Data mining:WormMart

Introduction

WormMart (http://caprica.caltech.edu:9002/biomart/martview/) provides easy and interactive access to data en masse. In particular, WormMart enables users to retrieve sequences and genome annotations using a variety of filters to constrain retrieved results. Filters include such things as genomic location and the presence or absence of specific annotations. Data can be returned in a variety of formats, inluding HTML, text, FASTA, and even Microsoft Excel. It is expected that WormMart will eventually replace the Batch Genes and Batch Sequences pages.

WormMart is the WormBase implementation of BioMart. Read more about BioMart at its official home page.

WormMart Video Tutorial

http://www.youtube.com/watch?v=BrbMAbxUseo

WormMart Worked Examples

• Example 1 List all synonyms for the following genes; bli-1, egl-43, lag-1.

• Example 2 From all genes in C.elegans that have an ortholog in C. briggsae, are located in chromosome III, are sterile in an RNAi screen, and have annotated UTRs, provide a FASTA file containing peptide sequence.

• Example 3 Download the set of all RNAi experiments that resulted in an Emb phenotype, and in which the target genes are classified as serine/threonine kinases.

• Example 4 Retrieve 1.5 kb promoter region upstream of a bunch of genes.

• Example 5 How do I retrieve a list of transcription factors which when mutated or targeted by RNAi cause embryonic lethal phenotype?

• Example 6 What genes are EXCLUSIVELY expressed in touch cell neurons?