[annotation] [Fwd:What evidence code to use?]

Wed Nov 28 11:24:35 PST 2007

ok with me if we need to make the distinction.  I took it to mean the 
difference between a simple  alignment report and a more comprehensive 
analysis.  Phylogenetic analyses employ powerful algorithms, but at the 
core of the analysis are manually curated multiple alignments from 
hundreds of species.  These could be RCA for me.  At the end of the day, 
I think it doesn't matter :) since all these measures are predictive and 
not experimental determinations.

Judy

Karen Christie wrote:
> My recollection is that RCA was proposed by SGD to handle papers such 
> as Samanta and Liang 2003 (url below) where they did computational 
> analysis of large-scale protein interaction data.
>
> http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000074191
>
> The original documentation for RCA explicitly stated that it was not 
> to be used for sequence data. At the St. Croix meeting, Sue Rhee 
> brought up the point that some computational analyses combined 
> sequence data into the types of analyses done by Samanta and Liang. On 
> that basis, it was agreed that RCA could include sequence data, but 
> was not intended for analyses that were entirely sequence based.
>
> -Karen
>
>
> On Wed, 28 Nov 2007, Mike Cherry wrote:
>
>> I believe RCA was proposed by SGD to use with analyzes like Biopixie.
>>
>> Cheers, Mike
>>
>>
>> On Nov 27, 2007, at 9:00 PM, Judith Blake 
>> <jblake at informatics.jax.org> wrote:
>>
>>> This is exactly what RCA was originally used for.  With the FANTOM 
>>> project [mouse full length cDNA annotatons], participants employed a 
>>> series of algorithmic approaches combined with manual inspection and 
>>> evaluation to provide annotations.  Actually, I think RCA was 
>>> created as a result of the FANTOM project.
>>>
>>> Judy
>>>
>>> Tanya Berardini wrote:
>>>> Forwarding this from the evidence code discussion group. Apologies 
>>>> to those who are on both lists.  I've sorted the emails from top to 
>>>> bottom in chronological order for easier reading:
>>>>
>>>> ----------
>>>> My original email:
>>>>
>>>>> Ah, the eternal question:  Is it ISS, is it RCA?
>>>>>
>>>>> I've got a paper that describes the identification of a nice big set
>>>>> of transcription factors in Arabidopsis.
>>>>>
>>>>> http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=11118137&dopt=AbstractPlus 
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> The authors use a combination of motif searches + BLAST + sequence
>>>>> alignment and review those by eye and came up with 1500 or so genes
>>>>> that they call 'transcription factors.'
>>>>>
>>>>> Right now, we've got these annotated to 'transcription factor
>>>>> activity' with the evidence code ISS but nothing in the evidence_with
>>>>> column.  If I leave these as ISS, I'd like to put something in the
>>>>> with column, but what?  Does this type of a combination of sequence
>>>>> analysis methods that's reviewed manually make it RCA?  Not according
>>>>> to the current RCA documentation:
>>>>>
>>>>> "Examples where the RCA evidence code should not be used:
>>>>>
>>>>>     * Annotations based on more than one type of gene product 
>>>>> sequence
>>>>> based evidence, including such things as BLAST, profile HMMs, TMHMM,
>>>>> SignalP, PROSITE, InterPro, mapping files such as interpro2go etc.
>>>>> should use the ISS code. "
>>>>>
>>>>> Should I wait till ISS comes to a resolution?
>>>>>
>>>>> Help!
>>>>
>>>> ---------
>>>> Ben's reply:
>>>>
>>>> If you can't put something USEFUL in the WITH column, I think this 
>>>> has to be RCA.
>>>> I guess under the new, non-documented system, this would be ISS/no 
>>>> "With" ISA/ISO/ISM would require withs... (either seq ids or model 
>>>> aka interpro ids).
>>>>
>>>>
>>>> Ben
>>>>
>>>> ----------
>>>>
>>>> Val's reply:
>>>>
>>>> This is *exactly* the type of data why I was orginally suggesting 
>>>> that RCA should not be restricted to analysis which include some 
>>>> experimental component.  Unfortunately I couldn't come up with any 
>>>> good examples at the time.
>>>>
>>>> These would surely be  better as RCA, even though they are sequence 
>>>> based
>>>>
>>>> Val
>>>>
>>>> ----------
>>>>
>>>> Susan's reply:
>>>>
>>>> I've just hit another example...
>>>>
>>>> Enhanced function annotations for Drosophila serine proteases: A case
>>>> study for
>>>> systematic annotation of multi-member gene families.
>>>>
>>>> Shah PK, Tripathi LP, Jensen LJ, Gahnim M, Mason C, Furlong EE, 
>>>> Rodrigues V,
>>>> White KP, Bork P, Sowdhamini R.
>>>>
>>>> PMID: 17996400
>>>>
>>>> This is a functional classification of serine proteases based on a
>>>> 'function residue clustering' algorithm. The algorithm incorporates 
>>>> info
>>>> from sequence alignments, hydrophobicity plots and info about key
>>>> residues from 3D structures - all sequence based but no one thing 
>>>> to put
>>>> in the 'with'.
>>>>
>>>> Susan
>>>>
>>>> -----------
>>>>
>>>> Pascale's reply:
>>>>
>>>> Tanya,
>>>>
>>>> I thought we agreed that BLAST and InterPro were ISS, as you point 
>>>> out. I don't think ISS + ISS = RCA?? That is, I would say using 
>>>> InterPro or the BLAST result should be enough to make the 
>>>> annotation; we dont need to capture both? In this case, the easiest 
>>>> might be using ISS with an InterPro domain ID in the 'with',
>>>>
>>>> Similarly in the paper Susan cites, they mention several domains 
>>>> and also they have compared to several proteins whose 3D structure 
>>>> has been determined hence can be used in the 'with' - I would pick 
>>>> one of those example proteins and ISS to that.
>>>>
>>>> Pascale
>>>>
>>>> ---------
>>>>
>>>> Any other thoughts?
>>>>
>>>>
>>>> Thanks,
>>>>
>>>> Tanya
>>>>
>>>>
>>>>
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>>>>
>>>>
>>>> -------- Original Message --------
>>>> Subject: Re: [evidence] What evidence code to use?
>>>> Date: Wed, 21 Nov 2007 08:43:16 -0500
>>>> From: Pascale Gaudet <pgaudet at northwestern.edu>
>>>> Reply-To: pgaudet at northwestern.edu
>>>> Organization: Northwestern University
>>>> To: tberardi at acoma.stanford.edu
>>>> CC: evidence at genome.stanford.edu
>>>> References: <47437C88.5070204 at acoma.stanford.edu>
>>>>
>>>> Tanya,
>>>>
>>>> I thought we agreed that BLAST and InterPro were ISS, as you point 
>>>> out.
>>>> I don't think ISS + ISS = RCA?? That is, I would say using InterPro or
>>>> the BLAST result should be enough to make the annotation; we dont need
>>>> to capture both? In this case, the easiest might be using ISS with an
>>>> InterPro domain ID in the 'with',
>>>>
>>>> Similarly in the paper Susan cites, they mention several domains and
>>>> also they have compared to several proteins whose 3D structure has 
>>>> been
>>>> determined hence can be used in the 'with' - I would pick one of those
>>>> example proteins and ISS to that.
>>>>
>>>> Pascale
>>>>
>>>>
>>>>> ------------------------------------------------------------------------------------------ 
>>>>>
>>>>> Tanya Berardini, Ph.D.            tberardi at acoma.stanford.edu
>>>>> The Arabidopsis Information Resource    FAX: (650) 325-6857
>>>>> Carnegie Institution of Washington    Tel: (650) 325-1521 ext. 325
>>>>> Department of Plant Biology        URL: http://arabidopsis.org/
>>>>> 260 Panama St.
>>>>> Stanford, CA 94305
>>>>> ------------------------------------------------------------------------------------------ 
>>>>>
>>>>>
>>>>>
>>>>
>>