seek
Getting Started
Functional Networks
Method
Genomics data types
Evidence
Tissue-specific Networks
Functional interactions
Examples
IL1B in blood vessel
Functional module detection
Method
NetWAS - Network-wide Association Study
Method
GWAS File
NetWAS Results
Examples
Hypertension GWAS
Additional GWAS
Sei
Introduction
Input
File formats
Genome coordinates
Large submissions
Output
Sequence classes
Regulatory feature scores
DeepSEA (Beluga)
Introduction
Input
File formats
Genome coordinates
Large submissions
Output
Regulatory feature scores
Variant scores
In-silico mutagenesis
ExPecto
Introduction
Download
Predicted expression effects
Variation potential directionality scores
Method Details
SEEK - Search-Based Exploration of Expression Compendium
What is SEEK?
Cross-organism, cross platform, coexpression search
SEEK hubbiness correction
SEEK vs SPELL comparison
Getting Started
Starting a search
Viewing the retrieved genes and datasets
Gene-enrichment analysis
Limit search to tissue or disease related datasets
Case Studies
Case Study #1: Study a pathway of interest
i. Explore a pathway
ii. Find disease states and cancer types
iii. Discover other gene candidates in this pathway
Case Study #2: Study a differentially expressed gene-set, glean underlying pathways and processes
Case Study #3: Find functionally related gene pairs involving the query
Case Study #4: Model organisms can capture different processes of cancer
Evaluating your search result
Use the Gene Enrichment function to evaluate the coexpressed genes
Use the dataset enrichment chart to check for over-representation
Uses a clustering based evaluation
How do I improve the results?
FAQ
General questions
What is SEEK?
What is SEEK used for?
What are the advantages of SEEK?
Algorithm questions
What is the dataset weighting algorithm used by SEEK?
How does SEEK compute significance for dataset weight?
How is the score of each gene computed?
How do I know if the coexpressed genes retrieved by SEEK are significant?
How do I know if my query is coexpressed or not?
What is a dataset keyword?
Usage questions
How do I narrow down the scope of datasets used in the query?
How do I get the complete list of genes or datasets prioritized to the given query?
How can I check the rank for a gene or dataset of interest?
How can I visualize the expression for a particular gene of interest?
Which datasets were used for my query?
How large a query can SEEK handle?
How much time does searching a query take?
Citation
Citations
Tissue-specific networks, NetWAS
Variant effect predictions (ExPecto)
Autism gene predictions
Tissue-expression predictions
HumanBase
Docs
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