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: TBX1

Description: T-box 1

Entrez Gene ID: 6899

SwissProt Acc Number: O43435

RefSeq: NM_005992

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

..Tbx1 affects asymmetric cardiac morphogenesis by regulating?Pitx2?in the secondary heart field..

From PMID: 16556915, in Journal Development , 2006

References

There were 4 potential papers with TBX1 and CHD.

PMID	Title	Journals	Details
22318994	Human gene copy number spectra analysis in congenital heart malformations.	Physiological genomics	More Details
18583714	The del22q11.2 candidate gene Tbx1 controls regional outflow tract identity and coronary artery patterning.	Circulation research	More Details
15548583	ENU induced mutations causing congenital cardiovascular anomalies.	"Development (Cambridge, England)"	More Details
11242110	"DiGeorge syndrome phenotype in mice mutant for the T-box gene, Tbx1."	Nature genetics	More Details

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

PPI interactions

There were totally 2 unique genes interacted with TBX1. Show PPI network

Gene name	Interaction type	reference PMID	CHD relation
TERF1	Affinity Capture-MS	20811636	No
TERF2	Affinity Capture-MS	20811636	No

Involved FDA drugs

There was no drug associated with TBX1

Design by WLH