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Javier Santoyo, 05/30/2010 05:14 pm

SNOW input parameters

Input data.

First thing to choose is the type of analysis you want to perform. Basicaly, choose in the top section Define your input data the kind analysis you want to perform:
  • One list. Users may compare a list of proteins/genes versus a random set of lists
  • Comparing two lists. Compare two custom lists

Select your data.

Select the list of genes or proteins that are already stored in the server or choose to upload data from if your list has not been uploaded yet. If "Comparing two lists" option has been chosen in the "Input data" section there will be a second upload option

Select interactome

Select type of interactome you want to use for your analysis
  • Non filetered interactome. Interactions belonging to all methods will be used.
  • Filtered interactome. Interactions that are going to be used are present in at least two of the methods.
  • Users may also submit their own interactions. This option will help users with custom datasets or with non-human experiments to be analysed. When this option is enabled a new section appears beneath. Here you can choose the interactions file that you previously uploaded into the system. The interactions have to be specified according to the sif format (as follows):
    prot1 pp prot2
    prot1 pp prot3
    prot3 pp prot4
    prot3 pp prot5
    . . .
    . . .
    Column separator in this file is a single tab.

The option Proteins in interactions and list in same id? asks if proteins ids in the interaction file and in the list are the same. If this is not ticked SNOW will convert IDs in order to match interactions IDs with IDs on the list.

Nature of your lists
THis information should be in agreement with the uploaded data.The list of proteins or genes in usual Babelomics format, each entry in a row:

  1. Currently SNOW accepts lists of proteins/genes in the range of 3 to 500 proteins/genes mapped into our interactome of reference.
  1. Snow uses ensembl database for the id cross-reference. Supported IDs* on SNOW are:
    • affy_focus
    • affy_hcg110
    • affy_hugene
    • affy_u133
    • affy_u95
    • agilent_cgh
    • agilent_probe
    • biocarta
    • biocyc
    • ccds
    • cisred
    • codelink
    • embl
    • ensembl_gene
    • ensembl_prot
    • ensembl_transcript
    • ensembl_transcript_same_CDS
    • entrezgene
    • genbank
    • havana_transcript
    • hugo
    • illumina_v1
    • illumina_v2
    • imgt/gene_db
    • imgt/ligm_db
    • ipi
    • locuslink
    • pdb
    • refseq_dna
    • refseq_dna_predicted
    • refseq_peptide
    • refseq_peptide_predicted
    • ucsc
    • unigene
    • uniprot/splicevariant id
    • uniprot/swissprot id
    • uniprot/trembl id
  1. Do you submit genes or proteins?. Snow will use in consecuence either proteins interactome or the "genes interactome" Obviously we know there is not a "genes" interactome but most of our users may bring to the application lists of genes so we translate from databases entries to generate a interactome that could support genes to be mapped in it. Take into account that genes mapped into a preoteins interactome may give a higher connectivity just because a gene may result into different proteins.
    h2. Network generation

Choose the number of non-list proteins/genes that SNOW may introduce between two proteins to find a path. This is like choosing the maximum length of the shortest path to be able to introduce it into the Minimal Connected Network. The options are from 0 to 3.
List of proteins/genes

Job name and description
Put a name a your job and add a description (optional).