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

1.2.1.1. that not available elsewere and easy to use visualization

1.2.1.1.1. data warehouse

1.2.1.1.2. portals

1.2.1.1.3. cross-platform search tools

1.2.1.1.4. 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

1.4.1.1. ArrayExpress

1.4.1.2. CEO

1.5. avoid accepting new EST databases

1.5.1. those dealing with individual species

1.5.1.1. have a home

1.5.1.1.1. DDJB

1.5.1.1.2. GeneBank

1.5.1.1.3. European Nucleotide Archive databases

1.6. Boutique databases

1.6.1. cover narrow topics

1.6.1.1. useful beyond specialists

1.6.1.2. useful introduction for general public

2. Number available

2.1. Online molecular database collection

2.1.1. 1512 online databases

2.1.1.1. 14 main catagories

2.1.1.2. 41 subcategories

2.2. Metabase collection (MB)

2.2.1. 1795 entries

2.3. Bioinformatics link directory

2.3.1. 1794 links

2.3.1.1. 455 database

2.3.1.2. 134 resouces

2.3.1.3. 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

3.1.1.1. DDBJ - DNA Data Bank of Japan

3.1.1.2. European Nucleotide Archive

3.1.1.3. GeneBank

3.1.2. Coding and non-coding DNA

3.1.2.1. Dfam

3.1.2.2. SINEBase

3.1.2.3. UNCEBase

3.1.2.4. DoriC

3.1.3. Gene structure, introns, and exons, splice sites

3.1.3.1. APPRIS

3.1.3.2. ChiTaRS

3.1.3.3. GeneTack

3.1.3.4. HEXEvent

3.1.3.5. SpliceAid-F

3.1.3.6. Spliceosome Database

3.1.4. Transcriptional regular sites and transcription factors

3.1.4.1. ChIPBase

3.1.4.2. Factorbook

3.1.4.3. HOCOMOCO

3.1.4.4. 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

3.3.1.1. UniProt

3.3.2. Protein Properties

3.3.2.1. ePros

3.3.2.2. SwissSidechain

3.3.2.3. TOPPR

3.3.3. Protein Localization and Targeting

3.3.3.1. ValidNESs

3.3.4. Protein Sequence Motifs and Active Sites

3.3.5. Protein Domain Databases; Protein Classification

3.3.5.1. OtholugeDB

3.3.6. Databases of individual protein families

3.3.6.1. Cyanolyase

3.3.6.2. DoBISCUIT

3.3.6.3. EENdb

3.3.6.4. KIDFamMap

3.3.6.5. UUCD

3.4. Structural Databases

3.4.1. Small molecules

3.4.2. Carbohydrates

3.4.2.1. Glycan Fragment DB

3.4.3. Nucleic acid structure

3.4.3.1. MetalPDB

3.4.3.2. Voronoia4RNA

3.4.4. Protein structure

3.4.4.1. D2P2

3.4.4.2. Genome3D

3.4.4.3. SIFTS

3.4.4.4. 2P2Idb

3.4.4.5. NPIDB

3.4.4.6. PDBe

3.4.4.7. CATH

3.4.4.8. SCOP

3.5. Genomics Databases (non-vertebrate)

3.5.1. Genome annotation terms, ontologies and nomenclature

3.5.1.1. dcGO

3.5.1.2. DGA

3.5.1.3. BioGPS

3.5.2. Taxonomy and identification

3.5.3. General genomics databases

3.5.4. Viral genome databases

3.5.4.1. HBVdb

3.5.4.2. Papillomavirus Episteme

3.5.4.3. Papillomavirus Episteme

3.5.5. Prokaryotic genome databases

3.5.5.1. meta.MicrobesOnline

3.5.5.2. SecReT4

3.5.5.3. SEVA

3.5.5.4. Microscope

3.5.5.5. EcoCyc

3.5.5.6. EcoGene

3.5.5.7. RegulonDB

3.5.5.8. EcoCyc

3.5.6. Fungal genome databases

3.5.6.1. NetwoRx

3.5.7. Unicellular eukaryotes genome databases

3.5.7.1. PR2

3.5.8. Invertebrate eurkayotes genome databases

3.5.8.1. MonarchBase

3.5.8.2. WDDD

3.5.8.3. WormQTL

3.5.8.4. FlyAtlas

3.5.8.5. FlyAtlas

3.6. Metabolic and Signaling Pathways

3.6.1. Enzymes and enzyme nomenclature

3.6.1.1. EBI Enzyme Portal

3.6.2. Metabolic Pathways

3.6.2.1. ClusterMine360

3.6.2.2. ECMDB

3.6.2.3. LAMP

3.6.2.4. MetaboLights

3.6.2.5. RNApathwaysDB

3.6.2.6. WholeCellKB

3.6.2.7. LAMP

3.6.2.8. MetaboLights

3.6.3. Protein-protein interactions

3.6.3.1. prePPI

3.6.3.2. PTMcode

3.6.3.3. SynSysNet

3.6.3.4. TissueNet

3.6.4. Signalling Pathway

3.6.4.1. Quorumpeps

3.7. Human and other Vertebrate Genomes

3.7.1. Model organisms, comparative genomics

3.7.1.1. H2DB

3.7.1.2. NHPRTR

3.7.1.3. OikoBase

3.7.1.4. RhesusBase

3.7.1.5. ZInC

3.7.1.6. 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

3.8.1.1. dbVar

3.8.1.2. DGVar

3.8.1.3. ClinVar

3.8.2. Cancer gene databases

3.8.2.1. CellLine Navigator

3.8.2.2. TSGene

3.8.2.3. TSGene

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

3.8.3.1. LncRNADisease

3.8.4. General Human genetics databases

3.8.4.1. 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

3.11.1.1. BioLip

3.11.1.2. G4LDB

3.11.1.3. GDSC

3.11.1.4. NPACT

3.11.1.5. StreptomeDB

3.11.1.6. SwissBiosostere

3.11.2. TCMID

3.12. Organelle Databases

3.13. Plant Databases

3.13.1. General plant databases

3.13.1.1. PGDD

3.13.1.2. PIECE

3.13.2. Rice

3.13.2.1. OrysPSSP

3.13.2.2. 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

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

4.1.1.1.1. http://www.ncbi.nlm.nih.gov/genbank/

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.

4.2.1.1. http://rdp.cme.msu.edu/

4.3. Protein Sequence

4.3.1. UniProt

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

4.3.1.1.1. http://www.uniprot.org/

4.4. Protein Structure

4.4.1. Protein Data Bank (PDB)

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

4.4.1.2. simple and advanced searches based on annotations relating to sequence, structure and function, and to visualize, download, and analyze molecules.

4.4.1.2.1. http://www.rcsb.org/pdb/home/home.do

4.5. Metabolic pathway and Protein Function

4.5.1. BRENDA

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

4.5.1.1.1. http://www.brenda-enzymes.info/

4.6. Genome

4.6.1. Ensembl

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

4.6.1.1.1. http://www.ensembl.org/index.html

4.7. Specialised

4.7.1. HGMD

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

4.7.1.1.1. http://www.hgmd.cf.ac.uk/ac/index.php

4.8. Proteomic

4.8.1. PRIDE

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

4.8.1.1.1. http://www.ebi.ac.uk/pride/archive/

5. Prepared by

5.1. KONG PUI SAN

5.2. PEGGY KWAN DICT SHAN

5.3. TAN SHENG HAO

5.4. WONG SIEW FONG

5.5. YING CHOI YIENG

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

6.1.3.1. knowledge of protein-protein interactions expand

6.1.3.2. the references databases

6.1.3.2.1. human protein interactions

6.1.3.2.2. signaling pathways

6.1.4. 7 principal proteins successful collected for insulin signaling pathway

6.1.4.1. INS

6.1.4.2. INSR

6.1.4.3. IRS2

6.1.4.4. IRS1

6.1.4.4.1. using 7 protein

6.1.4.5. PIK3CA

6.1.4.6. Akt2

6.1.4.7. GLUT4

6.1.5. sucessfully constructed phylogenetic tree

6.1.5.1. also modified phylogenetic tree

6.1.5.1.1. with node

6.1.5.1.2. distance

6.1.6. sequence logo

6.1.7. protein-protein interaction network.

6.1.7.1. direct

6.1.7.1.1. physical

6.1.7.2. indirect

6.1.7.2.1. functional