wanglab

kegg

KEGG pathway entries paired with variant annotations for training and evaluating multimodal biological reasoning models (used by the BioReason work).

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Updated: Jun 2

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Over 1,159 rows of default/train

answer

string_label

alzheimer's disease15%
parkinson's disease14%
amyotrophic lateral sclerosis13%

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string_label

Chromosome Number: 14 Network Definition of the pathway: ATXN3* // (BECN1+PIK3C3+ATG14+PIK3R4+AMBRA1) Genes in the pathway: ATXN3; ataxin 3 | BECN1; beclin 1 | PIK3C3; phosphatidylinositol 3-kinase catalytic subunit type 3 | ATG14; autophagy related 14 | PIK3R4; phosphoinositide-3-kinase regulatory subunit 4 | AMBRA1; autophagy and beclin 1 regulator 1 Given this context, what is the biological effect of this ATXN3 allele, specifically what disease does this contribute to?2%
Chromosome Number: 14 Network Definition of the pathway: "Glutamate -> GRM1 -> GNAQ -> PLCB -> IP3 -> (ITPR1+(ATXN2*,ATXN3*)) -> Ca2+ -- MCU -> Ca2+(mito) -- MPTP -> CYCS" Genes in the pathway: GRM1; glutamate metabotropic receptor 1 | GNAQ; G protein subunit alpha q | PLCB1; phospholipase C beta 1 | PLCB2; phospholipase C beta 2 | PLCB3; phospholipase C beta 3 | PLCB4; phospholipase C beta 4 | ITPR1; inositol 1,4,5-trisphosphate receptor type 1 | ATXN2; ataxin 2 | ATXN3; ataxin 3 | MCU; mitochondrial calcium uniporter | VDAC1; voltage dependent anion channel 1 | VDAC2; voltage dependent anion channel 2 | VDAC3; voltage dependent anion channel 3 | SLC25A4; solute carrier family 25 member 4 | SLC25A5; solute carrier family 25 member 5 | SLC25A6; solute carrier family 25 member 6 | SLC25A31; solute carrier family 25 member 31 | CYCS; cytochrome c, somatic Given this context, what is the biological effect of this ATXN3 allele, specifically what disease does this contribute to?2%
Chromosome Number: 14 Network Definition of the pathway: PSEN1* -> ITPR -> Ca2+ -- MCU -> Ca2+(mito) -- MPTP -> CYCS Genes in the pathway: PSEN1; presenilin 1 | ITPR1; inositol 1,4,5-trisphosphate receptor type 1 | ITPR2; inositol 1,4,5-trisphosphate receptor type 2 | ITPR3; inositol 1,4,5-trisphosphate receptor type 3 | MCU; mitochondrial calcium uniporter | VDAC1; voltage dependent anion channel 1 | VDAC2; voltage dependent anion channel 2 | VDAC3; voltage dependent anion channel 3 | SLC25A4; solute carrier family 25 member 4 | SLC25A5; solute carrier family 25 member 5 | SLC25A6; solute carrier family 25 member 6 | SLC25A31; solute carrier family 25 member 31 | CYCS; cytochrome c, somatic Given this context, what is the biological effect of this PSEN1 allele, specifically what disease does this contribute to?1%

kegg

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reasoning

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