Hi Perry,

Sorry for the delay in responding. I should explain that the annotation
packages that we provide are built upon the results of an in-house Perl
script (described in Barbosa-Morais et al) where we map probes to the
genome and transcriptome separately and collate the results. As you point
out, the resources used are not well-documented so it took a while to get
the relevant information from the people that actually run the script. We
hope to improve on this for future releases. As for your query, we were
essentially using an old version of Unigene for cross-referencing.

The last time the Perl script was run in September 2011, we used UniGene
v230 which had an entry Hs.466662 with the gene symbol C1orf151 and Entrez
gene ID 440574. The way these get associated with Illumina probes is
through sequence cross-references in the UniGene entry. So, for example,
the top BLAST hit in RefSeq for the first probe, ILMN_2064311, was the
transcript NM_001204083 which is one of the cross-references in the UniGene
record. The second of the four probes matches the same transcript while the
other two match another RefSeq transcript, NM_001204089, that is also among
the cross-reference sequences in the same UniGene record.

In the current version of UniGene (v236) the gene symbol for that same
record is now MINOS1. It still contains the same RefSeq transcript links so
assuming those still came up as the top BLAST hits for these probes then we
would still end up with all having the same Entrez Gene ID.

The Ensembl gene IDs come directly from the BLAST search against the
Ensembl transcripts.


Mark


On Fri, Nov 15, 2013 at 8:43 PM, P.D. Moerland <p.d.moerland@amc.uva.nl>wrote:

>  Dear all, dear Mark,
>
> I'm a grateful user of the illuminaHumanv4.db annotation package. One of
> my collaborators is interested in probes mapping to C1orf151 according to
> the reannotation provided by the package. However, the re-annotation for
> these probes seems inconsistent:
>
> > Illids = get("C1orf151",revmap(illuminaHumanv4SYMBOLREANNOTATED))
> > Illids
> [1] "ILMN_2064311" "ILMN_1657860" "ILMN_1789599" "ILMN_2405009"
>
> > indx = match(Illids,illuminaHumanv4fullReannotation()[,1])
> > tab  =  illuminaHumanv4fullReannotation()[indx,]
> > tab[,c(1,4,11:13,16)]
>          IlluminaID       ProbeQuality EntrezReannotated
> GenomicLocation SymbolReannotated EnsemblReannotated
>   4615 ILMN_2064311          Bad            440574
>  chr1:19954844:19954893:+          C1orf151    ENSG00000173436
> 24195 ILMN_1657860      Perfect            440574
> chr1:19954399:19954448:+          C1orf151    ENSG00000173436
> 39363 ILMN_1789599      Perfect            440574
> chr1:19984747:19984796:+          C1orf151    ENSG00000158747
> 46631 ILMN_2405009      Perfect            440574
> chr1:19984595:19984644:+          C1orf151    ENSG00000158747
>
> As you can see two probes map to ENSG00000173436 and the other two probes
> to ENSG00000158747. This is in agreement with their annotation on the
> Ensembl website. The reannotated Entrez Gene ID and the reannotated symbol,
> however, seem inconsistent with this. According to the Ensembl website and
> according to org.Hs.eg.db the annotation of the two ENSG IDs is:
>
> > IDs = unlist(mget(tab$EnsemblReannotated,org.Hs.egENSEMBL2EG))
> > IDs
>  ENSG00000173436  ENSG00000173436 ENSG000001587471 ENSG000001587472
> ENSG000001587471 ENSG000001587472
>         "440574"                 "440574"
> "4681"                    "100532736"           "4681"
> "100532736"
> unlist(mget(IDs,org.Hs.egSYMBOL))
>        440574        440574                4681
> 100532736               4681     100532736
>      "MINOS1"      "MINOS1"        "NBL1" "MINOS1-NBL1"        "NBL1"
> "MINOS1-NBL1"
>
> Note that C1orf151 is an alias for MINOS1 and that MINOS1 and NBL1 are
> neighboring genes on chromosome 1, MINOS-NBL1 is the readthrough
> transcript.
>
> How come that illuminaHumanv4.db links all 4 probes to a single Entrez
> Gene ID (440574) and a single symbol (C1orf151)? The more general question
> is probably, how identifier conversion is performed for the re-annotation.
> I tried to find a description in the package documentation and in
> Barbosa-Morais et al. (2010) but without success.
>
> best wishes,
> Perry
>
>  ---
>
> Perry Moerland, PhD
>
> Room J1B-215
>
> Bioinformatics Laboratory, Department of Clinical Epidemiology,
> Biostatistics and Bioinformatics
>
> Academic Medical Center, University of Amsterdam
>
> Postbus 22660, 1100 DD Amsterdam, The Netherlands
>
> tel: +31 20 5666945
>
> p.d.moerland@amc.uva.nl, http://www.bioinformaticslaboratory.nl/
>
>
>
> > sessionInfo()
>
> R version 3.0.2 (2013-09-25)
>
> Platform: i386-w64-mingw32/i386 (32-bit)
>
>
>
> locale:
>
> [1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United
> Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
>
> [4] LC_NUMERIC=C                            LC_TIME=English_United
> Kingdom.1252
>
>
>
> attached base packages:
>
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> base
>
>
>
> other attached packages:
>
> [1] illuminaHumanv4.db_1.20.0 org.Hs.eg.db_2.10.1
> RSQLite_0.11.4            DBI_0.2-7
>
> [5] AnnotationDbi_1.24.0      Biobase_2.22.0
> BiocGenerics_0.8.0
>
>
>
> loaded via a namespace (and not attached):
>
> [1] AnnotationForge_1.4.0 IRanges_1.20.4        stats4_3.0.2
>
>
>
>  ------------------------------
>
> AMC Disclaimer : http://www.amc.nl/disclaimer
> ------------------------------
>
>

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