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: GATA5

Description: GATA binding protein 5

Entrez Gene ID: 140628

SwissProt Acc Number: Q9BWX5

RefSeq: NM_080473

It was supported literatures to be a novel CHD related gene:

..The results unravel a critical cell-autonomous role for endocardial Gata5 in aortic valve formation and identify GATA5 as a potential gene responsible for congenital heart disease in humans...

From PMID: 21633169, in Journal J Clin Invest , 2011

References

There were 1 potential papers with GATA5 and CHD.

PMID	Title	Journals	Details
21633169	Loss of Gata5 in mice leads to bicuspid aortic valve.	The Journal of clinical investigation	More Details

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

PPI interactions

There were totally 3 unique genes interacted with GATA5. Show PPI network

Gene name	Interaction type	reference PMID	CHD relation
KLF2	Two-hybrid	11375995	CHD related
HNF1A	in vitro;in vivo	12011060,14715527	CHD related
EP300	in vitro;in vivo	10567378	CHD related

Involved FDA drugs

There was no drug associated with GATA5

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