FAQ

What is MAS?

Molecule Annotation System (MAS) is a web-based software toolkit for a whole data mining and function annotation solution to extract & analyze biological molecules relationships from public knowledgebase of biological molecules and signification. MAS uses relational database of biological networks created from millions of individually modeled relationships between genes, proteins, disease and tissues. MAS allow a view on your data, integrated in biological networks according to different biological context. This unique feature results from multiple lines of evidence which are integrated in MASCORE. MAS Helps to understand relationship of gene expression data through the given molecular symbols list, and provides thorough, unbiased and visible results.

What is "MAS-Core"?

MAS-Core is the primary databases of MAS integrated various well-known biological resources such as Genbank, EMBL, SwissProt, Gene Ontology, KEGG, BioCarta, GenMapp, mirBase, EPD, HPRD, MIND, BIND, Intact, TRANSFAC, UniGene, dbSNP, OMIM, InterPro, HUGO, MGI and RGD.

Why should we use MAS?

Various high-throughput experiments are becoming more and more important in this post-genomic era. However, high-throughput also indicates highly-complex and noise-generating. To easily understand the underlining biological relevance of a high-throughput experiment result, say a set of interesting genes/proteins/mrna/array probes/promoter/TF/cpg-island, we have to find significantly enriched function of them and get rid of those might be selected by chance. Selecting the significantly enriched GO or Pathway terms would be helpful a lot to understand our results. There have been quite many similar tools to annotation the molecular function. Nevertheless, MAS has several crucial unique features compared with them.

• 26 databases integration (total number: 26)
• Supporting multi-species (21 species now, and more coming soon)
• Supporting multi-function query (14 functions around genes)
• Supporting multi-experiment data input
• Proteins/Genes mapping in GO/pathway
• User-defined query function module (for the registered and the non-registered)
• Significantly enriched GO, pathway terms analysis
• GO and pathway Clustering analysis
• More graphic result display
• Supporting multiple projects and analysis, allowing user’ data saved at server side
• Analysis result and visit trace saved in server
• Export of results in csv format

In general, MAS is an easy-to-use, comprehensive, unbiased and visible tool suit providing strong power in meta-analysis of various high-throughput experiment results. MAS offers various query entries, graphics result display, comparative genome information and free word search. The system represents an alternative approach to mining and catch on biological signification for high through array data.

Who would be benefit from MAS?

MAS is quite compatible for various high-throughput experiment results. Thus, users who use these techniques, such as microarray, 2-D gel electrophoresis of proteome, protein microarray, SAGE, MPSS, deep sequencing, would find MAS very helpful. MAS would save you a lot of time and funds!

How does MAS utilize genes/proteins/mrna/array probes/promoter/TF/cpg-island/Unigene/disease information?

MAS parses the genes/proteins/mrna/array probes/SNP/promoter/TF/cpg-island/Unigene/disease relationship in the latest related database files. The results are stored in MASCORE. All of these information are updated regularly, currently at every month according species.

How does MAS map gene/protein identifiers to Pathway/GO terms?

MAS intents to map gene/protein identifiers from the original data resources. Thus, commercial microarray probe identifiers are mapped to Pathway/GO terms by their annotation files, and gene identifiers of various species are mapped to Pathway/GO terms by gene-association files obtained from Pathway/GO original Website or ftp. MAS will follow this discipline to map genes/proteins to Pathway/GO terms, if it involved in future new tools.

How many queries types does MAS support?

• Analysis of high-throughput array data. Analysis of thousands of molecular symbols and no more than 10 experiment’s records can be rapidly run to get their overall biological annotation.
• Self-defined query. When creating an analysis, the queried species, molecular symbol and databases used are selected to limit the annotation.

How often does MAS update?

The functionality of MAS is relatively stable, and small changes would be made irregularly. However, MAS updates its own database for each species and different annotation level have different updating frequencies, based their own data. The data version help document shows you that all database version and download information.

What input symbols does MAS support?

Molecular type	DataBase	Example
Gene	NCBI,Ensembl,HUGO,TIGR,TAIR,FlyBase,SGD,RGD,MGI,WormBase	P53,1002,ENSG001,FBgn0037312, AZM4_102706, LOC_Os08g42520, S000000786, AT5G17050
mRNA	NCBI, Ensembl	NM_012,AY_012,ENST002
Protein	NCBI,Ensembl,Uniprot	NP_013,ENSP003,Q58HF3
Probe	CapitalBio,AffyMetrix	H200100,231225_at

What ID formats dose MAS support?

How many annotation levels does MAS support?

MAS mascore integrates 26 public biological databases. KEGG and Biocarta are well known for high-quality pathway annotation. Gene Ontology for gene relationship and classification by there function, mirBase for comprehensive information of miRNA, EPD for eukaryotic promoter information collection, and TRANSFAC for transcription factor information.An network relationship exists between these integration data sources, such as interaction, expression and regulation.

MAS supports multi-species biological information query. 21 species were included such as Homo sapiens, Mus musculus, Rattus norvegicus, Arabidopsis thaliana, Zea mays, Oryza sativa, Saccharomyces cerevisiae, Drosophila melanogaster, Sus scrofa. Molecular annotation information for the species derives from mascore.Some special species databases were also involved, such as HUGO, MGI and RGD.

What to do when you forget your password?

Login->forget your password?

Enter your email address and the check words, and you will receive a letter including a new password generated by MAS.

How many symbols in the list in one analysis?

1000 for ordinary user,3000 for internal and 5000 for advance.Supporting Gene,mRNA,protein and probe for the time being.

Which web browsers does MAS support?

All MAS web pages follow the W3C recommended XHTML1.0 DTD standard, and compatible with most modern web browsers, including Internet Explorer, Firefox, Mozilla, the World, etc.

How fast does MAS work?

Analysis time cost depends on species and annotation levels that user chosen.The analysis will wait in the analysis queue after starting. For example, 4,000 genes analysis takes 2~50 minutes especially the function for drawing graphs were selected. Please try again later or get connect with our technical support,if your analysis got an error or still waiting for long time, .