Download Annotation

Annotation
EPP 245/298
Statistical Analysis of
Laboratory Data
1
Annotation
• Given that one has found one of more
genes that are differentially expressed,
there are a number useful things to know
– What is the putative function?
– What pathways are know to contain this
gene?
– What other proteins interact with the given
protein?
– etc.
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EPP 245 Statistical Analysis of
Laboratory Data
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Two-color array example
> alldata[1,]
[1] 473 888 170 1137
86 290 109 226 370 659
[16] 324 196 638 102 293
> geneID[1,]
Name
ID
1 NM_006182 discoidin domain receptor family, member
359
484
102
293
174
http://www.ncbi.nlm.nih.gov/genome/guide/human/resources.shtml
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EPP 245 Statistical Analysis of
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Affy Example
> library(annaffy)
Loading required package: GO
Loading required package: KEGG
Loading required package: annotate
> probeids <- geneNames(eset.rma)[allp1adj < .05]
> symbols <- aafSymbol(probeids,"hgu95av2")
Loading required package: hgu95av2
> symbols[[1]]
An object of class "aafSymbol"
[1] "DDR1"
> getText(symbols[[1]])
[1] "DDR1"
> gos <- aafGO(probeids,"hgu95av2")
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> gos[[1]]
An object of class "aafGO"
[[1]]
An object of class "aafGOItem"
@id
"GO:0005524"
@name "ATP binding"
@type "Molecular Function"
@evid "IEA"
[[2]]
An object of class "aafGOItem"
@id
"GO:0007155"
@name "cell adhesion"
@type "Biological Process"
@evid "IEA"
[[3]]
An object of class "aafGOItem"
@id
"GO:0007155"
@name "cell adhesion"
@type "Biological Process"
@evid "TAS"
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[[4]]
An object of class "aafGOItem"
@id
"GO:0005887"
@name "integral to plasma membrane"
@type "Cellular Component"
@evid "TAS"
[[5]]
An object of class "aafGOItem"
@id
"GO:0016020"
@name "membrane"
@type "Cellular Component"
@evid "IEA"
[[6]]
An object of class "aafGOItem"
@id
"GO:0006468"
@name "protein amino acid phosphorylation"
@type "Biological Process"
@evid "IEA"
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EPP 245 Statistical Analysis of
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[[7]]
An object of class "aafGOItem"
@id
"GO:0004674"
@name "protein serine/threonine kinase activity"
@type "Molecular Function"
@evid "IEA"
[[8]]
An object of class "aafGOItem"
@id
"GO:0004872"
@name "receptor activity"
@type "Molecular Function"
@evid "IEA"
[[9]]
An object of class "aafGOItem"
@id
"GO:0016740"
@name "transferase activity"
@type "Molecular Function"
@evid "IEA"
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EPP 245 Statistical Analysis of
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[[10]]
An object of class "aafGOItem"
@id
"GO:0004714"
@name "transmembrane receptor protein tyrosine kinase activity"
@type "Molecular Function"
@evid "IEA"
[[11]]
An object of class "aafGOItem"
@id
"GO:0004714"
@name "transmembrane receptor protein tyrosine kinase activity"
@type "Molecular Function"
@evid "TAS"
[[12]]
An object of class "aafGOItem"
@id
"GO:0007169"
@name "transmembrane receptor protein tyrosine kinase signaling pathway"
@type "Biological Process"
@evid "IEA"
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EPP 245 Statistical Analysis of
Laboratory Data
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GO Evidence Codes
• IEA = inferred from electronic annotation
(e.g., BLAST). Uncurated
• TAS = traceable author statement (i.e.,
someone said so).
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EPP 245 Statistical Analysis of
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•
•
•
•
•
•
•
•
•
IDA = inferred from direct assay
IEP = inferred from expression pattern
IGI = inferred from genetic interaction
IMP = inferred from mutant phenotype
IPI = inferred from physical interaction
ISS = inferred from sequence similarity
NAS = non-traceable author statement
ND = no biological data available
NR = not recorded
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EPP 245 Statistical Analysis of
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Online Access
> gbs <- aafGenBank(probeids,"hgu95av2")
> getURL(gbs[[1]])
[1]
"http://www.ncbi.nlm.nih.gov/entrez/query.
fcgi?cmd=search&db=nucleotide&term=U48705%
5BACCN%5D&doptcmdl=GenBank"
> lls <- aafLocusLink(probeids,"hgu95av2")
> getURL(lls[[1]])
[1]
"http://www.ncbi.nlm.nih.gov/entrez/query.
fcgi?db=gene&cmd=Retrieve&dopt=Graphics&li
st_uids=780"
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EPP 245 Statistical Analysis of
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Abstracts
> pmids <- aafPubMed(probeids,"hgu95av2")
> pmids[[1]]
An object of class "aafPubMed"
[1] 15111304 14764702 14500648 12935821 12477932
9659899 8977099 8796349 8682498 8622863
8390675 8302582
[13] 8226977 7848919 7789998 7774938
> getURL(pmids[[1]])
[1]
"http://www.ncbi.nih.gov/entrez/query.fcgi?tool=bi
oconductor&cmd=Retrieve&db=PubMed&list_uids=151113
04%2c14764702%2c14500648%2c12935821%2c12477932%2c9
659899%2c8977099%2c8796349%2c8682498%2c8622863%2c8
390675%2c8302582%2c8226977%2c7848919%2c7789998%2c7
774938“
> browseURL(getURL(lls[[1]]))
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EPP 245 Statistical Analysis of
Laboratory Data
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