Bioconductor注释专题：Inparanoid

Inparanoid简介

Inparanoid packages收集了通过 inparanoid 算法获得的同源基因组。该算法主要通过Blast算法比较一对不同物种蛋白质组（proteome）的相似性，获得orthology group，而在orthology group里的seed orthologs作为参考，用于遍历寻找和比对其他物种间更为相似的序列。orthology group里面的所有同源蛋白的数目称为inparalogs，每组orthology group的inparalog都有和seed ortholog的相似性打分。目前这个数据库已经比对了35个物种之间的同源蛋白，而在bioconductor上则有5个物种每个相比所有35个物种之间的同源蛋白数据集，分别是：

• hom.Hs.inp.db for human mappings to the other 35 species

• hom.Mm.inp.db for mouse mappings to the other 35 species

• hom.Rn.inp.db for rat mappings to the other 35 species

• hom.Dm.inp.db for fly mappings to the other 35 species

• hom.Sc.inp.db for yeast mappings to the other 35 species

今天主要讲讲如何用这些注释包的使用，比如何获得某个基因的同源基因，同源基因之间的seed pairs。

以人（hom.Hs.inp.db）为例讲讲信息提取方法

每个注释包都有对应每个物种的信息，物种两两对应，比如人对小鼠，同样地，和小鼠对人的包内的信息保持一致，可以通过seed pair获得他们的交集。 hom.Hs.inp.db包里的数据主要包括：

• hom.Hs.inp_dbconn：Collect information about the package annotation DB

• hom.Hs.inpHOMSA ：Map between IDs for genes in one organism to their predicted paralogs in another hom.Hs.inpRATNO map would provide mappings between human and rat.

• hom.Hs.inpMAPCOUNTS：number of mapped keys for the maps in package hom.Hs.inp.db

• hom.Hs.inpORGANISM：The Organism for hom.Hs.inp

包的组成如下图所示，人相对其他物种的paralog的对象名称为hom.Hs.inpXXXXX，XXXXX五个字符就是对应物种的缩写：

1. 通过基因直接检索

假如想看人和鼠的同源基因：

1. > as.list(hom.Hs.inpMUSMU[1:4])

2. $ENSP00000364178

3. [1] "ENSMUSP00000097561"

4. $ENSP00000356224

5. [1] "ENSMUSP00000051825"

6. $ENSP00000386259

7. [1] "ENSMUSP00000074773"

8. $ENSP00000271588

9. [1] "ENSMUSP00000074340"

既然都是annotation db系列，从hom db里提取出来的信息也可以到org.db里查询：

1. #随便挑个人的基因

2. > # load the organism annotation data for human

3. > library(org.Hs.eg.db)

4. > # get the entrex gene ID and ensembl protein id for gene symbol "MSX2"

5. > select(org.Hs.eg.db,

6. + keys="MSX2",

7. + columns=c("ENTREZID","ENSEMBLPROT"),

8. + keytype="SYMBOL")

9. SYMBOL ENTREZID ENSEMBLPROT

10. 1 MSX2 4488 ENSP00000239243

11. 2 MSX2 4488 ENSP00000427425

12. #找同源

13. > # use the inparanoid package to get the mouse gene that is considered

14. > # equivalent to ensembl protein ID "ENSP00000239243"

15. > select(hom.Hs.inp.db,

16. + keys="ENSP00000239243",

17. + columns="MUS_MUSCULUS",

18. + keytype="HOMO_SAPIENS")

19. HOMO_SAPIENS MUS_MUSCULUS

20. 1 ENSP00000239243 ENSMUSP00000021922

21. # load the organism annotation data for mouse

22. > library(org.Mm.eg.db)

23. > # get the entrez gene ID and gene Symbol for "ENSMUSP00000021922"

24. > select(org.Mm.eg.db,

25. + keys="ENSMUSP00000021922",

26. + columns=c("ENTREZID","SYMBOL"),

27. + keytype="ENSEMBLPROT")

28. ENSEMBLPROT ENTREZID SYMBOL

29. 1 ENSMUSP00000021922 17702 Msx2

2.通过dbi接口以seed pair方式进行查询

连接数据库

1. > # make a connection to the human database

2. > mycon <- hom.Hs.inp_dbconn()

3. > # make a list of all the tables that are available in the DB

4. > head(dbListTables(mycon))

5. [1] "Acyrthosiphon_pisum" "Aedes_aegypti"

6. [3] "Anopheles_gambiae" "Apis_mellifera"

7. [5] "Arabidopsis_thaliana" "Aspergillus_fumigatus"

8. > # make a list of the columns in the table of interest

9. > dbListFields(mycon, "mus_musculus") ##获得数据库的名字mus_musculus

10. [1] "inp_id" "clust_id" "species" "score"

11. [5] "seed_status"

通过SQL语句查询mus_musculus中ENSP00000301011对应的种子“cluster ID”

1. > #make a query that will let us see which clust_id we need #

2. > sql <- "SELECT * FROM mus_musculus WHERE inp_id = 'ENSP00000301011';"

3. > #retrieve the data

4. > dataOut <- dbGetQuery(mycon, sql)

5. > dataOut

6. inp_id clust_id species score seed_status

7. 1 ENSP00000301011 2084 HOMSA 1 100%

又或者想通过cluster ID查询inparanoid里基因名

1. > #make a query that will let us see all the data that is affiliated with a clust id

2. > sql <- "SELECT * FROM mus_musculus WHERE clust_id = '1731';"

3. > #retrieve the data

4. > dataOut <- dbGetQuery(mycon, sql)

5. > dataOut

6. inp_id clust_id species score seed_status

7. 1 ENSP00000273857 1731 HOMSA 1 100%

8. 2 ENSMUSP00000005352 1731 MUSMU 1 100%

id 1731对应的物种同源蛋白分别是ENSP00000273857 和 ENSMUSP00000005352

其他

AnnotationDbi也提供了一个函数inpIDMapper可以快速提取物种间同源蛋白，比较方便。

REF http://bioconductor.org/packages/release/data/annotation/manuals/hom.Hs.inp.db/man/hom.Hs.inp.db.pdf http://www.imsbio.co.jp/RGM/Rrdfile?f=hom.Hs.inp.db/man/hom.Hs.inpORGVSORGMAP.Rd&d=RBC https://www.rdocumentation.org/packages/AnnotationDbi/versions/1.34.4/topics/inpIDMapper

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