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: FXN

Description: frataxin

Entrez Gene ID: 2395

SwissProt Acc Number: Q16595

RefSeq: NM_000144

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

.."Finally, we tested these 24 SNPs in a third study (475 cases and 619 controls) and found that 5 SNPs in 4 genes (ENO1, FXN (2 SNPs), HLA-DPB2, and LPA) were associated with MI in the third study (1-sided P<0.05),"..

From PMID: 18682748, in Journal PLoS One. , 2008

References

There were 1 potential papers with FXN and CHD.

PMID	Title	Journals	Details
18682748	"Analysis of 17,576 potentially functional SNPs in three case-control studies of myocardial infarction."	PloS one	More Details

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

PPI interactions

There were totally 4 unique genes interacted with FXN. Show PPI network

Gene name	Interaction type	reference PMID	CHD relation
ACTN1	Two-hybrid	16713569	No
PICK1	Two-hybrid	16713569\|16713569	No
PMPCB	Two-hybrid	9700204\|9700204\|9700204	No
UBC	Affinity Capture-MS	21890473	No

Involved FDA drugs

There was no drug associated with FXN

Design by WLH