PathwayResources

Table of Contents

1. Overview
2. Links to Pathway Resources
3. Links to Non-Pathway Resources

Overview

This Wiki topic is intended to capture and present the ever-changing list of recommended online pathway and gene network resources. Most resources do not contain tools for gene set analysis, however they almost all promote browsing through the pathways visually.

Links to Pathway Resources

• Science_Signaling -- Science magazine's online resource entitled "Signal Transduction Knowledge Environment"
• Science_Netwatch - a list with their opinion on useful resources
• Reactome.org - a very comprehensive set of metabolic pathways.
• The key strength of Reactome is that it has the huge overview map, whereas most resources chop such data into so-called "canonical pathways."
• Note that metabolic pathways are not always representative of signaling cascades, nor of tissue-specificity. What may appear as "one big connected pathway" may in fact take place in multiple tissues, with blood plasma as an intermediate.
• Reactome has gallus gallus (chicken) pathways, however the pathway views appear under human -- compare Cell cycle Control for human and rat for example.
• Biocyc - This resource contains 500+ pathways, but is as comprehensive as most other resources are currently.
• Biocyc contains numerous tools, click a few example links on their front page.
• Biocyc_Omics_Analysis - This tools allows you to submit a gene set for analysis and visualization on their pathway viewer. It also allows submitting a timecourse and watching the pathways change over time.
• Humancyc - a human-specific pathway view of Biocyc.
• Biopax - Biopax another "comprehensive" pathway resource, and in fact its "Level 2" data feeds Biocyc (above.) Level 3 is its best content, however, and seems more biologically relevant than individual metabolic pathways.
• Biopax is mainly a data download site, however it has great data for download.
• Pathwaycommons - Another "mirror" of Biopax data, it does feature a query-browse workflow, which may prove fruitful when starting with one critical gene.
• Pathguide - A list of all individual pathway databases, roughly the precursor to comprehensive resources such as Biopax.
• Individual resources often have specialty expertise far beyond the "big picture" resources.
• CA1_Cell_Hippocampal_Pathways may be a useful specialty resource.

Links to Non-Pathway Resources

Not all gene sets come from pathways or gene networks, and yet some non-pathway resources may give the best indication of the biology happening within a cell.

• Nextbio - This resource is founded on curated expression data from highly relevant biological studies.
• Consider Nextbio the absolute leading (if only) resource on biologically relevant expression data. They pull in thousands of studies from around the world, and curate annotation consistently across studies to make it queriable.
• Nextbio is also perhaps the only resource of its kind to start with the query tool first.
• The general workflow is: gene set → expression studies → biological context from the studies showing similar gene changes
• Expression studies are more sensitive and accurate (correct) than gene set analyses because they compare gene change directions, which clearly separates out many pathways one finds with very commonly changing genes.
• Martini - gene set to gene set comparision tool.
• It uses literature keyword mining as its method of enrichment detection, though it does require two gene sets as input.
• The workflow appears to be: gene set from experiment A, gene set from experiment B, keywords from each set, overlapping keywords identified, unique keywords identified and summarized.