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This Wiki is a collection of online information about the analysis pipelines, web applications and databases developed by the Mood Disorders Center of the Johns Hopkins Department of Psychiatry. In addition, some useful notes for developers is included for solving common programming problems. Users are welcome to send suggestions for improving this site.

Metamoodics
 Metamoodics.org (PMID:24018898) is a bioinformatics resource that synthesizes the findings from genetic association studies of mood disorders, including bipolar disorder and major depression.

SynaptomeDB
 SynaptomeDB (PMID:22285564) is an integrated database to retreive, compile, and annotate genes comprising the synaptome. These genes encode components of the synapse including neurotransmitters and their receptors, adhesion/cytoskeletal proteins, scaffold proteins, transporters, and others.

Bioinformoodics
 The database server and applications were developed by previous development team. Although the server will be maintained, there would be no further update and development on these applications. 1. QuickSNP (PMID:17517769)  was developed to help researchers select SNPs for association studies in a cost-effective and efficient manner. It allows for gene-centric SNP selection from a chromosomal region in an automated fashion, automated selection of coding non-synonymous SNPs, and SNP filtering based on inter-SNP distance. It also provides information on availability of genotyping assays for SNPs, and availability of SNPs on whole genome chips, and it produces user-friendly summary tables and results as well as a link to a UCSC Genome Browser track, illustrating the position of the selected tagSNPs in relation to genes and other genomic features. 2. The Bipolar Disorder Phenome database (PMID:17671286)  is meant to complement the large bodies of genetic data that are being generated through the Human Genome Project, The International HapMap Consortium, the Genetic Analysis Information Network, and similar efforts. Johns Hopkins and NIMH researchers have jointly created this database, which posts the clinical phenotypes of over 5,000 people recruited for bipolar disorder genetics studies. The goal is to accelerate discovery of genes that contribute to this common and often disabling disease, by promoting the genetic analysis of clinical subtypes. Researchers can now explore connections between clinical variables and genetics with adequate numbers of subjects to detect even moderate genetic effects. 3. Chromosome 8 SNP Data (PMID:18163389) : Research at Johns Hopkins University and University of Michigan collaborated to genotype 1,461 SNPs on chromosome 8q24 in 3,512 individuals, of whom 1,954 were affected with bipolar disorder. These individuals came from 737 families that consisted of 1,142 nuclear families and broke down into 1,840 parent affected offspring triads (573 with zero genotyped parents, 641 with one genotyped parent, and 626 with two genotyped parents) and 333 discordant sib-pairs. The individuals were ascertained and assessed through the Mood Disorders Research Program at Johns Hopkins University and as part of the National Institute of Mental Health Genetics Initiative on Bipolar Disorder. Chromosome 8q24 is one of the most promising regions of linkage in bipolar disorder, and this data was generated to fine map the region and search for associations.

SVAw
The SVAw (PMID:23497726) (Surrogate Variable Analysis web application)   is a web application dedicated primarily to solve the gene expression heterogeneity caused by factors such as environmental, demographic, genetic and technical factors. It is based on the SVA algorithm developed by Leek JT and Storey JD, (PMID: 20428335 ) A general framework for multiple testing dependence.

BatchBlastExtractor
BatchBlastExtractor (PMID: 18831775): a Java GUI program for parsing information from BLASTX output.

* : not yet publicly available

NGS


Whole Exome Sequencing

 * Whole Exome Sequencing Analysis Pipeline
 * Variants Annotation and Analysis Pipeline *
 * Family Data *
 * Case/Control Collapsing *
 * Synaptome Project
 * Mega-analysis
 * Gene-burden analysis

Whole Genome Sequencing

 * Whole Genome Sequencing Analysis Pipeline *

RNA-Seq

 * RNA-Seq Analysis Pipeline

ChIP-Seq

 * Pipeline for comparative ChIP-seq analysis *

CNV analysis

 * CNV Analysis Pipeline *

GWAS



 * GWAS - CEL to Intensity
 * GWAS - CEL to call
 * GWAS - impute_pipe

Gene Expression

 * Gene Expression Pipeline:

http://metamoodics.igm.jhmi.edu/metamoodics/ge.php * : not yet publicly available

Tools & Scripts

 * VCF to BED
 * plink to VCF
 * BAM to FASTQ
 * SeattleSeq Annotation
 * Manhattan Plot
 * Sort chr_bp file
 * VCF to Excel *
 * 1K Genomes annotation for Annovar
 * Compare 2 tped files
 * Merge duplicates
 * liftOver hg18/19
 * Query_STRING