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GEMINI interactions (version 0.20.1)
Only files with version 0.20.1 are accepted.
This tool requires a catalogue of known protein-protein interactions. Such interaction data, obtained from the Human Protein Reference Database (HPRD), is part of GEMINI's own annotation data, but you can choose to provide your own interactions data instead.
By default, the tool finds all genes affected by loss-of-function variants in your input, then, for every such gene, reports its interaction partners if they are also affected by any variant. If you specify the name of a gene of interest (e.g. PTPN22) here, you get the affected interaction partners of only this particular gene reported, irrespective of whether your gene of interest itself is affected by any variant or not.
A value of 1, for example, means: report only affected direct interaction partners. A value of 0 restricts the report to just variants in the query gene itself.

What it does

Integrating the knowledge of the known protein-protein interactions would be useful in explaining variation data. Meaning to say that a damaging variant in an interacting partner of a potential protein may be equally interesting as the protein itself. We have used the HPRD binary interaction data to build a p-p network graph which can be explored by GEMINI.

Details

interactions: Find genes among variants that are interacting partners.

Integrating the knowledge of the known protein-protein interactions would be useful in explaining variation data. Meaning to say that a damaging variant in an interacting partner of a potential protein may be equally interesting as the protein itself. We have used the HPRD binary interaction data to build a p-p network graph which can be explored by GEMINI.

Examples

EXAMPLE with setting -g CTBP2 and -r 3:

sample   gene    order_of_interaction    interacting_gene
M128215  CTBP2   0_order:                CTBP2
M128215  CTBP2   1_order:                RAI2
M128215  CTBP2   2_order:                RB1
M128215  CTBP2   3_order:                TGM2,NOTCH2NL

Return CTBP2 (-g) interacting gene variants till the third order (-r)

EXAMPLE lof_interactions (use this option to restrict your analysis to only LoF variants); lof_interactions and -r 3:

sample    lof_gene    order_of_interaction    interacting_gene
M128215   TGM2        1_order:                RB1
M128215   TGM2        2_order:                none
M128215   TGM2        3_order:                NOTCH2NL,CTBP2

Meaning to say return all LoF gene TGM2 (in sample M128215) interacting partners to a 3rd order of interaction.

EXAMPLE --var. An extended variant information (chrom, start, end etc.) for the interacting gene may be achieved with the –var option for both the interactions and the lof_interactions. Settings '-g CTBP2', '-r 3' and '--var':

sample   gene    order_of_interaction    interacting_gene    var_id  chrom   start           end             impact          biotype         in_dbsnp    clinvar_sig   clinvar_disease_name    aaf_1kg_all     aaf_esp_all
M128215  CTBP2   0                       CTBP2               5       chr10   126678091       126678092       stop_gain       protein_coding  1           None          None                    None            None
M128215  CTBP2   1                       RAI2                9       chrX    17819376        17819377        non_syn_coding  protein_coding  1           None          None                    1               0.000473
M128215  CTBP2   2                       RB1                 7       chr13   48873834        48873835        upstream        protein_coding  1           None          None                    0.94            None
M128215  CTBP2   3                       NOTCH2NL            1       chr1    145273344       145273345       non_syn_coding  protein_coding  1           None          None                    None            None
M128215  CTBP2   3                       TGM2                8       chr20   36779423        36779424        stop_gain       protein_coding  0           None          None                    None            None

EXAMPLE with the following settings; '-r 3', '--var':

sample    lof_gene   order_of_interaction   interacting_gene   var_id   chrom   start         end             impact          biotype         in_dbsnp   clinvar_sig   clinvar_disease_name    aaf_1kg_all     aaf_esp_all
M128215   TGM2       1                      RB1                7        chr13   48873834      48873835        upstream        protein_coding  1          None          None                    0.94            None
M128215   TGM2       3                      NOTCH2NL           1        chr1    145273344     145273345       non_syn_coding  protein_coding  1          None          None                    None            None
M128215   TGM2       3                      CTBP2              5        chr10   126678091     126678092       stop_gain       protein_coding  1          None          None                    None            None