Files

Columns

Description

experiment.txt.gz

Organism

Experimental organism. The current version of NeuroGeM includes D. melanogaster, S. cerevisiae or C. elegans.

GeneID

Common genome database IDs (FlyBase, WormBase, SGD).

Type of modification

This field has one of S, E, and No effect, denoting suppressor, enhancer, and non-modifier, respectively.

Disease model

Disease model name. Current NeuroGeM includes Alzheimer's disease (AD), Huntington's disease (HD), Parkinson's disease (PD), Spinocerebellar ataxia type 1 (SCA1), Spinocerebellar ataxia type 3 (SCA3), Spinocerebellar ataxia type 7 (SCA7), Amyotrophic lateral sclerosis (ALS), or PolyQ disease (PolyQ).

Disease induction

This field describes prion-expression cassette including promoter and prion gene.

Modulation method

This field describes how the expression of a target gene was modulated, and has one of Overexpression, Gain-of-function, Knockdown, Knockout, and Loss-of-function. Overexpression and gain-of-function denote increase of expression level, while knockdown, knockout, and loss-of-function denote decrease or complete deletion of expression level.

Cell type

This field describes information cell or organism assayed.

Experimental scale

This field describe the scale of experiment, and has one of High-throughput, primary, High-throughput, secondary, or Low-throughput.

Pubmed ID

This field contains a pubmed ID which links to the original paper.

Note

This field contains additional experimental information.

Measurement

This field describes how the change in symptom was measured.

Mode of action

This field describes whether the gene changes the size/number of protein aggregates (aggregation modifier, denoted by 'A') or disease symptoms (toxicity modifier, denoted by 'T').

gene_ontology.txt.gz

GO ID

GeneOntology ID.

Definition

GO ID description.

Parent node IDs

This field contains GO IDs in parent relation. This information is utilized to search genes in a similar pathway or with a similar function.

gene.txt.gz

Organism

Experimental organism. The current version of NeuroGeM has one of D. melanogaster, S. cerevisiae or C. elegans.

GeneID

Common genome database IDs (FlyBase, WormBase, SGD).

Gene name

The official name of a gene used in respective genome databases. Some genes may not have a gene name.

Secondary IDs

This field contains comma-separated synonyms.

Description

This field briefly describes the function of a gene. This information was extracted from original genome databases and STRING.

Gene Ontology

This field contains comma separated GeneOntology IDs.

STRING ID

This field contains the corresponding STRING ID

Uniprot ID

This field contains the corresponding comma-separated Uniprot IDs

homologene.txt.gz

Group ID

This field describes a group of homologous genes.

Gene ID

Common genome database IDs (FlyBase, WormBase, SGD).

Homologous genes

This field contains a tab-separated list of genes included in the same homologous gene group. For easy access, the gene list is redundantly iterated.

interaction.txt.gz

Two Gene IDs

This contains tab-separated IDs of interacting gene pairs.

Confidence score

This field contains a confidence score stored in STRING.