computeIA: Compute information accretion for an ontology
In SemDist: Information Accretion-based Function Predictor Evaluation
Description
Usage
Arguments
Value
Note
Author(s)
See Also
Examples
Description
Calculates information accretion for each term in the specified ontology using either user
-specified data or the sequence annotations for the organisms specified (note that organism-specific pacakges must be downloaded separately. See "note" section).
Usage
1
2
3
Arguments
ont
Character representation of ontology version to use. One of "CC", "MF", or "BP"
, corresponding to Cellular Component, Molecular Function, and Biological
Process.
organism
A character vector indicating which organism's annotation data to use.
evcodes
A character vector specifying which evidence codes to use in the ontology
data. Default NULL value causes all codes to be used.
specify.ont
A boolean indicating whether the user wants to specify their own version
of the ontology.
myont
Character object indicating what file to read in the specified ontology from.
The ontology should be specified as a tab-delimited file with 2 columns (no header).
Each row in the file should indicate a parent-child relationship between two GO accessions (e.g. "GO:0003674 GO:0004000")
specify.annotations
Boolean indicating whether the user wants to specify sequence
annotations from a file. Should only be TRUE if specify.ont is TRUE.
annotfile
Character object indicating which file to read sequence annotations from.
Should be a tab-delimited file with 2 columns. The first column is a
list of sequences, the second is a list of GO accessions in the same rows
as the sequences they annotate.
Value
Does not return a specific value. Saves the information accretion values for each term in the ontology
in a .rda file that specifies the organism and the ont version. Parent count and term count
objects are also saved in similarly formatted files so that IA calculations from multiple
organisms can be combined.
Note
In order to compute IA for an organism, the specific annotation data set for that organism must be installed by the user. Here is a list of supported organisms (names in the format that should be passed to computeIA) and the correspoinding packages needed:
anopheles = org.Ag.eg.db
arabidopsis = org.At.tair.db
bovine = org.Bt.eg.db
canine = org.Cf.eg.db
chicken = org.Gg.eg.db
chimp = org.Pt.eg.db
ecolik12 = org.EcK12.eg.db
fly = org.Dm.eg.db
human = org.Hs.eg.db
malaria = org.Pf.plasmo.db
mouse = org.Mm.eg.db
pig = org.Ss.eg.db
rat = org.Rn.eg.db
rhesus = org.Mmu.eg.db
worm = org.Ce.eg.db
xenopus = org.Xl.eg.db
yeast = org.Sc.sgd.db
zebrafish = org.Dr.eg.db
Author(s)
Ian Gonzalez and Wyatt Clark
See Also
Examples
1
2
3
4
5
6
7
# Calculate IA, specify ontology and annotations
ontfile <- system.file("extdata", "mfo_ontology.txt", package="SemDist")
annotations <- system.file("extdata", "MFO_LABELS_TEST.txt", package="SemDist")
computeIA("my", "values", specify.ont=TRUE,
myont=ontfile, specify.annotations=TRUE,
annotfile=annotations)
Example output
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: GO.db
Loading required package: annotate
Loading required package: XML
GO:0000030 GO:0000036 GO:0000099 GO:0000146 GO:0000149 GO:0000150 GO:0000166
2.0000000 4.1699250 1.8073549 0.0000000 7.2915544 6.7279205 4.6412307
GO:0000287 GO:0000339 GO:0000702 GO:0000739 GO:0000822 GO:0000900 GO:0000975
2.1292830 3.3923174 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
GO:0000988 GO:0000989 GO:0001067 GO:0001071 GO:0001595 GO:0001596 GO:0001601
5.8132879 0.0000000 2.8073549 5.1917995 1.5849625 0.0000000 0.0000000
GO:0001602 GO:0001607 GO:0001614 GO:0001637 GO:0001640 GO:0001641 GO:0001646
0.0000000 0.0000000 0.0000000 1.5849625 0.0000000 0.0000000 0.0000000
GO:0001653 GO:0001664 GO:0001671 GO:0001848 GO:0001871 GO:0001882 GO:0001883
0.0000000 2.0874628 0.0000000 7.8765169 6.5156998 5.5156998 0.0000000
GO:0001948 GO:0001965 GO:0002020 GO:0002039 GO:0002046 GO:0002161 GO:0002162
6.8765169 7.8765169 2.5025003 7.8765169 7.8765169 0.5849625 1.0000000
GO:0002166 GO:0003674 GO:0003676 GO:0003677 GO:0003678 GO:0003682 GO:0003684
0.0000000 0.0000000 3.2933074 0.5594274 0.5849625 6.2933074 4.2479275
GO:0003690 GO:0003697 GO:0003700 GO:0003702 GO:0003704 GO:0003712 GO:0003713
0.7369656 0.7369656 0.0000000 1.5849625 1.8744691 0.0000000 0.8930848
GO:0003714 GO:0003723 GO:0003724 GO:0003725 GO:0003727 GO:0003729 GO:0003730
1.1154772 1.4150375 1.0000000 2.3923174 2.3923174 2.8073549 0.5849625
GO:0003735 GO:0003743 GO:0003755 GO:0003756 GO:0003774 GO:0003779 GO:0003785
1.4474590 0.0000000 0.0000000 0.0000000 3.3923174 0.8930848 1.8073549
GO:0003810 GO:0003823 GO:0003824 GO:0003837 GO:0003869 GO:0003885 GO:0003887
0.0000000 7.5156998 1.7858071 1.8073549 2.7004397 0.0000000 0.0000000
GO:0003899 GO:0003906 GO:0003924 GO:0003952 GO:0003954 GO:0003978 GO:0003993
0.0000000 1.5849625 1.2223924 0.0000000 1.3219281 0.0000000 2.7004397
GO:0003995 GO:0004003 GO:0004004 GO:0004016 GO:0004029 GO:0004030 GO:0004032
1.3219281 0.0000000 0.0000000 0.0000000 0.0000000 0.5849625 0.4150375
GO:0004033 GO:0004046 GO:0004089 GO:0004091 GO:0004092 GO:0004107 GO:0004112
0.8073549 1.8073549 1.0000000 3.1154772 0.0000000 0.0000000 1.3219281
GO:0004113 GO:0004130 GO:0004132 GO:0004143 GO:0004144 GO:0004161 GO:0004175
0.0000000 1.0000000 0.0000000 3.2479275 0.0000000 0.0000000 0.7004397
GO:0004177 GO:0004180 GO:0004185 GO:0004190 GO:0004197 GO:0004198 GO:0004222
0.4150375 1.0000000 0.0000000 0.0000000 0.0000000 1.0000000 0.0000000
GO:0004301 GO:0004303 GO:0004324 GO:0004337 GO:0004349 GO:0004363 GO:0004364
0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 2.4594316 1.0000000
GO:0004386 GO:0004392 GO:0004402 GO:0004407 GO:0004415 GO:0004435 GO:0004437
1.8073549 1.5849625 0.0000000 0.0000000 0.0000000 0.0000000 1.3785116
GO:0004438 GO:0004439 GO:0004445 GO:0004457 GO:0004459 GO:0004466 GO:0004468
0.0000000 0.0000000 0.0000000 1.7369656 0.0000000 0.0000000 0.0000000
GO:0004474 GO:0004476 GO:0004478 GO:0004497 GO:0004499 GO:0004514 GO:0004518
0.0000000 0.5849625 1.5849625 2.8073549 0.5849625 0.5849625 1.8930848
GO:0004519 GO:0004520 GO:0004521 GO:0004527 GO:0004529 GO:0004531 GO:0004536
0.4854268 0.0000000 0.0000000 1.8073549 0.0000000 0.5849625 0.8073549
GO:0004540 GO:0004551 GO:0004553 GO:0004555 GO:0004559 GO:0004565 GO:0004582
1.8073549 3.5849625 0.2895066 0.0000000 0.0000000 0.0000000 0.0000000
GO:0004586 GO:0004594 GO:0004601 GO:0004619 GO:0004620 GO:0004623 GO:0004629
1.0000000 3.2479275 0.0000000 0.0000000 0.0000000 0.0000000 0.4150375
GO:0004630 GO:0004631 GO:0004633 GO:0004634 GO:0004645 GO:0004650 GO:0004653
1.0000000 0.0000000 1.0000000 1.0000000 2.0000000 2.1699250 0.0000000
GO:0004659 GO:0004672 GO:0004674 GO:0004679 GO:0004683 GO:0004694 GO:0004697
1.5849625 0.1604647 0.1805722 2.9068906 2.3219281 2.3219281 2.9068906
GO:0004702 GO:0004707 GO:0004713 GO:0004714 GO:0004721 GO:0004722 GO:0004725
0.0000000 0.0000000 3.0874628 0.0000000 0.8930848 0.4854268 1.2223924
GO:0004729 GO:0004748 GO:0004772 GO:0004774 GO:0004775 GO:0004776 GO:0004791
0.0000000 0.0000000 1.0000000 0.0000000 0.0000000 0.0000000 0.0000000
GO:0004792 GO:0004796 GO:0004797 GO:0004807 GO:0004812 GO:0004819 GO:0004832
0.0000000 1.5849625 0.0000000 0.5849625 0.0000000 0.5849625 0.5849625
GO:0004833 GO:0004835 GO:0004842 GO:0004843 GO:0004857 GO:0004859 GO:0004860
0.7369656 2.4594316 0.0000000 0.3219281 1.5145732 0.0000000 0.0000000
GO:0004866 GO:0004867 GO:0004869 GO:0004871 GO:0004872 GO:0004874 GO:0004875
0.0000000 0.3219281 1.3219281 0.0000000 0.1979394 4.0874628 0.0000000
GO:0004879 GO:0004888 GO:0004890 GO:0004896 GO:0004930 GO:0004945 GO:0004967
4.0874628 0.3870231 0.0000000 0.0000000 0.7935491 0.0000000 2.9068906
GO:0004983 GO:0004984 GO:0004993 GO:0005007 GO:0005034 GO:0005041 GO:0005047
0.5849625 2.9068906 0.0000000 0.0000000 3.7004397 0.5849625 0.5849625
GO:0005057 GO:0005070 GO:0005083 GO:0005085 GO:0005087 GO:0005088 GO:0005089
3.2854022 0.0000000 0.3219281 1.3219281 0.5849625 0.0000000 0.5849625
GO:0005092 GO:0005096 GO:0005097 GO:0005099 GO:0005100 GO:0005102 GO:0005125
2.0000000 0.0000000 1.3219281 0.2630344 1.3219281 3.7890541 3.0874628
GO:0005126 GO:0005132 GO:0005134 GO:0005148 GO:0005149 GO:0005150 GO:0005152
1.9175378 2.1699250 1.0000000 2.1699250 1.0000000 0.0000000 0.0000000
GO:0005172 GO:0005178 GO:0005179 GO:0005184 GO:0005198 GO:0005200 GO:0005201
1.0000000 0.0000000 3.0874628 1.0000000 4.6068370 2.5849625 2.3219281
GO:0005212 GO:0005215 GO:0005216 GO:0005244 GO:0005245 GO:0005246 GO:0005247
3.3219281 4.1214102 0.0000000 0.0000000 0.0000000 1.3219281 0.0000000
GO:0005249 GO:0005251 GO:0005253 GO:0005254 GO:0005261 GO:0005262 GO:0005267
0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 1.2223924 1.8073549
GO:0005272 GO:0005275 GO:0005290 GO:0005313 GO:0005315 GO:0005319 GO:0005342
1.8073549 0.7004397 0.0000000 0.0000000 0.0000000 3.5849625 2.0995357
GO:0005353 GO:0005355 GO:0005372 GO:0005375 GO:0005381 GO:0005384 GO:0005388
0.5849625 0.0000000 3.3219281 0.0000000 0.0000000 0.0000000 0.0000000
GO:0005432 GO:0005471 GO:0005487 GO:0005488 GO:0005496 GO:0005506 GO:0005507
0.5849625 1.0000000 4.3923174 0.4130653 1.5849625 1.5849625 1.1255309
GO:0005509 GO:0005515 GO:0005516 GO:0005522 GO:0005524 GO:0005525 GO:0005529
2.3219281 0.2241454 7.2915544 7.8765169 0.0000000 0.0000000 1.3219281
GO:0005536 GO:0005537 GO:0005539 GO:0005540 GO:0005542 GO:0005543 GO:0005544
1.0000000 1.0000000 0.0000000 1.5849625 0.5849625 0.8479969 1.3219281
GO:0005546 GO:0005549 GO:0008009 GO:0008013 GO:0008017 GO:0008022 GO:0008026
0.4150375 8.1006623 0.0000000 7.2915544 0.3219281 6.2915544 0.0000000
GO:0008047 GO:0008066 GO:0008080 GO:0008081 GO:0008083 GO:0008084 GO:0008092
1.0000000 3.7004397 0.0000000 1.8479969 2.5025003 1.5849625 5.1760772
GO:0008093 GO:0008094 GO:0008134 GO:0008135 GO:0008137 GO:0008138 GO:0008140
0.0000000 1.1699250 5.7065919 3.3923174 0.0000000 1.2223924 1.8073549
GO:0008144 GO:0008146 GO:0008168 GO:0008170 GO:0008172 GO:0008173 GO:0008186
7.5156998 0.7369656 0.0000000 0.4854268 1.8073549 1.8073549 1.5849625
GO:0008187 GO:0008188 GO:0008194 GO:0008200 GO:0008201 GO:0008227 GO:0008233
1.0000000 0.0000000 1.0000000 0.0000000 0.5849625 2.9068906 2.4964258
GO:0008234 GO:0008236 GO:0008237 GO:0008238 GO:0008252 GO:0008254 GO:0008270
0.8930848 0.0000000 2.7004397 1.7004397 2.7004397 0.0000000 2.0000000
GO:0008273 GO:0008276 GO:0008289 GO:0008307 GO:0008308 GO:0008324 GO:0008327
0.0000000 0.8073549 5.9307373 3.3219281 0.0000000 0.3625701 0.0000000
GO:0008330 GO:0008374 GO:0008375 GO:0008376 GO:0008378 GO:0008381 GO:0008395
1.8073549 0.5849625 1.3219281 0.7369656 2.0000000 0.0000000 1.5849625
GO:0008409 GO:0008415 GO:0008419 GO:0008420 GO:0008430 GO:0008446 GO:0008453
0.0000000 0.0000000 0.0000000 1.3219281 8.1006623 1.0000000 0.0000000
GO:0008469 GO:0008480 GO:0008483 GO:0008503 GO:0008509 GO:0008519 GO:0008528
0.0000000 1.0000000 0.0000000 1.0000000 2.1699250 0.0000000 0.0000000
GO:0008532 GO:0008534 GO:0008556 GO:0008565 GO:0008641 GO:0008649 GO:0008705
0.0000000 0.0000000 0.0000000 3.5849625 6.7279205 0.0000000 0.0000000
GO:0008757 GO:0008792 GO:0008832 GO:0008863 GO:0008900 GO:0008905 GO:0008928
0.2223924 1.0000000 0.0000000 0.5849625 0.0000000 0.0000000 0.0000000
GO:0008934 GO:0008937 GO:0008990 GO:0009007 GO:0009008 GO:0009044 GO:0009055
1.3219281 0.0000000 0.0000000 0.0000000 1.8073549 2.1699250 7.1917995
GO:0009378 GO:0009673 GO:0009824 GO:0009927 GO:0009973 GO:0009975 GO:0009982
1.0000000 0.5849625 1.5849625 1.0000000 1.3219281 6.7279205 0.4150375
GO:0010011 GO:0010178 GO:0010179 GO:0010181 GO:0010436 GO:0010471 GO:0010472
0.5849625 2.1699250 0.0000000 2.0000000 1.3219281 0.0000000 0.0000000
GO:0010473 GO:0010474 GO:0010475 GO:0010698 GO:0010843 GO:0015026 GO:0015035
0.0000000 0.0000000 0.0000000 2.3219281 0.0000000 4.0874628 0.0000000
GO:0015036 GO:0015075 GO:0015077 GO:0015078 GO:0015079 GO:0015081 GO:0015085
1.3219281 0.7369656 1.0000000 1.0000000 0.4150375 0.4150375 0.2630344
GO:0015086 GO:0015087 GO:0015093 GO:0015094 GO:0015099 GO:0015101 GO:0015103
0.0000000 0.0000000 0.0000000 1.5849625 0.0000000 2.8073549 0.4150375
GO:0015114 GO:0015144 GO:0015145 GO:0015146 GO:0015148 GO:0015149 GO:0015171
0.0000000 2.9068906 0.0000000 1.0000000 0.0000000 0.4150375 0.0000000
GO:0015172 GO:0015174 GO:0015175 GO:0015179 GO:0015186 GO:0015187 GO:0015193
1.8073549 1.8073549 0.4854268 0.4854268 0.5849625 1.3219281 0.5849625
GO:0015197 GO:0015198 GO:0015203 GO:0015204 GO:0015248 GO:0015250 GO:0015267
4.1699250 0.0000000 2.0000000 0.0000000 0.5849625 0.0000000 0.0000000
GO:0015276 GO:0015280 GO:0015288 GO:0015291 GO:0015297 GO:0015298 GO:0015300
0.0000000 0.0000000 0.0000000 1.5849625 0.3219281 0.0000000 0.0000000
GO:0015368 GO:0015399 GO:0015405 GO:0015459 GO:0015464 GO:0015491 GO:0015562
0.0000000 1.9068906 0.0000000 0.3219281 0.0000000 0.0000000 4.0874628
GO:0015578 GO:0015591 GO:0015606 GO:0015631 GO:0015662 GO:0015923 GO:0015925
0.5849625 0.0000000 0.0000000 1.3785116 0.0000000 2.1699250 2.1699250
GO:0015927 GO:0015929 GO:0016151 GO:0016162 GO:0016165 GO:0016175 GO:0016208
2.1699250 2.1699250 3.0000000 2.1699250 1.3219281 0.0000000 2.1699250
GO:0016209 GO:0016229 GO:0016247 GO:0016248 GO:0016251 GO:0016273 GO:0016274
7.1917995 4.3923174 7.1917995 1.3219281 1.1375035 0.7369656 0.0000000
GO:0016277 GO:0016278 GO:0016279 GO:0016298 GO:0016301 GO:0016314 GO:0016405
0.5849625 1.3219281 0.0000000 2.3785116 0.3985494 0.0000000 0.0000000
GO:0016406 GO:0016407 GO:0016410 GO:0016411 GO:0016413 GO:0016435 GO:0016455
1.0000000 1.0000000 1.0000000 1.0000000 0.0000000 0.0000000 1.3219281
GO:0016462 GO:0016491 GO:0016499 GO:0016502 GO:0016520 GO:0016563 GO:0016564
0.0000000 2.3356030 1.5849625 3.7004397 2.9068906 1.2370392 1.4594316
GO:0016565 GO:0016566 GO:0016597 GO:0016614 GO:0016616 GO:0016620 GO:0016627
2.5849625 2.0000000 0.0000000 2.0703893 0.5145732 0.0000000 3.0703893
GO:0016628 GO:0016634 GO:0016645 GO:0016647 GO:0016651 GO:0016655 GO:0016667
1.3219281 0.7369656 3.3923174 1.0000000 3.0703893 1.3219281 3.0703893
GO:0016668 GO:0016671 GO:0016684 GO:0016701 GO:0016702 GO:0016705 GO:0016706
0.0000000 1.3219281 3.3923174 3.0703893 0.0000000 2.8073549 1.5849625
GO:0016707 GO:0016709 GO:0016712 GO:0016725 GO:0016728 GO:0016730 GO:0016731
0.0000000 0.4150375 1.0000000 4.3923174 0.0000000 4.3923174 0.0000000
GO:0016740 GO:0016741 GO:0016746 GO:0016747 GO:0016755 GO:0016757 GO:0016758
1.7971831 3.1233824 2.9307373 0.4150375 2.0000000 2.6088092 0.3219281
GO:0016763 GO:0016765 GO:0016769 GO:0016772 GO:0016773 GO:0016774 GO:0016776
1.7369656 3.3457748 4.9307373 1.0727563 0.6100535 3.8579810 3.8579810
GO:0016779 GO:0016780 GO:0016782 GO:0016783 GO:0016787 GO:0016788 GO:0016791
2.0506261 3.8579810 3.6088092 0.7369656 1.4241397 1.6033410 0.4694853
GO:0016793 GO:0016796 GO:0016798 GO:0016799 GO:0016801 GO:0016803 GO:0016810
3.1699250 0.0000000 2.8443491 1.8744691 5.3037807 0.0000000 3.1338557
GO:0016811 GO:0016814 GO:0016817 GO:0016818 GO:0016820 GO:0016829 GO:0016830
0.3625701 2.1699250 1.7188182 0.0000000 0.0000000 4.4059924 1.3219281
GO:0016831 GO:0016835 GO:0016836 GO:0016838 GO:0016849 GO:0016853 GO:0016854
0.0000000 0.7369656 0.5849625 1.5849625 2.3219281 4.0274807 2.1154772
GO:0016857 GO:0016859 GO:0016860 GO:0016861 GO:0016862 GO:0016864 GO:0016866
0.0000000 2.1154772 1.1154772 1.0000000 1.0000000 1.0000000 1.7004397
GO:0016868 GO:0016874 GO:0016875 GO:0016876 GO:0016877 GO:0016878 GO:0016879
1.0000000 3.8210299 2.3219281 0.0000000 2.9068906 0.0000000 0.3219281
GO:0016881 GO:0016884 GO:0016887 GO:0016889 GO:0016891 GO:0016893 GO:0016894
0.1255309 2.5849625 0.8073549 0.0000000 0.0000000 1.3219281 0.7369656
GO:0016895 GO:0016899 GO:0016903 GO:0016917 GO:0016922 GO:0016929 GO:0016936
0.0000000 2.3219281 3.8073549 3.7004397 4.0874628 1.3219281 1.0000000
GO:0016986 GO:0017017 GO:0017025 GO:0017046 GO:0017076 GO:0017089 GO:0017110
4.0443941 0.0000000 7.8765169 0.0000000 0.4594316 0.5849625 3.5849625
GO:0017111 GO:0017123 GO:0017124 GO:0017134 GO:0017147 GO:0017171 GO:0018024
0.1926451 1.3219281 2.9068906 0.4150375 7.8765169 5.3037807 0.0000000
GO:0019001 GO:0019003 GO:0019104 GO:0019136 GO:0019137 GO:0019139 GO:0019144
1.4150375 0.0000000 0.5849625 0.0000000 2.1699250 1.0000000 3.5849625
GO:0019153 GO:0019154 GO:0019199 GO:0019202 GO:0019205 GO:0019206 GO:0019207
0.0000000 2.3219281 0.0000000 3.4594316 3.4594316 0.0000000 2.7369656
GO:0019210 GO:0019213 GO:0019239 GO:0019783 GO:0019787 GO:0019789 GO:0019825
0.0000000 4.7188182 6.7279205 0.4854268 0.2895066 2.1699250 7.5156998
GO:0019829 GO:0019838 GO:0019842 GO:0019843 GO:0019870 GO:0019887 GO:0019894
0.5849625 6.8765169 7.5156998 3.3923174 0.0000000 0.0000000 2.7004397
GO:0019899 GO:0019900 GO:0019901 GO:0019902 GO:0019903 GO:0019904 GO:0019905
4.7890541 1.0874628 0.1926451 3.0874628 0.0000000 4.9696264 0.0000000
GO:0019911 GO:0019948 GO:0019955 GO:0020037 GO:0022803 GO:0022804 GO:0022821
3.9068906 0.0000000 6.8765169 0.0000000 1.5025003 1.1805722 0.0000000
GO:0022829 GO:0022832 GO:0022833 GO:0022834 GO:0022836 GO:0022838 GO:0022843
2.5849625 0.5849625 1.5849625 1.5849625 1.0000000 0.0000000 0.0000000
GO:0022857 GO:0022890 GO:0022891 GO:0022892 GO:0030020 GO:0030116 GO:0030145
0.3048546 0.8073549 0.0000000 0.2223924 1.0000000 1.5849625 3.0000000
GO:0030151 GO:0030165 GO:0030169 GO:0030228 GO:0030234 GO:0030246 GO:0030247
3.5849625 1.9068906 0.0000000 0.0000000 5.1917995 5.7787342 0.0000000
GO:0030276 GO:0030331 GO:0030332 GO:0030347 GO:0030371 GO:0030414 GO:0030528
7.2915544 0.5849625 7.8765169 0.5849625 0.0000000 0.0000000 4.4693335
GO:0030545 GO:0030547 GO:0030551 GO:0030552 GO:0030554 GO:0030594 GO:0030674
7.9287651 0.0000000 3.4594316 0.0000000 0.1255309 0.0000000 0.0000000
GO:0030675 GO:0030695 GO:0030984 GO:0031072 GO:0031177 GO:0031369 GO:0031406
0.0000000 0.1375035 7.8765169 6.8765169 0.0000000 7.8765169 6.2933074
GO:0031419 GO:0031432 GO:0031490 GO:0031625 GO:0031628 GO:0031690 GO:0031699
0.0000000 2.7004397 0.0000000 3.0874628 2.0000000 2.0000000 0.0000000
GO:0031711 GO:0031726 GO:0031851 GO:0032182 GO:0032403 GO:0032427 GO:0032553
2.0000000 0.0000000 0.0000000 7.2915544 6.0691620 2.9068906 0.6520767
GO:0032555 GO:0032559 GO:0032561 GO:0032810 GO:0032947 GO:0033222 GO:0033229
0.0000000 0.0000000 0.0000000 2.0000000 2.1154772 1.0000000 0.0000000
GO:0033300 GO:0033549 GO:0033558 GO:0033592 GO:0033691 GO:0033699 GO:0033764
0.0000000 1.2223924 0.0000000 0.0000000 1.0000000 0.0000000 0.0000000
GO:0034061 GO:0034062 GO:0034450 GO:0034593 GO:0034594 GO:0034595 GO:0034711
1.2223924 1.2223924 2.1699250 0.7369656 1.3219281 1.3219281 7.8765169
GO:0034737 GO:0034738 GO:0035064 GO:0035091 GO:0035241 GO:0035242 GO:0035251
0.0000000 0.0000000 0.4150375 0.3219281 0.5849625 0.5849625 0.0000000
GO:0035257 GO:0035258 GO:0035312 GO:0035586 GO:0035591 GO:0035639 GO:0042007
0.0000000 0.4150375 0.0000000 3.7004397 0.5849625 0.2223924 1.0000000
GO:0042054 GO:0042084 GO:0042123 GO:0042124 GO:0042156 GO:0042162 GO:0042165
0.4150375 1.8073549 4.9307373 0.0000000 2.8073549 3.2479275 6.5156998
GO:0042166 GO:0042277 GO:0042379 GO:0042393 GO:0042562 GO:0042577 GO:0042578
0.0000000 5.5156998 0.4150375 6.8765169 7.5156998 2.7004397 0.5305147
GO:0042605 GO:0042623 GO:0042625 GO:0042626 GO:0042800 GO:0042802 GO:0042803
0.0000000 0.4150375 0.0000000 0.0000000 0.0000000 3.3846639 0.0000000
GO:0042826 GO:0042887 GO:0042903 GO:0042923 GO:0042924 GO:0042936 GO:0043021
3.0874628 3.9068906 0.5849625 2.0000000 0.5849625 0.0000000 7.5156998
GO:0043022 GO:0043130 GO:0043138 GO:0043140 GO:0043167 GO:0043169 GO:0043176
0.5849625 0.0000000 0.4150375 0.0000000 3.9713793 0.0000000 5.7787342
GO:0043178 GO:0043208 GO:0043295 GO:0043424 GO:0043425 GO:0043492 GO:0043498
8.1006623 0.0000000 0.0000000 1.8073549 2.1699250 1.1699250 8.1006623
GO:0043565 GO:0043566 GO:0043621 GO:0043892 GO:0044212 GO:0045182 GO:0045294
1.0000000 2.9259994 7.8765169 1.8073549 0.0000000 7.9287651 6.8765169
GO:0045296 GO:0045437 GO:0045499 GO:0045549 GO:0046030 GO:0046527 GO:0046556
0.0000000 0.5849625 8.5137276 0.0000000 1.3219281 2.0000000 2.1699250
GO:0046568 GO:0046592 GO:0046625 GO:0046703 GO:0046870 GO:0046872 GO:0046873
0.5849625 0.0000000 2.1699250 4.0874628 3.5849625 0.0000000 1.0000000
GO:0046906 GO:0046912 GO:0046914 GO:0046915 GO:0046943 GO:0046982 GO:0046983
6.1006623 2.0000000 0.5443205 1.8073549 0.0000000 1.2630344 4.2915544
GO:0047196 GO:0047485 GO:0047493 GO:0047499 GO:0047631 GO:0047710 GO:0048019
1.0000000 7.2915544 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
GO:0048020 GO:0048029 GO:0048037 GO:0048155 GO:0048186 GO:0048187 GO:0048306
0.5849625 0.0000000 6.1006623 7.2915544 0.0000000 0.0000000 7.8765169
GO:0048407 GO:0048487 GO:0050126 GO:0050136 GO:0050263 GO:0050291 GO:0050577
1.0000000 0.7369656 1.8073549 0.0000000 0.5849625 0.5849625 1.8073549
GO:0050660 GO:0050661 GO:0050662 GO:0050664 GO:0050681 GO:0050699 GO:0050733
0.0000000 1.0000000 0.0000000 1.3219281 0.5849625 2.9068906 2.9068906
GO:0050750 GO:0050839 GO:0050897 GO:0051015 GO:0051082 GO:0051087 GO:0051119
0.0000000 7.8765169 2.5849625 0.8073549 6.2915544 7.8765169 0.0000000
GO:0051183 GO:0051213 GO:0051219 GO:0051287 GO:0051378 GO:0051381 GO:0051427
4.0874628 3.0703893 7.8765169 1.0000000 2.3219281 2.3219281 3.0874628
GO:0051635 GO:0051717 GO:0051721 GO:0051800 GO:0051861 GO:0051879 GO:0051990
0.0000000 1.3219281 0.0000000 0.0000000 2.1699250 1.0000000 2.3219281
GO:0052579 GO:0052580 GO:0055056 GO:0055102 GO:0060089 GO:0060090 GO:0060589
0.0000000 0.0000000 0.5849625 1.8073549 4.2283254 6.5156998 0.8624965
GO:0060590 GO:0061134 GO:0061135 GO:0070001 GO:0070008 GO:0070011 GO:0070016
2.4594316 2.0000000 0.0000000 2.1154772 0.0000000 0.1069152 2.9068906
GO:0070026 GO:0070035 GO:0070063 GO:0070087 GO:0070181 GO:0070325 GO:0070330
8.1006623 0.0000000 3.0874628 2.9068906 0.0000000 4.0874628 0.0000000
GO:0070402 GO:0070491 GO:0070567 GO:0070568 GO:0070635 GO:0070636 GO:0070818
0.4150375 2.1699250 1.8073549 1.8073549 0.5849625 0.5849625 0.7369656
GO:0070851 GO:0071813 GO:0071814 GO:0072341 GO:0072349 GO:0072509 GO:0080025
2.5025003 0.0000000 7.5156998 0.4854268 1.8073549 0.4150375 1.0000000
GO:0080046 GO:0080048 GO:0080118 GO:0090079
0.0000000 0.0000000 0.5849625 0.0000000
SemDist documentation built on Nov. 8, 2020, 8:27 p.m.
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Description Usage Arguments Value Note Author(s) See Also Examples
Description
Calculates information accretion for each term in the specified ontology using either user -specified data or the sequence annotations for the organisms specified (note that organism-specific pacakges must be downloaded separately. See "note" section).
Usage
1 2 3 |
Arguments
ont |
Character representation of ontology version to use. One of "CC", "MF", or "BP" , corresponding to Cellular Component, Molecular Function, and Biological Process. |
organism |
A character vector indicating which organism's annotation data to use. |
evcodes |
A character vector specifying which evidence codes to use in the ontology data. Default NULL value causes all codes to be used. |
specify.ont |
A boolean indicating whether the user wants to specify their own version of the ontology. |
myont |
Character object indicating what file to read in the specified ontology from. The ontology should be specified as a tab-delimited file with 2 columns (no header). Each row in the file should indicate a parent-child relationship between two GO accessions (e.g. "GO:0003674 GO:0004000") |
specify.annotations |
Boolean indicating whether the user wants to specify sequence annotations from a file. Should only be TRUE if specify.ont is TRUE. |
annotfile |
Character object indicating which file to read sequence annotations from. Should be a tab-delimited file with 2 columns. The first column is a list of sequences, the second is a list of GO accessions in the same rows as the sequences they annotate. |
Value
Does not return a specific value. Saves the information accretion values for each term in the ontology in a .rda file that specifies the organism and the ont version. Parent count and term count objects are also saved in similarly formatted files so that IA calculations from multiple organisms can be combined.
Note
In order to compute IA for an organism, the specific annotation data set for that organism must be installed by the user. Here is a list of supported organisms (names in the format that should be passed to computeIA) and the correspoinding packages needed:
anopheles = org.Ag.eg.db
arabidopsis = org.At.tair.db
bovine = org.Bt.eg.db
canine = org.Cf.eg.db
chicken = org.Gg.eg.db
chimp = org.Pt.eg.db
ecolik12 = org.EcK12.eg.db
fly = org.Dm.eg.db
human = org.Hs.eg.db
malaria = org.Pf.plasmo.db
mouse = org.Mm.eg.db
pig = org.Ss.eg.db
rat = org.Rn.eg.db
rhesus = org.Mmu.eg.db
worm = org.Ce.eg.db
xenopus = org.Xl.eg.db
yeast = org.Sc.sgd.db
zebrafish = org.Dr.eg.db
Author(s)
Ian Gonzalez and Wyatt Clark
See Also
Examples
1 2 3 4 5 6 7 |
# Calculate IA, specify ontology and annotations
ontfile <- system.file("extdata", "mfo_ontology.txt", package="SemDist")
annotations <- system.file("extdata", "MFO_LABELS_TEST.txt", package="SemDist")
computeIA("my", "values", specify.ont=TRUE,
myont=ontfile, specify.annotations=TRUE,
annotfile=annotations)
|
Example output
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: GO.db
Loading required package: annotate
Loading required package: XML
GO:0000030 GO:0000036 GO:0000099 GO:0000146 GO:0000149 GO:0000150 GO:0000166
2.0000000 4.1699250 1.8073549 0.0000000 7.2915544 6.7279205 4.6412307
GO:0000287 GO:0000339 GO:0000702 GO:0000739 GO:0000822 GO:0000900 GO:0000975
2.1292830 3.3923174 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
GO:0000988 GO:0000989 GO:0001067 GO:0001071 GO:0001595 GO:0001596 GO:0001601
5.8132879 0.0000000 2.8073549 5.1917995 1.5849625 0.0000000 0.0000000
GO:0001602 GO:0001607 GO:0001614 GO:0001637 GO:0001640 GO:0001641 GO:0001646
0.0000000 0.0000000 0.0000000 1.5849625 0.0000000 0.0000000 0.0000000
GO:0001653 GO:0001664 GO:0001671 GO:0001848 GO:0001871 GO:0001882 GO:0001883
0.0000000 2.0874628 0.0000000 7.8765169 6.5156998 5.5156998 0.0000000
GO:0001948 GO:0001965 GO:0002020 GO:0002039 GO:0002046 GO:0002161 GO:0002162
6.8765169 7.8765169 2.5025003 7.8765169 7.8765169 0.5849625 1.0000000
GO:0002166 GO:0003674 GO:0003676 GO:0003677 GO:0003678 GO:0003682 GO:0003684
0.0000000 0.0000000 3.2933074 0.5594274 0.5849625 6.2933074 4.2479275
GO:0003690 GO:0003697 GO:0003700 GO:0003702 GO:0003704 GO:0003712 GO:0003713
0.7369656 0.7369656 0.0000000 1.5849625 1.8744691 0.0000000 0.8930848
GO:0003714 GO:0003723 GO:0003724 GO:0003725 GO:0003727 GO:0003729 GO:0003730
1.1154772 1.4150375 1.0000000 2.3923174 2.3923174 2.8073549 0.5849625
GO:0003735 GO:0003743 GO:0003755 GO:0003756 GO:0003774 GO:0003779 GO:0003785
1.4474590 0.0000000 0.0000000 0.0000000 3.3923174 0.8930848 1.8073549
GO:0003810 GO:0003823 GO:0003824 GO:0003837 GO:0003869 GO:0003885 GO:0003887
0.0000000 7.5156998 1.7858071 1.8073549 2.7004397 0.0000000 0.0000000
GO:0003899 GO:0003906 GO:0003924 GO:0003952 GO:0003954 GO:0003978 GO:0003993
0.0000000 1.5849625 1.2223924 0.0000000 1.3219281 0.0000000 2.7004397
GO:0003995 GO:0004003 GO:0004004 GO:0004016 GO:0004029 GO:0004030 GO:0004032
1.3219281 0.0000000 0.0000000 0.0000000 0.0000000 0.5849625 0.4150375
GO:0004033 GO:0004046 GO:0004089 GO:0004091 GO:0004092 GO:0004107 GO:0004112
0.8073549 1.8073549 1.0000000 3.1154772 0.0000000 0.0000000 1.3219281
GO:0004113 GO:0004130 GO:0004132 GO:0004143 GO:0004144 GO:0004161 GO:0004175
0.0000000 1.0000000 0.0000000 3.2479275 0.0000000 0.0000000 0.7004397
GO:0004177 GO:0004180 GO:0004185 GO:0004190 GO:0004197 GO:0004198 GO:0004222
0.4150375 1.0000000 0.0000000 0.0000000 0.0000000 1.0000000 0.0000000
GO:0004301 GO:0004303 GO:0004324 GO:0004337 GO:0004349 GO:0004363 GO:0004364
0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 2.4594316 1.0000000
GO:0004386 GO:0004392 GO:0004402 GO:0004407 GO:0004415 GO:0004435 GO:0004437
1.8073549 1.5849625 0.0000000 0.0000000 0.0000000 0.0000000 1.3785116
GO:0004438 GO:0004439 GO:0004445 GO:0004457 GO:0004459 GO:0004466 GO:0004468
0.0000000 0.0000000 0.0000000 1.7369656 0.0000000 0.0000000 0.0000000
GO:0004474 GO:0004476 GO:0004478 GO:0004497 GO:0004499 GO:0004514 GO:0004518
0.0000000 0.5849625 1.5849625 2.8073549 0.5849625 0.5849625 1.8930848
GO:0004519 GO:0004520 GO:0004521 GO:0004527 GO:0004529 GO:0004531 GO:0004536
0.4854268 0.0000000 0.0000000 1.8073549 0.0000000 0.5849625 0.8073549
GO:0004540 GO:0004551 GO:0004553 GO:0004555 GO:0004559 GO:0004565 GO:0004582
1.8073549 3.5849625 0.2895066 0.0000000 0.0000000 0.0000000 0.0000000
GO:0004586 GO:0004594 GO:0004601 GO:0004619 GO:0004620 GO:0004623 GO:0004629
1.0000000 3.2479275 0.0000000 0.0000000 0.0000000 0.0000000 0.4150375
GO:0004630 GO:0004631 GO:0004633 GO:0004634 GO:0004645 GO:0004650 GO:0004653
1.0000000 0.0000000 1.0000000 1.0000000 2.0000000 2.1699250 0.0000000
GO:0004659 GO:0004672 GO:0004674 GO:0004679 GO:0004683 GO:0004694 GO:0004697
1.5849625 0.1604647 0.1805722 2.9068906 2.3219281 2.3219281 2.9068906
GO:0004702 GO:0004707 GO:0004713 GO:0004714 GO:0004721 GO:0004722 GO:0004725
0.0000000 0.0000000 3.0874628 0.0000000 0.8930848 0.4854268 1.2223924
GO:0004729 GO:0004748 GO:0004772 GO:0004774 GO:0004775 GO:0004776 GO:0004791
0.0000000 0.0000000 1.0000000 0.0000000 0.0000000 0.0000000 0.0000000
GO:0004792 GO:0004796 GO:0004797 GO:0004807 GO:0004812 GO:0004819 GO:0004832
0.0000000 1.5849625 0.0000000 0.5849625 0.0000000 0.5849625 0.5849625
GO:0004833 GO:0004835 GO:0004842 GO:0004843 GO:0004857 GO:0004859 GO:0004860
0.7369656 2.4594316 0.0000000 0.3219281 1.5145732 0.0000000 0.0000000
GO:0004866 GO:0004867 GO:0004869 GO:0004871 GO:0004872 GO:0004874 GO:0004875
0.0000000 0.3219281 1.3219281 0.0000000 0.1979394 4.0874628 0.0000000
GO:0004879 GO:0004888 GO:0004890 GO:0004896 GO:0004930 GO:0004945 GO:0004967
4.0874628 0.3870231 0.0000000 0.0000000 0.7935491 0.0000000 2.9068906
GO:0004983 GO:0004984 GO:0004993 GO:0005007 GO:0005034 GO:0005041 GO:0005047
0.5849625 2.9068906 0.0000000 0.0000000 3.7004397 0.5849625 0.5849625
GO:0005057 GO:0005070 GO:0005083 GO:0005085 GO:0005087 GO:0005088 GO:0005089
3.2854022 0.0000000 0.3219281 1.3219281 0.5849625 0.0000000 0.5849625
GO:0005092 GO:0005096 GO:0005097 GO:0005099 GO:0005100 GO:0005102 GO:0005125
2.0000000 0.0000000 1.3219281 0.2630344 1.3219281 3.7890541 3.0874628
GO:0005126 GO:0005132 GO:0005134 GO:0005148 GO:0005149 GO:0005150 GO:0005152
1.9175378 2.1699250 1.0000000 2.1699250 1.0000000 0.0000000 0.0000000
GO:0005172 GO:0005178 GO:0005179 GO:0005184 GO:0005198 GO:0005200 GO:0005201
1.0000000 0.0000000 3.0874628 1.0000000 4.6068370 2.5849625 2.3219281
GO:0005212 GO:0005215 GO:0005216 GO:0005244 GO:0005245 GO:0005246 GO:0005247
3.3219281 4.1214102 0.0000000 0.0000000 0.0000000 1.3219281 0.0000000
GO:0005249 GO:0005251 GO:0005253 GO:0005254 GO:0005261 GO:0005262 GO:0005267
0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 1.2223924 1.8073549
GO:0005272 GO:0005275 GO:0005290 GO:0005313 GO:0005315 GO:0005319 GO:0005342
1.8073549 0.7004397 0.0000000 0.0000000 0.0000000 3.5849625 2.0995357
GO:0005353 GO:0005355 GO:0005372 GO:0005375 GO:0005381 GO:0005384 GO:0005388
0.5849625 0.0000000 3.3219281 0.0000000 0.0000000 0.0000000 0.0000000
GO:0005432 GO:0005471 GO:0005487 GO:0005488 GO:0005496 GO:0005506 GO:0005507
0.5849625 1.0000000 4.3923174 0.4130653 1.5849625 1.5849625 1.1255309
GO:0005509 GO:0005515 GO:0005516 GO:0005522 GO:0005524 GO:0005525 GO:0005529
2.3219281 0.2241454 7.2915544 7.8765169 0.0000000 0.0000000 1.3219281
GO:0005536 GO:0005537 GO:0005539 GO:0005540 GO:0005542 GO:0005543 GO:0005544
1.0000000 1.0000000 0.0000000 1.5849625 0.5849625 0.8479969 1.3219281
GO:0005546 GO:0005549 GO:0008009 GO:0008013 GO:0008017 GO:0008022 GO:0008026
0.4150375 8.1006623 0.0000000 7.2915544 0.3219281 6.2915544 0.0000000
GO:0008047 GO:0008066 GO:0008080 GO:0008081 GO:0008083 GO:0008084 GO:0008092
1.0000000 3.7004397 0.0000000 1.8479969 2.5025003 1.5849625 5.1760772
GO:0008093 GO:0008094 GO:0008134 GO:0008135 GO:0008137 GO:0008138 GO:0008140
0.0000000 1.1699250 5.7065919 3.3923174 0.0000000 1.2223924 1.8073549
GO:0008144 GO:0008146 GO:0008168 GO:0008170 GO:0008172 GO:0008173 GO:0008186
7.5156998 0.7369656 0.0000000 0.4854268 1.8073549 1.8073549 1.5849625
GO:0008187 GO:0008188 GO:0008194 GO:0008200 GO:0008201 GO:0008227 GO:0008233
1.0000000 0.0000000 1.0000000 0.0000000 0.5849625 2.9068906 2.4964258
GO:0008234 GO:0008236 GO:0008237 GO:0008238 GO:0008252 GO:0008254 GO:0008270
0.8930848 0.0000000 2.7004397 1.7004397 2.7004397 0.0000000 2.0000000
GO:0008273 GO:0008276 GO:0008289 GO:0008307 GO:0008308 GO:0008324 GO:0008327
0.0000000 0.8073549 5.9307373 3.3219281 0.0000000 0.3625701 0.0000000
GO:0008330 GO:0008374 GO:0008375 GO:0008376 GO:0008378 GO:0008381 GO:0008395
1.8073549 0.5849625 1.3219281 0.7369656 2.0000000 0.0000000 1.5849625
GO:0008409 GO:0008415 GO:0008419 GO:0008420 GO:0008430 GO:0008446 GO:0008453
0.0000000 0.0000000 0.0000000 1.3219281 8.1006623 1.0000000 0.0000000
GO:0008469 GO:0008480 GO:0008483 GO:0008503 GO:0008509 GO:0008519 GO:0008528
0.0000000 1.0000000 0.0000000 1.0000000 2.1699250 0.0000000 0.0000000
GO:0008532 GO:0008534 GO:0008556 GO:0008565 GO:0008641 GO:0008649 GO:0008705
0.0000000 0.0000000 0.0000000 3.5849625 6.7279205 0.0000000 0.0000000
GO:0008757 GO:0008792 GO:0008832 GO:0008863 GO:0008900 GO:0008905 GO:0008928
0.2223924 1.0000000 0.0000000 0.5849625 0.0000000 0.0000000 0.0000000
GO:0008934 GO:0008937 GO:0008990 GO:0009007 GO:0009008 GO:0009044 GO:0009055
1.3219281 0.0000000 0.0000000 0.0000000 1.8073549 2.1699250 7.1917995
GO:0009378 GO:0009673 GO:0009824 GO:0009927 GO:0009973 GO:0009975 GO:0009982
1.0000000 0.5849625 1.5849625 1.0000000 1.3219281 6.7279205 0.4150375
GO:0010011 GO:0010178 GO:0010179 GO:0010181 GO:0010436 GO:0010471 GO:0010472
0.5849625 2.1699250 0.0000000 2.0000000 1.3219281 0.0000000 0.0000000
GO:0010473 GO:0010474 GO:0010475 GO:0010698 GO:0010843 GO:0015026 GO:0015035
0.0000000 0.0000000 0.0000000 2.3219281 0.0000000 4.0874628 0.0000000
GO:0015036 GO:0015075 GO:0015077 GO:0015078 GO:0015079 GO:0015081 GO:0015085
1.3219281 0.7369656 1.0000000 1.0000000 0.4150375 0.4150375 0.2630344
GO:0015086 GO:0015087 GO:0015093 GO:0015094 GO:0015099 GO:0015101 GO:0015103
0.0000000 0.0000000 0.0000000 1.5849625 0.0000000 2.8073549 0.4150375
GO:0015114 GO:0015144 GO:0015145 GO:0015146 GO:0015148 GO:0015149 GO:0015171
0.0000000 2.9068906 0.0000000 1.0000000 0.0000000 0.4150375 0.0000000
GO:0015172 GO:0015174 GO:0015175 GO:0015179 GO:0015186 GO:0015187 GO:0015193
1.8073549 1.8073549 0.4854268 0.4854268 0.5849625 1.3219281 0.5849625
GO:0015197 GO:0015198 GO:0015203 GO:0015204 GO:0015248 GO:0015250 GO:0015267
4.1699250 0.0000000 2.0000000 0.0000000 0.5849625 0.0000000 0.0000000
GO:0015276 GO:0015280 GO:0015288 GO:0015291 GO:0015297 GO:0015298 GO:0015300
0.0000000 0.0000000 0.0000000 1.5849625 0.3219281 0.0000000 0.0000000
GO:0015368 GO:0015399 GO:0015405 GO:0015459 GO:0015464 GO:0015491 GO:0015562
0.0000000 1.9068906 0.0000000 0.3219281 0.0000000 0.0000000 4.0874628
GO:0015578 GO:0015591 GO:0015606 GO:0015631 GO:0015662 GO:0015923 GO:0015925
0.5849625 0.0000000 0.0000000 1.3785116 0.0000000 2.1699250 2.1699250
GO:0015927 GO:0015929 GO:0016151 GO:0016162 GO:0016165 GO:0016175 GO:0016208
2.1699250 2.1699250 3.0000000 2.1699250 1.3219281 0.0000000 2.1699250
GO:0016209 GO:0016229 GO:0016247 GO:0016248 GO:0016251 GO:0016273 GO:0016274
7.1917995 4.3923174 7.1917995 1.3219281 1.1375035 0.7369656 0.0000000
GO:0016277 GO:0016278 GO:0016279 GO:0016298 GO:0016301 GO:0016314 GO:0016405
0.5849625 1.3219281 0.0000000 2.3785116 0.3985494 0.0000000 0.0000000
GO:0016406 GO:0016407 GO:0016410 GO:0016411 GO:0016413 GO:0016435 GO:0016455
1.0000000 1.0000000 1.0000000 1.0000000 0.0000000 0.0000000 1.3219281
GO:0016462 GO:0016491 GO:0016499 GO:0016502 GO:0016520 GO:0016563 GO:0016564
0.0000000 2.3356030 1.5849625 3.7004397 2.9068906 1.2370392 1.4594316
GO:0016565 GO:0016566 GO:0016597 GO:0016614 GO:0016616 GO:0016620 GO:0016627
2.5849625 2.0000000 0.0000000 2.0703893 0.5145732 0.0000000 3.0703893
GO:0016628 GO:0016634 GO:0016645 GO:0016647 GO:0016651 GO:0016655 GO:0016667
1.3219281 0.7369656 3.3923174 1.0000000 3.0703893 1.3219281 3.0703893
GO:0016668 GO:0016671 GO:0016684 GO:0016701 GO:0016702 GO:0016705 GO:0016706
0.0000000 1.3219281 3.3923174 3.0703893 0.0000000 2.8073549 1.5849625
GO:0016707 GO:0016709 GO:0016712 GO:0016725 GO:0016728 GO:0016730 GO:0016731
0.0000000 0.4150375 1.0000000 4.3923174 0.0000000 4.3923174 0.0000000
GO:0016740 GO:0016741 GO:0016746 GO:0016747 GO:0016755 GO:0016757 GO:0016758
1.7971831 3.1233824 2.9307373 0.4150375 2.0000000 2.6088092 0.3219281
GO:0016763 GO:0016765 GO:0016769 GO:0016772 GO:0016773 GO:0016774 GO:0016776
1.7369656 3.3457748 4.9307373 1.0727563 0.6100535 3.8579810 3.8579810
GO:0016779 GO:0016780 GO:0016782 GO:0016783 GO:0016787 GO:0016788 GO:0016791
2.0506261 3.8579810 3.6088092 0.7369656 1.4241397 1.6033410 0.4694853
GO:0016793 GO:0016796 GO:0016798 GO:0016799 GO:0016801 GO:0016803 GO:0016810
3.1699250 0.0000000 2.8443491 1.8744691 5.3037807 0.0000000 3.1338557
GO:0016811 GO:0016814 GO:0016817 GO:0016818 GO:0016820 GO:0016829 GO:0016830
0.3625701 2.1699250 1.7188182 0.0000000 0.0000000 4.4059924 1.3219281
GO:0016831 GO:0016835 GO:0016836 GO:0016838 GO:0016849 GO:0016853 GO:0016854
0.0000000 0.7369656 0.5849625 1.5849625 2.3219281 4.0274807 2.1154772
GO:0016857 GO:0016859 GO:0016860 GO:0016861 GO:0016862 GO:0016864 GO:0016866
0.0000000 2.1154772 1.1154772 1.0000000 1.0000000 1.0000000 1.7004397
GO:0016868 GO:0016874 GO:0016875 GO:0016876 GO:0016877 GO:0016878 GO:0016879
1.0000000 3.8210299 2.3219281 0.0000000 2.9068906 0.0000000 0.3219281
GO:0016881 GO:0016884 GO:0016887 GO:0016889 GO:0016891 GO:0016893 GO:0016894
0.1255309 2.5849625 0.8073549 0.0000000 0.0000000 1.3219281 0.7369656
GO:0016895 GO:0016899 GO:0016903 GO:0016917 GO:0016922 GO:0016929 GO:0016936
0.0000000 2.3219281 3.8073549 3.7004397 4.0874628 1.3219281 1.0000000
GO:0016986 GO:0017017 GO:0017025 GO:0017046 GO:0017076 GO:0017089 GO:0017110
4.0443941 0.0000000 7.8765169 0.0000000 0.4594316 0.5849625 3.5849625
GO:0017111 GO:0017123 GO:0017124 GO:0017134 GO:0017147 GO:0017171 GO:0018024
0.1926451 1.3219281 2.9068906 0.4150375 7.8765169 5.3037807 0.0000000
GO:0019001 GO:0019003 GO:0019104 GO:0019136 GO:0019137 GO:0019139 GO:0019144
1.4150375 0.0000000 0.5849625 0.0000000 2.1699250 1.0000000 3.5849625
GO:0019153 GO:0019154 GO:0019199 GO:0019202 GO:0019205 GO:0019206 GO:0019207
0.0000000 2.3219281 0.0000000 3.4594316 3.4594316 0.0000000 2.7369656
GO:0019210 GO:0019213 GO:0019239 GO:0019783 GO:0019787 GO:0019789 GO:0019825
0.0000000 4.7188182 6.7279205 0.4854268 0.2895066 2.1699250 7.5156998
GO:0019829 GO:0019838 GO:0019842 GO:0019843 GO:0019870 GO:0019887 GO:0019894
0.5849625 6.8765169 7.5156998 3.3923174 0.0000000 0.0000000 2.7004397
GO:0019899 GO:0019900 GO:0019901 GO:0019902 GO:0019903 GO:0019904 GO:0019905
4.7890541 1.0874628 0.1926451 3.0874628 0.0000000 4.9696264 0.0000000
GO:0019911 GO:0019948 GO:0019955 GO:0020037 GO:0022803 GO:0022804 GO:0022821
3.9068906 0.0000000 6.8765169 0.0000000 1.5025003 1.1805722 0.0000000
GO:0022829 GO:0022832 GO:0022833 GO:0022834 GO:0022836 GO:0022838 GO:0022843
2.5849625 0.5849625 1.5849625 1.5849625 1.0000000 0.0000000 0.0000000
GO:0022857 GO:0022890 GO:0022891 GO:0022892 GO:0030020 GO:0030116 GO:0030145
0.3048546 0.8073549 0.0000000 0.2223924 1.0000000 1.5849625 3.0000000
GO:0030151 GO:0030165 GO:0030169 GO:0030228 GO:0030234 GO:0030246 GO:0030247
3.5849625 1.9068906 0.0000000 0.0000000 5.1917995 5.7787342 0.0000000
GO:0030276 GO:0030331 GO:0030332 GO:0030347 GO:0030371 GO:0030414 GO:0030528
7.2915544 0.5849625 7.8765169 0.5849625 0.0000000 0.0000000 4.4693335
GO:0030545 GO:0030547 GO:0030551 GO:0030552 GO:0030554 GO:0030594 GO:0030674
7.9287651 0.0000000 3.4594316 0.0000000 0.1255309 0.0000000 0.0000000
GO:0030675 GO:0030695 GO:0030984 GO:0031072 GO:0031177 GO:0031369 GO:0031406
0.0000000 0.1375035 7.8765169 6.8765169 0.0000000 7.8765169 6.2933074
GO:0031419 GO:0031432 GO:0031490 GO:0031625 GO:0031628 GO:0031690 GO:0031699
0.0000000 2.7004397 0.0000000 3.0874628 2.0000000 2.0000000 0.0000000
GO:0031711 GO:0031726 GO:0031851 GO:0032182 GO:0032403 GO:0032427 GO:0032553
2.0000000 0.0000000 0.0000000 7.2915544 6.0691620 2.9068906 0.6520767
GO:0032555 GO:0032559 GO:0032561 GO:0032810 GO:0032947 GO:0033222 GO:0033229
0.0000000 0.0000000 0.0000000 2.0000000 2.1154772 1.0000000 0.0000000
GO:0033300 GO:0033549 GO:0033558 GO:0033592 GO:0033691 GO:0033699 GO:0033764
0.0000000 1.2223924 0.0000000 0.0000000 1.0000000 0.0000000 0.0000000
GO:0034061 GO:0034062 GO:0034450 GO:0034593 GO:0034594 GO:0034595 GO:0034711
1.2223924 1.2223924 2.1699250 0.7369656 1.3219281 1.3219281 7.8765169
GO:0034737 GO:0034738 GO:0035064 GO:0035091 GO:0035241 GO:0035242 GO:0035251
0.0000000 0.0000000 0.4150375 0.3219281 0.5849625 0.5849625 0.0000000
GO:0035257 GO:0035258 GO:0035312 GO:0035586 GO:0035591 GO:0035639 GO:0042007
0.0000000 0.4150375 0.0000000 3.7004397 0.5849625 0.2223924 1.0000000
GO:0042054 GO:0042084 GO:0042123 GO:0042124 GO:0042156 GO:0042162 GO:0042165
0.4150375 1.8073549 4.9307373 0.0000000 2.8073549 3.2479275 6.5156998
GO:0042166 GO:0042277 GO:0042379 GO:0042393 GO:0042562 GO:0042577 GO:0042578
0.0000000 5.5156998 0.4150375 6.8765169 7.5156998 2.7004397 0.5305147
GO:0042605 GO:0042623 GO:0042625 GO:0042626 GO:0042800 GO:0042802 GO:0042803
0.0000000 0.4150375 0.0000000 0.0000000 0.0000000 3.3846639 0.0000000
GO:0042826 GO:0042887 GO:0042903 GO:0042923 GO:0042924 GO:0042936 GO:0043021
3.0874628 3.9068906 0.5849625 2.0000000 0.5849625 0.0000000 7.5156998
GO:0043022 GO:0043130 GO:0043138 GO:0043140 GO:0043167 GO:0043169 GO:0043176
0.5849625 0.0000000 0.4150375 0.0000000 3.9713793 0.0000000 5.7787342
GO:0043178 GO:0043208 GO:0043295 GO:0043424 GO:0043425 GO:0043492 GO:0043498
8.1006623 0.0000000 0.0000000 1.8073549 2.1699250 1.1699250 8.1006623
GO:0043565 GO:0043566 GO:0043621 GO:0043892 GO:0044212 GO:0045182 GO:0045294
1.0000000 2.9259994 7.8765169 1.8073549 0.0000000 7.9287651 6.8765169
GO:0045296 GO:0045437 GO:0045499 GO:0045549 GO:0046030 GO:0046527 GO:0046556
0.0000000 0.5849625 8.5137276 0.0000000 1.3219281 2.0000000 2.1699250
GO:0046568 GO:0046592 GO:0046625 GO:0046703 GO:0046870 GO:0046872 GO:0046873
0.5849625 0.0000000 2.1699250 4.0874628 3.5849625 0.0000000 1.0000000
GO:0046906 GO:0046912 GO:0046914 GO:0046915 GO:0046943 GO:0046982 GO:0046983
6.1006623 2.0000000 0.5443205 1.8073549 0.0000000 1.2630344 4.2915544
GO:0047196 GO:0047485 GO:0047493 GO:0047499 GO:0047631 GO:0047710 GO:0048019
1.0000000 7.2915544 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
GO:0048020 GO:0048029 GO:0048037 GO:0048155 GO:0048186 GO:0048187 GO:0048306
0.5849625 0.0000000 6.1006623 7.2915544 0.0000000 0.0000000 7.8765169
GO:0048407 GO:0048487 GO:0050126 GO:0050136 GO:0050263 GO:0050291 GO:0050577
1.0000000 0.7369656 1.8073549 0.0000000 0.5849625 0.5849625 1.8073549
GO:0050660 GO:0050661 GO:0050662 GO:0050664 GO:0050681 GO:0050699 GO:0050733
0.0000000 1.0000000 0.0000000 1.3219281 0.5849625 2.9068906 2.9068906
GO:0050750 GO:0050839 GO:0050897 GO:0051015 GO:0051082 GO:0051087 GO:0051119
0.0000000 7.8765169 2.5849625 0.8073549 6.2915544 7.8765169 0.0000000
GO:0051183 GO:0051213 GO:0051219 GO:0051287 GO:0051378 GO:0051381 GO:0051427
4.0874628 3.0703893 7.8765169 1.0000000 2.3219281 2.3219281 3.0874628
GO:0051635 GO:0051717 GO:0051721 GO:0051800 GO:0051861 GO:0051879 GO:0051990
0.0000000 1.3219281 0.0000000 0.0000000 2.1699250 1.0000000 2.3219281
GO:0052579 GO:0052580 GO:0055056 GO:0055102 GO:0060089 GO:0060090 GO:0060589
0.0000000 0.0000000 0.5849625 1.8073549 4.2283254 6.5156998 0.8624965
GO:0060590 GO:0061134 GO:0061135 GO:0070001 GO:0070008 GO:0070011 GO:0070016
2.4594316 2.0000000 0.0000000 2.1154772 0.0000000 0.1069152 2.9068906
GO:0070026 GO:0070035 GO:0070063 GO:0070087 GO:0070181 GO:0070325 GO:0070330
8.1006623 0.0000000 3.0874628 2.9068906 0.0000000 4.0874628 0.0000000
GO:0070402 GO:0070491 GO:0070567 GO:0070568 GO:0070635 GO:0070636 GO:0070818
0.4150375 2.1699250 1.8073549 1.8073549 0.5849625 0.5849625 0.7369656
GO:0070851 GO:0071813 GO:0071814 GO:0072341 GO:0072349 GO:0072509 GO:0080025
2.5025003 0.0000000 7.5156998 0.4854268 1.8073549 0.4150375 1.0000000
GO:0080046 GO:0080048 GO:0080118 GO:0090079
0.0000000 0.0000000 0.5849625 0.0000000
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