human protein reference database
Recently Published Documents


TOTAL DOCUMENTS

13
(FIVE YEARS 0)

H-INDEX

8
(FIVE YEARS 0)

2017 ◽  
Author(s):  
Yonggang Tan ◽  
Yongqiang Tan ◽  
Lin Lu ◽  
Heying Zhang ◽  
Cheng Sun ◽  
...  

AbstractWe have established a database of Human Pancreatic Cancer (HPCDb) through effectively mining, extracting, analyzing, and integrating PC-related genes, single-nucleotide polymorphisms (SNPs), and microRNAs (miRNAs), now available online at http://www.pancancer.org/. Data were extracted from established databases, ≥5 published literature (PubMed), and microarray chips (screening of differentially expressed genes using limma package in R, |log2 fold change (FC)| > 1). Further, protein–protein interactions (PPIs) were investigated through the Human Protein Reference Database. miRNA–target relationships were also identified using the online software TargetScan. Currently, HPCDb contains 3284 genes, 120 miRNAs, 589 SNPs, 10,139 PPIs, and 3904 miRNA–target pairs. The detailed information on PC-related genes (e.g., gene identifier (ID), symbol, synonyms, full name, chip sets, expression alteration, PubMed ID, and PPIs), miRNAs (e.g., accession number, chromosome location, related disease, PubMed ID, and miRNA–target interactions), and SNPs (e.g., SNP ID, allele, gene, PubMed ID, chromosome location, and disease) is presented through user-friendly query interfaces or convenient links to NCBI GEO, NCBI PubMed, NCBI Gene, NCBI dbSNP, and miRBase. Overall, HPCDb provides biologists with relevant information on human PC-related molecules at multiple levels, helping to generate new hypotheses or identify candidate markers.



2012 ◽  
Vol 8 (2) ◽  
pp. 453-463 ◽  
Author(s):  
Renu Goel ◽  
H. C. Harsha ◽  
Akhilesh Pandey ◽  
T. S. Keshava Prasad


2010 ◽  
Vol 8 (57) ◽  
pp. 555-567 ◽  
Author(s):  
Yan Xu ◽  
Wen Hu ◽  
Zhiqiang Chang ◽  
Huizi DuanMu ◽  
Shanzhen Zhang ◽  
...  

Protein–protein interaction (PPI) prediction method has provided an opportunity for elucidating potential biological processes and disease mechanisms. We integrated eight features involving proteomic, genomic, phenotype and functional annotation datasets by a mixed model consisting of full connected Bayesian (FCB) model and naive Bayesian model to predict human PPIs, resulting in 40 447 PPIs which contain 2740 common PPIs with the human protein reference database (HPRD) by a likelihood ratio cutoff of 512. Then we applied them to exploring underlying pathway crosstalk where pathways were derived from the pathway interaction database. Two pathway crosstalk networks (PCNs) were constructed based on PPI sets. The PPI sets were derived from two different sources. One source was strictly the HPRD database while the other source was a combination of HPRD and PPIs predicted by our mixed Bayesian method. We demonstrated that PCNs based on the mixed PPI set showed much more underlying pathway interactions than the HPRD PPI set. Furthermore, we mapped cancer-causing mutated somatic genes to PPIs between significant pathway crosstalk pairs. We extracted highly connected clusters from over-represented subnetworks of PCNs, which were enriched for mutated gene interactions that acted as crosstalk links. Most of the pathways in top ranking clusters were shown to play important roles in cancer. The clusters themselves showed coherent function categories pertaining to cancer development.



2010 ◽  
Vol 48 (1) ◽  
pp. 87-95 ◽  
Author(s):  
Renu Goel ◽  
Babylakshmi Muthusamy ◽  
Akhilesh Pandey ◽  
T. S. Keshava Prasad


2009 ◽  
Vol 37 (Database) ◽  
pp. D767-D772 ◽  
Author(s):  
T. S. Keshava Prasad ◽  
R. Goel ◽  
K. Kandasamy ◽  
S. Keerthikumar ◽  
S. Kumar ◽  
...  


2006 ◽  
Vol 34 (90001) ◽  
pp. D411-D414 ◽  
Author(s):  
G. R. Mishra


2004 ◽  
Vol 5 (1) ◽  
pp. 4-4 ◽  
Author(s):  
Natalie Wilson


2004 ◽  
Vol 5 (1) ◽  
pp. 8-8 ◽  
Author(s):  
Natalie Wilson


Sign in / Sign up

Export Citation Format

Share Document