Welcome to the GeneNetwork Data Quality Control and Upload System. This system is provided to help in uploading your data onto GeneNetwork where you can do analysis on it.
The sections below provide an overview of what features the menu items on the left provide to you. Please peruse the information to get a good big-picture understanding of what the system provides you and how to get the most out of it.
You do need to be logged in to upload data onto this system. Please do that by clicking the "Log In" button at the top of the page.
Species
The GeneNetwork service provides datasets and tools for doing genetic studies — from its introduction:
GeneNetwork is a group of linked data sets and tools used to study complex networks of genes, molecules, and higher order gene function and phenotypes. …
With this in mind, it follows that the data in the system is centered aroud a variety of species. The species section will list the currently available species in the system, and give you the ability to add new ones, if the one you want to work on does not currently exist on GeneNetwork
Populations
Your studies will probably focus on a particular subset of the entire species you are interested in – your population.
Populations are a way to organise the species data so as to link data to specific know populations for a particular species, e.g. The BXD population of mice (Mus musculus)
In older GeneNetwork documentation, you might run into the term InbredSet. Should you run into it, it is a term that we've deprecated that essentially just means the population.
Samples
These are the samples or individuals (sometimes cases) that were involved in the experiment, and from whom the data was derived.
Genotype Data
This section will allow you to view and upload the genetic markers for your species, and the genotype encodings used for your particular population.
While, technically, genetic markers relate to the species in general, and not to a particular population, the data (allele information) itself relates to the particular population it was generated from – specifically, to the actual individuals used in the experiment.
This is the reason why the genotype data information comes under the population, and will check for the prior existence of the related samples/individuals before attempting an upload of your data.
Expression Data
TODO: Document this …
Phenotype Data
TODO: Document this …
Individual Data
TODO: Document this …
RNA-Seq Data
TODO: Document this …