How to Build CHD@ZJU

CHD related Articles were retrieved from Pubmed, by entering keywords "coronary heart disease" and constrict the publish date from 2000/1/1 to now (2013/1/23). As a result, totally 115898 articles were found and their abstracts were downloaded for text mining. Since some articles didn't contain abstracts, only 88396 abstracts remained.

The text-mining process to get CHD related genes could be divided in to 5 following steps:

1) Extracting all keywords from abstracts and ignoring those keywords start with numbers. 101402 keywords were extracted.

2) Input these keywords into Gene library in ArrayTrack and find possible related genes. 4674 genes were then found.

3) Put these 4674 genes again into pubmed abstracts to find related aticles. Only genes which offical name or there keyword description (such as prolactin for gene PRL) could be found in the abstract would be remained. As a result, 1247 genes were remained.

4) Manually examined on the 1247 genes to validate it was acutally related to CHD. Some genes would be filtered if it represents other meanings (such as gene CAD, Entrez ID:790, carbamoyl-phosphate synthetase 2, is mostly meant coronary arterial disease in articles). 681 genes were then validated with at least one reference.

5) All genes was compared with 1078 CHD genes in RGD database, and 370 genes were overlapped. These 370 genes were labels as "RGD_Supported" and the other 293 genes were labels as "REFERED". All 663 genes had supported references in CHD@ZJU which were examined by step 4.

How To contact Us

Collaboration Information: Prof. Xiaohui Fan (fanxh@zju.edu.cn)

Website using assistance : Leihong Wu (11019004@zju.edu.cn)

Basic Information

Gene Name: PTGDS

Description: prostaglandin D2 synthase 21kDa (brain)

Entrez Gene ID: 5730

SwissProt Acc Number: P41222

RefSeq: NM_000954

It was suspected to be CHD related:

.."Levels of the prostaglandin D2 synthase (PTGDS) gene, recently associated with the progression of atherosclerosis, were significantly different in the three pairwise comparisons (EAT>MAT>SAT)."..

From PMID: 21603615, in Journal PLoS One , 2011

References

There were 1 potential papers with PTGDS and CHD.

PMID	Title	Journals	Details
21603615	"The transcriptome of human epicardial, mediastinal and subcutaneous adipose tissues in men with coronary artery disease."	PloS one	More Details

NOTEs: These result is mostly from TEXT-MINING and there might have mismatches.

PPI interactions

There were totally 10 unique genes interacted with PTGDS. Show PPI network

Gene name	Interaction type	reference PMID	CHD relation
PTGER1	in vivo	8253813	No
EGFR	PCA	20029029	CHD related
CACNA1A	Two-hybrid	21078624	No
SHBG	Two-hybrid	15862967	CHD related
ATXN1	Two-hybrid	16713569	No
PTGER2	in vivo	8163486	No
PTGFR	in vivo	8300593	No
CAPN1	yeast 2-hybrid	12358155	No
HK2	in vitro;in vivo;yeast 2-hybrid	11068878	No
HK3	in vitro;in vivo;yeast 2-hybrid	11068878	No

Involved FDA drugs

There was no drug associated with PTGDS

Design by WLH