| Content | PTMD V2 | PTMD V1 | ||
|---|---|---|---|---|
| Known data | ||||
| PDAs | 342,624 | 1,950 | ||
| PTM Proteins | 15,105 | 749 | ||
| Modification Class | 49 | 9 | ||
| Modification Types | 93 | 23 | ||
| Disease Class | 34 | 26 | ||
| Disease Types | 2,083 | 275 | ||
| Data integration | ||||
| Data Size | ~8 GB | ~0.2 GB | ||
| Integrated Information | Basic information, protein sequence, disease-associated information, variation and mutation, protein-protein interaction, protein function, DNA & RNA element, protein structure, chemical-target relation, mRNA expression, protein expression/proteomics, subcellular localization, biological pathway, domain annotation, physicochemical property | Basic information, protein sequence, sequence annotation, domain, KEGG pathway | ||
Based on the distinct PTM states in diseases, we classified all disease-associated PTMs into six classes, including whether the up-regulation (U) or down-regulation (D) of PTM levels, the absence (A) or presence (P) of PTMs, and the creation (C) or disruption (N) of PTM sites are associated with diseases.
EXAMPLE:
P: WNT5A/JNK signaling regulates pancreatic cancer cells migration by Phosphorylating Paxillin (Wei, et al.,2013).
A: In normal tissues the phosphorylated form of Merlin was found to be the predominant one, while in the tumor tissues the unphosphorylated form was found to be more pronounced (Cacev, et al.,2014).
U: As shown in Figure 5A and Table 1, remarkably higher amounts of PDK1 and its phosphorylated form at Ser-241 were detected in most CLL samples but not in samples from healthy persons (Shehata, et al.,2010).
D: A dramatic increase in pGSK3β(Ser9) (inactive form of GSK3β) is observed in late papillomas and squamous cell carcinomas, while a significant decrease in pGSK3β(Tyr216) (active form of GSK3β) is detected in squamous cell carcinoma samples compared to normal tissues (Luo J, 2009).
C: We demonstrated that the expression of Tyr397 (main auto-phosphorylation of FAK) was strongly increased in FAK-Del33 overexpressed breast tumor cells compared to wild-type following FAK/Src RTK signaling activation (Fang, et al.,2014).
N: This mutation is gain-of-function, as it enhances the inhibitory capacity of IkappaBalpha by preventing its phosphorylation and degradation (Courtois, et al.,2003).
In PTMD 2.0, we try to make it more powerful and convenient to be used. The online service and local packages were provided. This USAGE is prepared for the online service. For usage of local packages, please download the Manual. The PTMD 2.0 provides the browse, search and advance options.
1. Browse. The PTMD 2.0 database offers three simple ways to browse proteins: by PTMs, by Diseases, or by PDAs.
Example: Please first click on a specific disease in the human body diagram to browse related diseases. Then by selecting disease, the related proteins which have association between PTMs and this disease will be presented.
2. Search. Three search options are provided, including simple search, advance search, batch search, and BLAST search.
3. API. Data can now be accessed via PTMDid using the following API link: https://ngdc.cncb.ac.cn/search/api/specific?db=ptmd&q={$ptmdid}
(1) Simple search. You can input one keyword to search the PTMD 2.0. The search fields include Any Field, PTMD ID, Uniprot Accession, Entrez Gene ID, Gene Name/Alias, Protein Name/Alias, PTM types, Organisms and Disease.
Example: You can click on the "Example" button to load an instance. All terms containing "p53" keyword will be shown by clicking on the "Submit" button.
(2) Advance search. allows you to input up to three terms to find the information more specifically. The three terms could be connected by the following operators:
AND: the term following this operator has to be included in the specified field(s).
OR: either the preceding or the following term to this operator should occur in the specified field(s).
NOT: If selected, the term following this operator must be not contained in the specified field(s).
Example: You can click on the "Example" button to load an instance; the human protein "p53" will be shown by clicking on the "Submit" button.
(3) Batch Search could be used to find a number of proteins such as a protein list. You can input keyword list, for example, a list of UniProt IDs to search the database. The list should be inputted as one keyword one line.
Example: You can click on the "Example" button to load an instance, which will show a list of Uniprot Accession. The result will be presented following by clicking on submit button.
(4) BLAST search. This option is used to find the specific protein and/or related homologues by sequence alignment. This search-option will help you to find the querying protein accurately and fast. Only one protein sequence in FASTA format is allowed per time. The E-value threshold could be user-defined while the default is set as 10.
Example: You can click on the "Example" button to load the protein sequence of human protein "p53". By clicking on the "Submit" button, you can find the related homologues in PTMD database.
* If there are any comments or suggestions, please contact the author: Dr. Yu Xue for details.