Standards for Common GeneSet Types

Type of Data: Differential Expression Profiling

Gene Set Name: Genes [upregulated/downregulated/differentially expressed] in [tissue] [comparison]. Example: Genes differentially expressed in striatum of C57Bl/6J compared to C57Bl/6C. Note: spell out anatomical terms as nouns, e.g. striatum, not striatal. Include complete strain names, e.g. C57BL/6J not B6.

Gene Set Figure Label: B6JvsB6CStriatum

Gene Set Description: Indicate which samples were compared. What experimental manipulations or tissue differences are being examined? Indicate statistical methodology, significance thresholds and which changes are reported here. Indicate if uploaded p-value, q-value, effect size or fold change and fold change reference. Example: Striatum gene expression differences between naive C57BL/6J and C57BL/6C substrains corresponding to a 5% FDR. A small number of genes are highly differentially expressed between B6 substrains, C57BL/6J (high alcohol consumption preference) and C57BL/6C (low alcohol consumption preference). Fold expression change are relative to B6/J.

Gene Set Contents: Gene identifier and statistical score for differential expression, e.g. p-value, q-value, correlation coefficient, binary score, effect size or fold change.

Type of Data: Published QTL Candidate Gene List

Gene Set Name: Description (name, Published QT Chr # MGI:#). Example: cocaine related behavior 10 (Cocrb10, Published QTL Chr #)

Gene Set Figure Label: (QTL-name-Organism-Chr #). Example: QTL-Cocrb10-Mouse-Chr 9

Gene Set Description: QTL Name Definition, candidate gene selection method (e.g. 1.5 LOD drop; inter-marker interval). Exact description of phenotype. Strains used for mapping should be included. Example: Rats were subjected to a forced swim test (FST) procedure in which they are placed in water for 5 min, and their behavior was scored every 5 sec as immobility, climbing, or swimming. Data were analyzed for each activity with consideration given to their non-independence. p-value:0.0002, Variance: 3.6, Peak Marker: D5Rat40 (BLAT 16538053) Spans 1-41538053. This interval was obtained by using a fixed interval width of 25 Mbp around the peak marker. Strains were WKY/NHsd and F344/NHsd. Also defined as Imm3.

Gene Set Contents: Gene identifier and binary score.

Type of Data: Co-Expression to Phenotype

Gene Set Name: Describe tissue and phenotype correlated. Example: Cerebellum gene expression correlates of acetic acid writhing behavior in BXD recombinant inbred mice.

Gene Set Figure Label: Co-expression writhing

Gene Set Description: Indicate what the comparison was that was made and any statistical cut-offs that were used. Example: Cerebellum gene co-expression with acetic acid writhing in BXD RI mice. Gene expression data was obtained from genenetwork.org SJUT Cerebellum mRNA M430 (Mar05) RMA data set. Behavioral phenotype data was collected by RMQ and consisted of the number of writhes in response to 0.6% acetic acid i.p.

Gene Set Contents: Gene identifier and statistical score for co-expression. e.g. R-squared, p-value, q-value, binary threshold.

Type of Data: Reference Ontology

Gene Set Name: Term # and name. Example: MP:XXXXXXX Abnormal.

Gene Set Figure Label: Term #. Example: Term #

Gene Set Description: Term Definition. Example: “Increase in the dose or concentration of a foreign compound required to induce a specific level of response” www.informatics.jax.org, 2010-12-01

Gene Set Contents: All gene sets include genes, mutant alleles or gene products annotated to an ontology term by a professional curator. Each gene directly annotated to the term is given a score of 1, each gene connected to a term through annotations to its higher order parents is given a score of 2. To use only direct annotations in an analysis assign a threshold of < 2 to each Gene Set.

Type of Data: Co-Expression Clusters

Gene Set Name: Co-Expression clusters. Example: Co-expression cluster of nicotine Dependence genes significantly expressed in the adolescent PFC, VS and Hippocampus.

Gene Set Figure Label: Abbreviated description. Example: Adolesc Rat Nic Dependence

Gene Set Description: Indicate what samples were compared and what was clustered. Example: Studies analyzing brain samples from female rats that had been injected with nicotine at four different ages show that nicotine exerts the greatest influence during adolescence. Using DNA microarrays, gene expression correlates were obtained from the prefrontal cortex (PFC), ventral striatum (VS), and hippocampus. Principal cluster analysis was then used to identify 76 genes that changed significantly in at least one of these three brain regions during the experiment.

Gene Set Contents: Gene identifier and statistical score for cluster analysis or binary threshold.

Type of Data: Genome Wide Association Study

Gene Set Name: GWAS of ... Example: GWAS of Alcohol and Nicotine Dependence in Australian DNA-Pools.

Gene Set Figure Label: Abbreviated description. Example: GWAS Alcohol Nicotine

Gene Set Description: List of positional candidate genes after correcting for multiple testing and controlling the false discovery rate from genome wide association study. Represents genes associated with a linked cytological region or genes ‘near’ an associated SNP. Example: Genome-wide association study identifies a locus at 7p15.2 associated with endometriosis.

Gene Set Contents: Gene identifier and binary threshold.