Pepsin A

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Pepsin A by Mind Map: Pepsin A

1. 1552 online databases up to date

1.1. 14 categories and 41 subcategories

1.1.1. 8 sections

1.1.1.1. Nucleic acid sequence and structure , transcriptional regulatio

1.1.1.1.1. Added five microRNA databases: miRBase, miRNEST, mirTarBase, PolymiRTS and starBASE, and on the NONCODE database of various types of non-coding RNA

1.1.1.1.2. Structural database

1.1.1.2. Protein sequence and structure, motifs and domains, protein-protein interactions

1.1.1.2.1. Protein database

1.1.1.2.2. Protein structure

1.1.1.3. Mettabolic and signaling pathways,enzymes,protein modification

1.1.1.3.1. Enzyme and metabolism

1.1.1.4. Viruses ,bacteria , protozoa,fungi

1.1.1.4.1. Transcriptional factor (TF) binding site (TFBSs)

1.1.1.5. Human genome , model organisms , comparative genomics

1.1.1.5.1. Phenotypic data table and genotypes

1.1.1.5.2. Model organism

1.1.1.6. Genomic variation,diseases and dug

1.1.1.7. Plant databases

1.1.1.8. Other molecular biology databases

1.2. 185 articles

1.2.1. 58 new molecular biology databases

1.2.2. Update on 100 databases previously featured in NAR

1.2.3. Update descriptions of 23 database that had been described in other journals

2. (B) Organisation of Nucleic Acids Research (NAR) databases and its major grouping

2.1. Nucleotide Sequence Databases

2.1.1. Coding and non-coding DNA

2.1.2. International Nucleotide Sequence Database Collaboration

2.1.3. Gene structure, introns and exons, splice sites

2.1.4. Transcriptional regulator sites and transcription factors

2.2. RNA sequences databases

2.3. Protein sequence databases

2.3.1. General sequence databases

2.3.2. Protein properties

2.3.3. Protein localization and targeting

2.3.4. Protein sequence motifs and active sites

2.3.5. Protein domain databases; protein classification

2.3.6. Databases of individual protein families

2.4. Structure Databases

2.4.1. Small molecules

2.4.2. BARD

2.4.3. Carbohydrates

2.4.4. Nucleic acid structure

2.4.5. Protein structure

2.5. Genomics Databases (non-vertebrate)

2.5.1. MGD - Mouse Genome Database

2.5.2. The Gene Indices

2.5.3. Genome annotation terms, ontologies and nomenclature

2.5.4. Taxonomy and identification

2.5.5. General genomics databases

2.5.6. Viral genome databases

2.5.7. Prokaryotic genome databases

2.5.8. Unicellular eukaryotes genome databases

2.5.9. Fungal genome databases

2.5.10. Invertebrate genome databases

2.6. Metabolic and Signaling Pathways

2.6.1. ChemProt

2.6.2. Prokaryotic genome databases

2.6.3. Enzymes and enzyme nomenclature

2.6.4. Metabolic pathways

2.6.5. Protein-protein interactions

2.6.6. Signalling pathways

2.7. Human and other Vertebrate Genomes

2.7.1. Model organisms, comparative genomics

2.7.2. Human genome databases, maps and viewers

2.7.3. Human ORFs

2.8. Human Genes and Diseases

2.8.1. CancerResource

2.8.2. Protein Mutant Database

2.8.3. General human genetics databases

2.8.4. General polymorphism databases

2.8.5. Cancer gene databases

2.8.6. Gene-, system- or disease-specific databases

2.9. Microarray Data and other Gene Expression Databases

2.10. Proteomics Resources

2.11. Other Molecular Biology Databases

2.11.1. Pubmed

2.11.2. SCLD

2.11.3. Drugs and drug design

2.11.4. Molecular probes and primers

2.12. Organelle databases

2.12.1. Chloroplast Genome Database

2.12.2. FUGOID

2.12.3. GOBASE

2.12.4. Mitochondrial genes and proteins

2.13. Plant databases

2.13.1. Chloroplast Genome Database

2.13.2. General plant databases

2.13.3. Arabidopsis thaliana

2.13.4. Rice

2.13.5. Other plants

2.14. Immunological databases

2.14.1. ALPSbase

2.14.2. MHCBN

2.15. Cell biology

2.15.1. NCBI Bookshelf

2.15.2. ExoCarta

3. (A) Introduction

4. Group members

4.1. Koh Teck Boon

4.1.1. A11QB0070

4.2. Lee Kong Shen

4.2.1. A11QB0095

4.3. Saw Shen Yee

4.3.1. A11QB0097

4.4. Teo Wee Siang

4.4.1. A11QB0078

4.5. Tham Wai Chun

4.5.1. A11QB0088

5. (C) Different types of databases

5.1. Primary nucleotide sequence databases

5.1.1. Repositories for nucleotide sequence data from all organisms

5.1.1.1. DNA Data Bank of Japan (National Institute of Genetics)

5.1.1.2. European Nucleotide Archive (European Bioinformatics Institute)

5.1.1.3. GenBank (National Center for Biotechnology Information)

5.2. Meta databases

5.2.1. With an emphasis on a particular disease or organism

5.2.1.1. Bioinformatic Harvester

5.2.1.1.1. Integrating 26 major protein/gene resources

5.2.1.2. Enzyme Portal

5.2.1.2.1. Integrates enzyme information such as small-molecule chemistry

5.2.1.3. Neuroscience Information Framework

5.2.1.3.1. Integrates hundreds of neuroscience relevant resources, many are listed below

5.3. Genome databases

5.3.1. Collect organism genome sequences and added with curation of experimental literature to improve computed annotations

5.3.1.1. CAMERA

5.3.1.1.1. Resource for microbial genomics and metagenomics

5.3.1.2. Saccharomyces Genome Database

5.3.1.2.1. Genome of the yeast model organism

5.4. Protein sequence database

5.4.1. Collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA.

5.4.1.1. PEDANT

5.4.1.1.1. Protein Extraction, Description and ANalysis Tool

5.4.1.2. PRINTS

5.4.1.2.1. A compendium of protein fingerprints from

5.4.1.3. SUPERFAMILY

5.4.1.3.1. Library of HMMs representing superfamilies and database of (superfamily and family) annotations for all completely sequenced organisms

5.5. Proteomics databases

5.5.1. A database and data analysis platform containing manually-curated details from the PubMed literature in a highly structured and easily searchable format

5.5.1.1. Proteomics Identifications Database (PRIDE)

5.5.1.1.1. A public repository for proteomics data, containing protein and peptide identifications and their associated supporting evidence as well as details of post-translational modifications

5.5.1.2. GelMap

5.5.1.2.1. A public database of proteins identified on 2D gels

5.6. Protein structure database

5.6.1. Database that is modeled around the various experimentally determined protein structures

5.6.1.1. Protein DataBank in Europe (PDBe)

5.6.1.2. ProteinDatabank in Japan(PDBj)

5.6.1.3. Research Collaboratory for Structural Bioinformatics (RCSB)

5.7. Protein model databases

5.7.1. A public resource aimed at storing manually built 3D models of proteins

5.7.1.1. Swiss-model

5.7.1.1.1. Server and Repository for Protein Structure Models

5.7.1.2. ModBase

5.7.1.2.1. Database of Comparative Protein Structure Models

5.7.1.3. Protein Model Portal (PMP)

5.7.1.3.1. Meta database that combines several databases of protein structure models

5.8. RNA databases

5.8.1. To analyze, search and update for the known RNA secondary structures

5.8.1.1. Rfam

5.8.1.1.1. A database of RNA families

5.8.1.2. miRBase

5.8.1.2.1. A microRNA database

5.8.1.3. tmRDB

5.8.1.3.1. A database of tmRNAs - transfer-messenger RNA

5.9. Carbohydrate structure databases

5.9.1. An open-access project that collects primary publication data on carbohydrate structures originating from eukaryotes & prokaryotes

5.9.1.1. EuroCarbDB

5.9.1.1.1. A repository for both carbohydrate sequences/structures and experimental data

5.10. Protein-protein interactions

5.10.1. A database to access establishment of two or more proteins which are intentional physical contacts & then biochemical events and/or electrostatic forces were resulted

5.10.1.1. CCSB Interactome

5.10.1.2. MINT: Molecular INTeraction database

5.10.1.3. BioGRID

5.10.1.3.1. A General Repository for Interaction Datasets

5.11. Signal transduction pathway databases

5.11.1. A database that searching & accessing difference types of cell responses resulted from the difference kind of signal transduction pathway

5.11.1.1. SignaLink Database

5.11.1.2. WikiPathways

5.11.1.2.1. A community resource for contributing and maintaining content dedicated to biological pathways

5.11.1.3. Netpath

5.11.1.3.1. A curated resource of signal transduction pathways in humans

5.12. Metabolic pathway and Protein Function databases

5.12.1. BRENDA

5.12.1.1. The Comprehensive Enzyme Information System, including FRENDA, AMENDA, DRENDA, and KENDA

5.12.2. MANET database

5.12.3. Metabolights

5.13. Microarray databases

5.13.1. As a “storehouse” containing microarray gene expression data

5.13.1.1. To store measurement data, and make them available for analysis and interpretation in other applications

5.13.1.1.1. GPX

5.13.1.1.2. ArrayExpress

5.13.1.1.3. Genevestigator

5.14. Exosomal databases

5.14.1. A manually curated databases of exosomal protein, RNA and lipids.Keep updated with exosome related studies

5.14.1.1. Exocarta

5.15. Mathematical model databases

5.15.1. A group of database which mainly focus on describing, building and publishing model on biological process with the help of computational data

5.15.1.1. Biomodels Databases

5.15.1.2. CellML

5.15.1.3. The Cell Collective

5.16. PCR and quantitative PCR primer databases

5.16.1. A group of databases which includes the primers, probes databases for real time PCR reaction, and also QPCR oligo databases for pathogens

5.16.1.1. PathoOligoDB

5.16.1.2. RTPrimerDB

5.17. Specialized databases

5.17.1. A collection of databases which include data on specific target such as protein, antibodies, DNA, etc

5.17.1.1. AntibodyRegistry

5.17.1.2. BioNumbers

5.17.1.3. Human Gene Mutation Databases

5.18. Taxonomic databases

5.18.1. A group of databases which have the data shown in taxonomy pattern and it is usually contain data for animal, plants and prokaryotes

5.18.1.1. Integrated Taxonomic Information System

5.18.1.2. Encyclopedia of Life

5.19. Wiki-style databases

5.19.1. A collection of databases which enable public to edit data in the databases.

5.19.1.1. EcoliWiki

5.19.1.2. GyDB

5.19.1.3. NeuroLex

5.20. Unsorted

5.20.1. Databases with information not grouping specifically or with any specific pattern compare to others

5.20.1.1. FINDbase

5.20.1.2. RIKEN integrated databases of mammals

6. (D) Why the databases useful in describing the proteins

6.1. Protein sequence databases (UniProt)

6.1.1. Clearly show the different Pepsin A in different organisms in a table

6.1.2. Can customize various aspect or classification to view

6.2. Protein structure databases (RCSB)

6.2.1. Structure and the summary can be viewed

6.2.2. The parameters are well categorize

6.2.3. The articles related to Pepsin A also shown

6.3. Primary nucleotide sequence databases (European Nucleotide Archive)

6.3.1. Clearly show how many results found in each categories

6.4. Meta databases (ConsensusPathDB)

6.4.1. ConsensusPathDB have integrates the interactions in Homo sapiens like proteins interaction, signalling reactions, gene regulations and etc

6.5. Genome databases (Ensembl)

6.5.1. No. of results shown in each categories

6.5.2. Can show in standard and table layout

6.6. Proteomics databases (PRIDE)

6.6.1. Able to search Pepsin A according to tissue and disease

6.7. Metabolic pathway and Protein Function databases (BRENDA)

6.7.1. Pepsin A can be viewed efficiently based on enzyme nomenclature, functional parameters, molecular properties, diseases and etc