Cell motility 56
22 Coenzyme transport and metabolism 89
9 Transcription 805
23 Nucleotide transport and metabolism 115
14 Nuclear structure 86
15 Replication, recombination and repair 392
11 RNA processing and modification 512
8 Chromatin structure and dynamics 257
2 Cell cycle control, cell division, chromosome partitioning 353
21 Carbohydrate transport and metabolism 433
20 Secondary metabolites biosynthesis, transport and catabolism 204
delta.rank pval padj
5 425 6.481483e-11 1.490741e-09
7 -820 1.110922e-06 1.277560e-05
1 -860 2.683092e-06 2.057037e-05
13 665 4.620272e-03 2.656656e-02
10 -331 1.188865e-02 5.468780e-02
17 269 3.536437e-02 1.355634e-01
18 313 5.090900e-02 1.539847e-01
12 -297 5.355989e-02 1.539847e-01
3 -163 7.925484e-02 2.025401e-01
16 -308 1.016494e-01 2.337936e-01
19 259 1.706526e-01 3.568191e-01
6 -186 2.128241e-01 3.876130e-01
4 -526 2.190856e-01 3.876130e-01
22 -321 3.443076e-01 5.656483e-01
9 -94 4.218868e-01 6.140175e-01
23 -238 4.271426e-01 6.140175e-01
14 241 4.851455e-01 6.387659e-01
15 111 4.999037e-01 6.387659e-01
11 -68 6.400061e-01 7.691819e-01
8 86 6.688538e-01 7.691819e-01
2 -17 9.195196e-01 9.783174e-01
21 7 9.638452e-01 9.783174e-01
20 6 9.783174e-01 9.783174e-01
[1] "Continuous measure of interest: will perform MWU test"
term nseqs
1 Energy production and conversion 310
15 Replication, recombination and repair 395
12 Amino acid transport and metabolism 448
7 Translation, ribosomal structure and biogenesis 370
5 Signal transduction mechanisms 3535
14 Nuclear structure 86
16 Extracellular structures 299
18 Lipid transport and metabolism 414
4 Cell motility 57
3 Posttranslational modification, protein turnover, chaperones 1338
13 Cell wall/membrane/envelope biogenesis 187
9 Transcription 803
19 Inorganic ion transport and metabolism 287
11 RNA processing and modification 508
20 Secondary metabolites biosynthesis, transport and catabolism 207
2 Cell cycle control, cell division, chromosome partitioning 354
21 Carbohydrate transport and metabolism 432
23 Nucleotide transport and metabolism 114
6 Defense mechanisms 474
17 Cytoskeleton 665
10 Intracellular trafficking, secretion, and vesicular transport 622
8 Chromatin structure and dynamics 258
22 Coenzyme transport and metabolism 89
delta.rank pval padj
1 -704 0.0001311754 0.003017033
15 -539 0.0009984303 0.010687775
12 -492 0.0013940577 0.010687775
7 -513 0.0023781220 0.013674201
5 171 0.0086021244 0.039569772
14 769 0.0260839752 0.099988572
16 364 0.0517464329 0.162198436
18 -305 0.0564168471 0.162198436
4 -731 0.0848350539 0.216800693
3 154 0.0984521437 0.226439931
13 345 0.1427622383 0.298502862
9 164 0.1610714849 0.308720346
19 230 0.2293518698 0.405776385
11 -160 0.2699350455 0.438847157
20 -239 0.2862046675 0.438847157
2 -166 0.3360102051 0.459203833
21 149 0.3433468206 0.459203833
23 -276 0.3593769131 0.459203833
6 128 0.3926991116 0.475372609
17 103 0.4197344377 0.482694603
10 -87 0.5083183209 0.549990823
8 128 0.5260781787 0.549990823
22 158 0.6427766368 0.642776637
KOGMWU documentation built on May 2, 2019, 4 p.m.
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Description Details Author(s) References Examples
Description
Rank-based tests for enrichment of KOG (euKaryotic Orthologous Groups) classes with up- or down-regulated genes based on a continuous measure. The meta-analysis is based on correlation of KOG delta-ranks across datasets (delta-rank is the difference between mean rank of genes belonging to a KOG class and mean rank of all other genes). With binary measure (1 or 0 to indicate significant and non-significant genes), one-tailed Fisher's exact test for over-representation of each KOG class among significant genes will be performed.
Details
| Package: | KOGMWU |
| Type: | Package |
| Version: | 1.2 |
| Date: | 2019-02-19 |
| License: | GPL-3 |
The most important function is kog.mwu, which performs a series of Mann-Whitney U tests when given two data tables: one, containing measures of interest for each gene (for example, log fold-change), and another, listing the association of each gene with a KOG class. The KOG class annotations for a collection of genes can be obtained using eggNOG-mapper: http://eggnogdb.embl.de/#/app/emapper. To extract KOG annotations understood by this package out of the eggNOG-mapper output, see here: https://github.com/z0on/emapper_to_GOMWU_KOGMWU
Author(s)
Mikhail V. Matz
Maintainer: Mikhail V. Matz <matz@utexas.edu>
References
Dixon, G. B., Davies, S. W., Aglyamova, G. V., Meyer, E., Bay, L. K. and Matz, M. V. Genomic determinants of coral heat tolerance across latitudes. Science 2015, 348:1460-1462. eggNOG-mapper to obtain KOG annotations: http://eggnogdb.embl.de/#/app/emapper To extract KOG annotations from eggNOG-mapper output: https://github.com/z0on/emapper_to_GOMWU_KOGMWU
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 | ## Not run:
data(adults.3dHeat.logFoldChange)
data(larvae.longTerm)
data(larvae.shortTerm)
data(gene2kog)
# Analyzing adult coral response to 3-day heat stress:
alfc.lth=kog.mwu(adults.3dHeat.logFoldChange,gene2kog)
alfc.lth
# coral larvae response to 5-day heat stress:
l.lth=kog.mwu(larvae.longTerm,gene2kog)
l.lth
# coral larvae response to 4-hour heat stress
l.sth=kog.mwu(larvae.shortTerm,gene2kog)
l.sth
# compiling a table of delta-ranks to compare these results:
ktable=makeDeltaRanksTable(list("adults.long"=alfc.lth,"larvae.long"=l.lth,"larvae.short"=l.sth))
# Making a heatmap with hierarchical clustering trees:
pheatmap(as.matrix(ktable),clustering_distance_cols="correlation")
# exploring correlations between datasets
pairs(ktable, lower.panel = panel.smooth, upper.panel = panel.cor)
# p-values of these correlations in the upper panel:
pairs(ktable, lower.panel = panel.smooth, upper.panel = panel.cor.pval)
# plotting individual delta-rank correlations:
corrPlot(x="adults.long",y="larvae.long",ktable)
corrPlot(x="larvae.short",y="larvae.long",ktable)
## End(Not run)
|
Example output
Loading required package: pheatmap
[1] "Continuous measure of interest: will perform MWU test"
term nseqs
6 Signal transduction mechanisms 4723
8 Translation, ribosomal structure and biogenesis 431
11 Inorganic ion transport and metabolism 387
1 Energy production and conversion 350
17 Cell wall/membrane/envelope biogenesis 235
13 Intracellular trafficking, secretion, and vesicular transport 713
3 Cell cycle control, cell division, chromosome partitioning 456
12 Transcription 926
22 Carbohydrate transport and metabolism 514
15 Cytoskeleton 808
10 Nucleotide transport and metabolism 124
9 Chromatin structure and dynamics 314
4 Posttranslational modification, protein turnover, chaperones 1663
5 Cell motility 66
23 Coenzyme transport and metabolism 99
2 Replication, recombination and repair 510
18 Nuclear structure 106
20 Secondary metabolites biosynthesis, transport and catabolism 246
7 Defense mechanisms 602
19 Lipid transport and metabolism 483
21 Extracellular structures 382
16 Amino acid transport and metabolism 551
14 RNA processing and modification 599
delta.rank pval padj
6 503 1.975290e-12 4.543167e-11
8 -1348 5.045068e-12 5.801828e-11
11 977 2.039699e-06 1.563769e-05
1 -916 2.208820e-05 1.270072e-04
17 1100 2.796245e-05 1.286273e-04
13 -609 7.164623e-05 2.746439e-04
3 743 9.132167e-05 3.000569e-04
12 -452 8.573269e-04 2.464815e-03
22 -496 5.664578e-03 1.447614e-02
15 327 2.391698e-02 5.388752e-02
10 -802 2.577229e-02 5.388752e-02
9 -463 4.185822e-02 7.699672e-02
4 -211 4.351989e-02 7.699672e-02
5 -899 6.794914e-02 1.116307e-01
23 -702 8.095447e-02 1.241302e-01
2 297 9.908850e-02 1.424397e-01
18 560 1.501987e-01 2.032100e-01
20 360 1.607049e-01 2.053451e-01
7 -214 1.971382e-01 2.386410e-01
19 204 2.689993e-01 3.007196e-01
21 226 2.745700e-01 3.007196e-01
16 -69 6.921105e-01 7.235701e-01
14 15 9.275128e-01 9.275128e-01
[1] "Continuous measure of interest: will perform MWU test"
term nseqs
5 Signal transduction mechanisms 3527
7 Translation, ribosomal structure and biogenesis 372
1 Energy production and conversion 312
13 Cell wall/membrane/envelope biogenesis 188
10 Intracellular trafficking, secretion, and vesicular transport 624
17 Cytoskeleton 661
18 Lipid transport and metabolism 411
12 Amino acid transport and metabolism 449
3 Posttranslational modification, protein turnover, chaperones 1336
16 Extracellular structures 296
19 Inorganic ion transport and metabolism 293
6 Defense mechanisms 475
4 Cell motility 56
22 Coenzyme transport and metabolism 89
9 Transcription 805
23 Nucleotide transport and metabolism 115
14 Nuclear structure 86
15 Replication, recombination and repair 392
11 RNA processing and modification 512
8 Chromatin structure and dynamics 257
2 Cell cycle control, cell division, chromosome partitioning 353
21 Carbohydrate transport and metabolism 433
20 Secondary metabolites biosynthesis, transport and catabolism 204
delta.rank pval padj
5 425 6.481483e-11 1.490741e-09
7 -820 1.110922e-06 1.277560e-05
1 -860 2.683092e-06 2.057037e-05
13 665 4.620272e-03 2.656656e-02
10 -331 1.188865e-02 5.468780e-02
17 269 3.536437e-02 1.355634e-01
18 313 5.090900e-02 1.539847e-01
12 -297 5.355989e-02 1.539847e-01
3 -163 7.925484e-02 2.025401e-01
16 -308 1.016494e-01 2.337936e-01
19 259 1.706526e-01 3.568191e-01
6 -186 2.128241e-01 3.876130e-01
4 -526 2.190856e-01 3.876130e-01
22 -321 3.443076e-01 5.656483e-01
9 -94 4.218868e-01 6.140175e-01
23 -238 4.271426e-01 6.140175e-01
14 241 4.851455e-01 6.387659e-01
15 111 4.999037e-01 6.387659e-01
11 -68 6.400061e-01 7.691819e-01
8 86 6.688538e-01 7.691819e-01
2 -17 9.195196e-01 9.783174e-01
21 7 9.638452e-01 9.783174e-01
20 6 9.783174e-01 9.783174e-01
[1] "Continuous measure of interest: will perform MWU test"
term nseqs
1 Energy production and conversion 310
15 Replication, recombination and repair 395
12 Amino acid transport and metabolism 448
7 Translation, ribosomal structure and biogenesis 370
5 Signal transduction mechanisms 3535
14 Nuclear structure 86
16 Extracellular structures 299
18 Lipid transport and metabolism 414
4 Cell motility 57
3 Posttranslational modification, protein turnover, chaperones 1338
13 Cell wall/membrane/envelope biogenesis 187
9 Transcription 803
19 Inorganic ion transport and metabolism 287
11 RNA processing and modification 508
20 Secondary metabolites biosynthesis, transport and catabolism 207
2 Cell cycle control, cell division, chromosome partitioning 354
21 Carbohydrate transport and metabolism 432
23 Nucleotide transport and metabolism 114
6 Defense mechanisms 474
17 Cytoskeleton 665
10 Intracellular trafficking, secretion, and vesicular transport 622
8 Chromatin structure and dynamics 258
22 Coenzyme transport and metabolism 89
delta.rank pval padj
1 -704 0.0001311754 0.003017033
15 -539 0.0009984303 0.010687775
12 -492 0.0013940577 0.010687775
7 -513 0.0023781220 0.013674201
5 171 0.0086021244 0.039569772
14 769 0.0260839752 0.099988572
16 364 0.0517464329 0.162198436
18 -305 0.0564168471 0.162198436
4 -731 0.0848350539 0.216800693
3 154 0.0984521437 0.226439931
13 345 0.1427622383 0.298502862
9 164 0.1610714849 0.308720346
19 230 0.2293518698 0.405776385
11 -160 0.2699350455 0.438847157
20 -239 0.2862046675 0.438847157
2 -166 0.3360102051 0.459203833
21 149 0.3433468206 0.459203833
23 -276 0.3593769131 0.459203833
6 128 0.3926991116 0.475372609
17 103 0.4197344377 0.482694603
10 -87 0.5083183209 0.549990823
8 128 0.5260781787 0.549990823
22 158 0.6427766368 0.642776637
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