(a­) Regulatory Pathways

There are some databases which provides the details various biological pathways.

 

Database

Description

Url

KEGG PATHWAY Database 

It is a collection of manually drawn pathway maps representing Knowledge on the molecular interaction and reaction networks

http://www.genome.jp/kegg/regulation.html

SPAD

( Signaling PAthway Database)

It is a collection of multiple signal transduction pathways

http://www.grt.kyushu-u.ac.jp/spad/

FlyNets

Database for molecular interactions in  Drosophila melanogaster

http://gifts.univ-mrs.fr:80/FlyNets/FlyNets_home_page.html

Klotho:

Biochemical Compounds Declarative Database

This database provides the details of various biochemical pathways.

http://www.biocheminfo.org/klotho/

BIOBASE

It is a combined source of various Pathways, diseases, Transcription factors and a collection of inherited disease mutations

http://www.biobase=international.com/

SMPDB

(Small Molecule Pathway Database )

SMPDB is an interactive, visual database which contains small molecule pathways in humans

http://www.smpdb.ca/

Reactome

Reactome is a database of biological pathways.

http://www.reactome.org/

INOH

INOH is a database on Signaling pathways..

http://www.inoh.org/

Metabolome.jp

It is a metabolic pathway-focused database

http://metabolome.jp/

Cancer Cell Map

This database provides the details of  various pathways related to cancer.

http://cancer.cellmap.org/cellmap/

 

(b) Microarray Databases

Some databases gives the data related to Microarray gene expressions. Some of them are listed below:

Database

Description

Url

Gene Expression Omnibus - NCBI

It is a functional genomic data repository of array and sequence based data

http://www.ncbi.nlm.nih.gov/geo/

Stanford Microarray database

t is a data repository of microaaray

http://smd.stanford.edu/

Genevestigator database 

This database gives the information related to microarray gene expression data.

https://www.genevestigator.com/gv/index.jsp

ArrayExpress at EBI

It is a database of functional genomics experiments.

http://www.ebi.ac.uk/arrayexpress/

UNC Microarray database

It is the database sct as a storage , retrieval and visualization portal of microarray data.

https://genome.unc.edu/

UNC modENCODE Microarray database

It is a microarray database

https://genome.unc.edu/

MUSC database

It is a repository of microarray data

http://proteogenomics.musc.edu/ma/musc_madb.php?page=home&act=manage

UPSC-BASE

The database is a repository for DNA microarray data generated by MUSC investigators as well as researchers in the global research community.

http://www.upscbase.db.umu.se/

ArrayTrack

It is a combined portal for managing, analyzing interoperating microarray data

http://www.fda.gov/ScienceResearch/BioinformaticsTools/Arraytrack//

 

(c) Enzyme Databases

These Databases provides various enzymes details. Some of the databases are as following:

Database

Description

Url

BRENDA

A database which provides with the information about various enzymes

http://www.brenda-enzymes.org/

KEGG LIGAND Database

KEGG LIGAND Database deals with the details of various enzymes.

http://www.genome.jp/dbget/ligand.html

ENZYME
Enzyme nomenclature database

This database gives the functions and details of the pathways in which enzymes are involved.

http://www.expasy.ch:80/enzyme/

PROMISE

It gives the Prosthetic groups and Metal Ions in Protein Active Sites

http://metallo.scripps.edu/promise/

ExplorEnz

 

It is an enzyme database through which various enzymes can be explored

http://www.enzyme-database.org/

Enzyme Structures Database

This database contains various enzymes details and their structures as well

http://www.ebi.ac.uk/thornton-srv/databases/enzymes/

BioChemWeb.org 

It is a database which provides with various enzymes details.

http://www.biochemweb.org/enzymes.shtml

Enzyme Structures Database - UCL

 

A database which provides with the enzymes details including their structures

http://www.biochem.ucl.ac.uk/bsm/enzymes/

IntEnz 

It is a database of various enzymes.

http://www.ebi.ac.uk/intenz/

Thermodynamics of Enzyme-Catalyzed Reactions

This database gives the thermodynamic information of enzyme-catalyzed reaction

http://xpdb.nist.gov/enzyme_thermodynamics/

 

 

(d) Immunological Databases

There are some databases which gives immunological data. Some of these databases are as following:

Database

Description

Url

AntiJen

An integrated database of kinetics, thermodynamic  and functional aspects of MHC Ligand, TCR-MHC Complexes, T Cell Epitope, TAP, B Cell Epitope molecules and immunological Protein-Protein interactions

http://www.darrenflower.info/antijen/

Conformational Epitope Database 

A collection of conformational epitopes, the immunological property of the epitope, the source antigen and corresponding antibody of the epitope

http://immunet.cn/ced/

European CD40L Defect Database 

A database of CD40 ligand defects leading to X-linked Hyper-IgM syndrome

http://www.expasy.ch/cd40lbase/

ImMunoGeneTics Database

Integrated databases of immunoglobulins, T cell receptors and the major histocompatibility complex (MHC) of all vertebrate species

http://www.ebi.ac.uk/imgt/

V BASE

Human antibody gene database

http://vbase.mrc-cpe.cam.ac.uk/

CYBBbase

Mutation registry for X-linked chronic granulomatous disease: Disease is characterized by a defect of intracellular bacterial killing in neutrophils and monocytes

http://bioinf.uta.fi/CYBBbase/

dbMinor

An overview of the identified minor Histocompatibility antigens

http://www.lumc.nl/rep/cod/redirect/5033/dbminor/

Epitome

Database of Structurally inferred Antigenic Epitopes in Proteins

http://cubic.bioc.columbia.edu/services/epitome/

ImmunoDeficiency Resource (IDR)

A storehouse of information on the immunodeficiencies

http://bioinf.uta.fi/idr/index.shtml

ImmunomeBase

A database for metazoan immunity genes and orthologs

http://bioinf.uta.fi/ImmunomeBase/home.html

Immune Epitope Database

Immune Epitope Database contains data related to antibody and T cell epitopes for humans, non-human primates, rodents, and other animal species

http://www.iedb.org/

BciPep

Database of B cell epitopes

http://www.imtech.res.in/raghava/bcipep/links.html