Nucleic Acid Research (NAR) Databases

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Nucleic Acid Research (NAR) Databases by Mind Map: Nucleic Acid Research (NAR) Databases

1. Criteria for selection into NAR database

1.1. act as general utility database to the scientific community

1.1.1. database is well curated

1.2. comprehenssiveness of coverage

1.2.1. web-accessible databases that not available elsewere and easy to use visualization data warehouse portals cross-platform search tools visualization tools

1.3. degree of value added

1.3.1. in the production of the databases

1.4. avoid accepting databases on gene expression

1.4.1. underlying data submitted to ArrayExpress CEO

1.5. avoid accepting new EST databases

1.5.1. those dealing with individual species have a home DDJB GeneBank European Nucleotide Archive databases

1.6. Boutique databases

1.6.1. cover narrow topics useful beyond specialists useful introduction for general public

2. Number available

2.1. Online molecular database collection

2.1.1. 1512 online databases 14 main catagories 41 subcategories

2.2. Metabase collection (MB)

2.2.1. 1795 entries

2.3. Bioinformatics link directory

2.3.1. 1794 links 455 database 134 resouces 1205 web server tools

3. Organization of databases and its major grouping

3.1. Nucleotide Sequence Databases

3.1.1. International Nucleotide Sequence Database Collaboration DDBJ - DNA Data Bank of Japan European Nucleotide Archive GeneBank

3.1.2. Coding and non-coding DNA Dfam SINEBase UNCEBase DoriC

3.1.3. Gene structure, introns, and exons, splice sites APPRIS ChiTaRS GeneTack HEXEvent SpliceAid-F Spliceosome Database

3.1.4. Transcriptional regular sites and transcription factors ChIPBase Factorbook HOCOMOCO TFClass

3.2. RNA Sequence Databases

3.2.1. BSRD

3.2.2. DIANA-LncBase

3.2.3. Lncipedia

3.2.4. PlantRNA

3.2.5. SomamiR

3.2.6. YM500

3.2.7. DARNED

3.2.8. Lncipedia

3.3. Protein Sequence Databases

3.3.1. General Sequence Databases UniProt

3.3.2. Protein Properties ePros SwissSidechain TOPPR

3.3.3. Protein Localization and Targeting ValidNESs

3.3.4. Protein Sequence Motifs and Active Sites

3.3.5. Protein Domain Databases; Protein Classification OtholugeDB

3.3.6. Databases of individual protein families Cyanolyase DoBISCUIT EENdb KIDFamMap UUCD

3.4. Structural Databases

3.4.1. Small molecules

3.4.2. Carbohydrates Glycan Fragment DB

3.4.3. Nucleic acid structure MetalPDB Voronoia4RNA

3.4.4. Protein structure D2P2 Genome3D SIFTS 2P2Idb NPIDB PDBe CATH SCOP

3.5. Genomics Databases (non-vertebrate)

3.5.1. Genome annotation terms, ontologies and nomenclature dcGO DGA BioGPS

3.5.2. Taxonomy and identification

3.5.3. General genomics databases

3.5.4. Viral genome databases HBVdb Papillomavirus Episteme Papillomavirus Episteme

3.5.5. Prokaryotic genome databases meta.MicrobesOnline SecReT4 SEVA Microscope EcoCyc EcoGene RegulonDB EcoCyc

3.5.6. Fungal genome databases NetwoRx

3.5.7. Unicellular eukaryotes genome databases PR2

3.5.8. Invertebrate eurkayotes genome databases MonarchBase WDDD WormQTL FlyAtlas FlyAtlas

3.6. Metabolic and Signaling Pathways

3.6.1. Enzymes and enzyme nomenclature EBI Enzyme Portal

3.6.2. Metabolic Pathways ClusterMine360 ECMDB LAMP MetaboLights RNApathwaysDB WholeCellKB LAMP MetaboLights

3.6.3. Protein-protein interactions prePPI PTMcode SynSysNet TissueNet

3.6.4. Signalling Pathway Quorumpeps

3.7. Human and other Vertebrate Genomes

3.7.1. Model organisms, comparative genomics H2DB NHPRTR OikoBase RhesusBase ZInC GenColors

3.7.2. Human genome databases, maps and views

3.7.3. Human ORFs

3.8. Human Genes and Diseases

3.8.1. General polymorphism databases dbVar DGVar ClinVar

3.8.2. Cancer gene databases CellLine Navigator TSGene TSGene

3.8.3. Gene-, system- or disease-specific databases LncRNADisease

3.8.4. General Human genetics databases NIH Genetic Testing Registry

3.9. Microarray Data and other Gene Expression Databases

3.9.1. CircaDB

3.9.2. HemaExplorer

3.9.3. METscout

3.9.4. Allen Brain Atlas

3.9.5. ArrayExpress

3.9.6. Gene Expression Omnibus

3.9.7. GPX

3.9.8. Stanford Microarray Database

3.10. Proteomics databases

3.10.1. Protein and peptide identifications and their associated supporting evidence

3.10.2. Details of post-translational modifications

3.10.3. e.g. Mito Miner

3.11. Other Molecular Biology databases

3.11.1. Drugs and drug design BioLip G4LDB GDSC NPACT StreptomeDB SwissBiosostere

3.11.2. TCMID

3.12. Organelle Databases

3.13. Plant Databases

3.13.1. General plant databases PGDD PIECE

3.13.2. Rice OrysPSSP RiceFREND

3.13.3. Arabidopsis thaliana

3.13.4. Other plants

3.14. Immunological databases

3.14.1. InnateDB

3.15. Cell Biology

3.15.1. CloneDB

3.15.2. LUCApedia

3.15.3. NCBI Bookshelf

4. Database for Insulin

4.1. Primary Nucleotide Sequence

4.1.1. GenBank genetic sequence database, an annotated collection of all publicly available DNA sequences

4.2. Ribosomal Database Project (RDP)

4.2.1. provides quality-controlled, aligned and annotated Bacterial and Archaeal 16S rRNA sequences, and Fungal 28S rRNA sequences, and a suite of analysis tools to the scientific community.

4.3. Protein Sequence

4.3.1. UniProt provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information.

4.4. Protein Structure

4.4.1. Protein Data Bank (PDB) provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information. simple and advanced searches based on annotations relating to sequence, structure and function, and to visualize, download, and analyze molecules.

4.5. Metabolic pathway and Protein Function

4.5.1. BRENDA comprises molecular and biochemical information on enzymes that have been classified by the IUBMB

4.6. Genome

4.6.1. Ensembl provides automatic annotation databases for human, mouse, other vertebrate and eukaryote genomes

4.7. Specialised

4.7.1. HGMD collate known (published) gene lesions responsible for human inherited disease.

4.8. Proteomic

4.8.1. PRIDE 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. Prepared by






6. Why it is important for insulin

6.1. through database

6.1.1. main component pathway of insulin can be detected.

6.1.2. large scale insulin proteomics information can analysed throughly

6.1.3. several biochemical pathway successful develop knowledge of protein-protein interactions expand the references databases human protein interactions signaling pathways

6.1.4. 7 principal proteins successful collected for insulin signaling pathway INS INSR IRS2 IRS1 using 7 protein PIK3CA Akt2 GLUT4

6.1.5. sucessfully constructed phylogenetic tree also modified phylogenetic tree with node distance

6.1.6. sequence logo

6.1.7. protein-protein interaction network. direct physical indirect functional