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Zhang L, Li X, Tai J, Li W, Chen L. Predicting candidate genes based on combined network topological features: a case study in coronary artery disease. PLoS One 2012; 7:e39542. [PMID: 22761820 PMCID: PMC3382204 DOI: 10.1371/journal.pone.0039542] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 05/22/2012] [Indexed: 11/26/2022] Open
Abstract
Predicting candidate genes using gene expression profiles and unbiased protein-protein interactions (PPI) contributes a lot in deciphering the pathogenesis of complex diseases. Recent studies showed that there are significant disparities in network topological features between non-disease and disease genes in protein-protein interaction settings. Integrated methods could consider their characteristics comprehensively in a biological network. In this study, we introduce a novel computational method, based on combined network topological features, to construct a combined classifier and then use it to predict candidate genes for coronary artery diseases (CAD). As a result, 276 novel candidate genes were predicted and were found to share similar functions to known disease genes. The majority of the candidate genes were cross-validated by other three methods. Our method will be useful in the search for candidate genes of other diseases.
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Affiliation(s)
- Liangcai Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province, China
- * E-mail: (LCZ); (LC)
| | - Xu Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Jingxie Tai
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Wan Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Lina Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province, China
- * E-mail: (LCZ); (LC)
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Chen JL. Randomized clinical trial of urokinase versus heparin in unstable angina. J Thromb Thrombolysis 1999; 8:223-6. [PMID: 10500312 DOI: 10.1023/a:1008918422293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The aim of this study was to evaluate the clinical effect of urokinase (UK) in unstable angina (UA). This study was a multicenter, single-blind, heparin-controlled, randomized clinical trial. Entry criteria was that effort angina was significantly aggravated within 96 hours and angina attack at rest within 24 hours. In addition to the control group, thrombolytic therapy was divided into two groups according to the dose of UK. The high-dose group was 18,000 IU/kg, and the total dose was no more than 1.5 million IU (no bolus of heparin in this dose). The low-dose group was 14,000 IU/kg, and the total dose was no more than 1 million IU. All patients were treated by aspirin 300 mg/day and heparin 3000 U IV bolus before thrombolytic therapy (except for the high-dose group), then subcutaneous heparin 7,500 U q12h. The primary endpoint for the comparison between the thrombolytic and control groups was death and AMI (cardiac event) within 30 days of enrollment. Five hundred and fifty-six patients with UA were selected, and 272 and 284 patients were enrolled in thrombolytic group and control groups, respectively. The 30-day incidence of cardiac events was a little higher, but not significantly, in the thrombolytic group than in the control group (7.0% vs. 5.3%, ns), but the rate for cardiac events was much lower in the low-dose UK group than in the high-dose UK group. The difference was significant (3.3% vs. 10.0%, P < 0.05). Even if the rate was also lower than in the control group, this difference was not significant (3.3% vs. 5.3%, P > 0.05). The time interval between enrollment and the AMIs was quite different in these two groups. The majority of AMIs (73.7%) occurred within 24 hours, including 37% of AMIs that occurred within 2 hours after the beginning of thrombolytic therapy in the UK group. However, only small number of AMIs (20%) occurred within 24 hours of enrollment in the control group. The increase in AMI risk on the first day of thrombolytic therapy in this study might be closely related to thrombolysis and to the lack of strong antithrombin therapy. The risk of AMI might be remarkably reduced by using low-dose UK in combination with antithrombin therapy before thrombolytic therapy.
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Affiliation(s)
- J L Chen
- Collaborative Research Group of National Project, Beijing, China
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3
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Scanlon PJ, Faxon DP, Audet AM, Carabello B, Dehmer GJ, Eagle KA, Legako RD, Leon DF, Murray JA, Nissen SE, Pepine CJ, Watson RM, Ritchie JL, Gibbons RJ, Cheitlin MD, Gardner TJ, Garson A, Russell RO, Ryan TJ, Smith SC. ACC/AHA guidelines for coronary angiography. A report of the American College of Cardiology/American Heart Association Task Force on practice guidelines (Committee on Coronary Angiography). Developed in collaboration with the Society for Cardiac Angiography and Interventions. J Am Coll Cardiol 1999; 33:1756-824. [PMID: 10334456 DOI: 10.1016/s0735-1097(99)00126-6] [Citation(s) in RCA: 665] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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4
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Ryan TJ, Anderson JL, Antman EM, Braniff BA, Brooks NH, Califf RM, Hillis LD, Hiratzka LF, Rapaport E, Riegel BJ, Russell RO, Smith EE, Weaver WD. ACC/AHA guidelines for the management of patients with acute myocardial infarction. A report of the American College of Cardiology/American Heart Association Task Force on Practice Guidelines (Committee on Management of Acute Myocardial Infarction). J Am Coll Cardiol 1996; 28:1328-428. [PMID: 8890834 DOI: 10.1016/s0735-1097(96)00392-0] [Citation(s) in RCA: 559] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- T J Ryan
- American College of Cardiology, Educational Services, Bethesda, MD 20814-1699, USA
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Lindahl B. Biochemical markers of myocardial damage for early diagnosis and prognosis in patients with acute coronary syndromes. Minireview based on a doctorial thesis. Ups J Med Sci 1996; 101:193-232. [PMID: 9055387 DOI: 10.3109/03009739609178922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
In patients with suspected AMI. Monitoring of a combination of myoglobin and CK-MB or tn-T allowed ruling-in AMI within 2-3 hours and ruling-out AMI within 3-6 hours in almost all patients admitted with chest pain and a nondiagnostic ECG. This might have a large impact on the early handling and treatment of these patients. The neural network methodology, with monitoring of myoglobin, CK-MB and tn-T allowed, within the first three hours, reliable diagnosis/exclusion of AMI/MMD and prediction of infarct size in patients admitted with suspicion of AMI. The computer system was faster than clinicians. Thus, neural network methodology might be a useful support for the early assessment of patients with suspected myocardial infarction. In patients with unstable CAD. The risk of subsequent cardiac events is increased by increasing maximal levels of tn-T obtained during the initial 24 hours. Thereby a normal, a slightly elevated and a clearly elevated tn-T level identified a low, intermediate and high risk group, respectively, for MI or death. The tn-T level was an independent prognostic variable for MI or death in a multivariate analysis comparing other early available risk indicators. Furthermore, tn-T seemed to be superior to CK-MB (mass) for risk stratification. In patients able to perform a predischarge ET both the tn-T level and the ET response were independent prognostic indicators for MI or death. The combination of tn-T and the ET response allowed a further improved risk stratification. In patients with tn-T elevation at inclusion, prolonged dalteparin treatment was beneficial. However, in patients without tn-T elevation, long term dalteparin treatment had no protective effect. Thus, tn-T determination provides independent and important prognostic information in unstable CAD. In the selection of treatment strategy for the individual patient, this simple, inexpensive and early available biochemical test might be useful.
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Affiliation(s)
- B Lindahl
- Department of Cardiology, University Hospital, Uppsala, Sweden
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Karlsson JE, Björkholm A, Nylander E, Ohlsson J, Wallentin L. Additional value of thallium-201 SPECT to a conventional exercise test for the identification of severe coronary lesions after an episode of unstable coronary artery disease. INTERNATIONAL JOURNAL OF CARDIAC IMAGING 1995; 11:127-37. [PMID: 7673760 DOI: 10.1007/bf01844710] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The additional value of thallium-201 SPECT to a conventional exercise test for the identification of patients with severe coronary lesions was evaluated in 170 men, one month after an episode of unstable coronary artery disease. Severe coronary lesions at coronary angiography--defined as three vessel disease, left main stenosis or proximal left anterior descending artery stenosis as part of two vessel disease--were observed in 45.9%. In the SPECT image, the left ventricular myocardium was divided into nine segments and each segment was classified as either normal (= 0), reduced uptake (= 1) or uptake defect (= 2). The sum of gradings in all segments post-exercise was denoted "SPECT score". The patients were divided into nine different groups regarding ST-depression during exercise (no ST-depression, ST-depression in 1-2 leads or > or = 3 leads) and "SPECT score" (no SPECT score, 1-3 scores or > or = 4 scores). Severe coronary lesions were, in 68% identified by SPECT score > or = 4 and in 65% by ST-depression in > or = 1 lead at exercise test. The specificity for identification of severe coronary lesions was, for both tests, 65%. SPECT score > or = 4 and/or ST-depression in > or = 3 leads identified 82% of the patients with severe coronary lesions with a specificity of 63%. Furthermore, SPECT score > or = 3 identified more patients with isolated proximal left anterior descending artery stenosis than ST-depression alone at exercise test.
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Affiliation(s)
- J E Karlsson
- Department of Cardiology, University Hospital, Linköping, Sweden
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Bär FW, Raynaud P, Renkin JP, Vermeer F, de Zwaan C, Wellens HJ. Coronary angiographic findings do not predict clinical outcome in patients with unstable angina. J Am Coll Cardiol 1994; 24:1453-9. [PMID: 7930275 DOI: 10.1016/0735-1097(94)90139-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
OBJECTIVES The presence of thrombus formation and type of coronary artery lesion were determined in patients with unstable angina and correlated with the angiographic findings and clinical outcome. BACKGROUND Some previous studies have suggested that thrombus formation and lesions are predictive of the angiographic and clinical findings. This was evaluated in a retrospective analysis of 159 patients participating in the placebo-controlled Unstable Angina Study Using Eminase (UNASEM) trial on the effect of thrombolysis in unstable angina. METHODS Patients without a previous myocardial infarction who presented with a typical history of unstable angina in the presence of abnormal findings on the electrocardiogram indicative of ischemia were included in the study. After baseline angiography, study medication (anistreplase or placebo) was given to 126 to 159 patients. Thirty-three patients did not receive medication because of significant main stem disease or normal coronary arteries or for other reasons. Angiography was repeated after 12 to 28 h. RESULTS Quantitative angiography showed a significant decrease in diameter stenosis in the anistreplase-treated group compared with the placebo-treated group (decrease 11% vs. 3%, p = 0.008). No differences in clinical outcome were found when thrombolytic treatment was compared with placebo (p = 0.98). Neither the presence nor absence of thrombus formation (p = 0.98) nor the type of lesion (p = 0.96) was related to the changes in diameter stenosis or to clinical outcome (p = 0.90 and p = 0.77, respectively). The power of these analyses to detect a 20% difference varied between 56% and 74%. CONCLUSIONS In this selected group of patients with unstable angina, type of coronary artery lesion and the presence or absence of thrombus formation does not predict clinical outcome.
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Affiliation(s)
- F W Bär
- Center of the Unstable Angina Study Using Eminase (UNASEM) Group Academic Hospital Maastricht, University of Limburg, The Netherlands
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Vaitkus PT, Laskey WK. Efficacy of adjunctive thrombolytic therapy in percutaneous transluminal coronary angioplasty. J Am Coll Cardiol 1994; 24:1415-23. [PMID: 7930268 DOI: 10.1016/0735-1097(94)90128-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Adjunctive thrombolysis has not been shown to improve angioplasty success or complication rates in elective angioplasty or myocardial infarction and may be detrimental in unstable angina. Thrombolysis of chronically occluded vessels achieves recanalization at a rate comparable to conventional angioplasty and is associated with a high rate of complications and limited long-term patency. Thrombolysis administered for thrombus or acute occlusion complicating angioplasty usually achieves coronary artery patency but is unable to forestall complications in many cases. A benefit of thrombolysis in reducing restenosis has not been conclusively demonstrated.
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Affiliation(s)
- P T Vaitkus
- Cardiology Unit, Medical Center Hospital of Vermont, University of Vermont, Burlington 05401
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Topol EJ, Fuster V, Harrington RA, Califf RM, Kleiman NS, Kereiakes DJ, Cohen M, Chapekis A, Gold HK, Tannenbaum MA. Recombinant hirudin for unstable angina pectoris. A multicenter, randomized angiographic trial. Circulation 1994; 89:1557-66. [PMID: 8149521 DOI: 10.1161/01.cir.89.4.1557] [Citation(s) in RCA: 115] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
BACKGROUND Coronary artery thrombosis plays an important pathophysiological role in unstable angina and non-Q-wave myocardial infarction. To date, heparin and thrombolytic therapy has not provided complete or consistent benefit. We hypothesized that recombinant hirudin, a direct thrombin inhibitor, would prevent accumulation of coronary artery thrombus in a manner superior to heparin. METHODS AND RESULTS Patients with rest ischemic pain, abnormal ECG, and baseline angiogram indicating a > or = 60% stenosis of a culprit coronary artery or saphenous vein graft with visual appearance of thrombus were randomized to one of two different doses of heparin (either a target activated partial thromboplastin time [aPTT] of 65 to 90 or 90 to 110 seconds) or one of four doses of hirudin (0.05, 0.10, 0.20, or 0.30 mg.kg-1.h-1 infusion) in a dose-escalating protocol. After 72 to 120 hours of study drug, a repeat coronary angiogram was obtained, and the paired studies underwent quantitative analysis. The primary end point was change in the average cross-sectional area of the culprit lesion. Other efficacy end points also involved changes in culprit lesion dimensions and TIMI flow grade. Recombinant hirudin led to a dose-dependent elevation of aPTT that appeared to plateau at the 0.2-mg/kg dose. A higher proportion of hirudin-treated patients had their aPTT within a 40-second range (16% heparin versus 71% hirudin, P < .001). Overall, the 116 patients treated with hirudin tended to show more improvement than the 50 patients receiving heparin relative to the primary efficacy variable--the average cross-sectional area (P = .08)--as well as minimal cross-sectional area (P = .028), minimal luminal diameter (P = .029), and percent diameter stenosis (P = .07). CONCLUSIONS Recombinant hirudin appears to be a promising antithrombotic intervention compared with heparin for inhibition of coronary artery thrombus. Large-scale comparative trials are warranted.
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Affiliation(s)
- E J Topol
- Department of Cardiology, Cleveland Clinic Foundation, OH 44195
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Abstract
This article discusses therapy with beta blockade and thrombolytic agents in acute myocardial infarction. In large and well-controlled studies both treatment strategies have been shown to increase survival. Both therapies have also been demonstrated to be safe in acute myocardial infarction. Historically, the 2 different treatment strategies have been tested during different time periods, resulting in few studies with the main objective to study the combined effects of the 2 agents. From the data that are presently available, however, there is a clear suggestion of additive beneficial effect and the 2 treatments given in combination are well tolerated.
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Affiliation(s)
- G Olsson
- Cardiovascular Medicine, Astra Hässle AB, Mölndal, Sweden
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Karlsson JE, Björkholm A, Blomstrand P, Ohlsson J, Wallentin L. Ambulatory ST-recording has no additional value to exercise test for identification of severe coronary lesions after an episode of unstable coronary artery disease in men. INTERNATIONAL JOURNAL OF CARDIAC IMAGING 1993; 9:281-9. [PMID: 8133126 DOI: 10.1007/bf01137155] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
One month after an episode of unstable coronary artery disease, 95 male patients performed coronary angiography, 48 hours ambulatory ST-recording and also an exercise test. ST-depression occurred in 29.5% during the ST-recording and in 44.2% during the exercise test (p < 0.05). In patients with ST-depression at ambulatory monitoring, 79% demonstrated the same finding at the exercise test. A high risk response at the exercise test--defined as either ST-depression in > or = 3 leads, ST-depression in 1-2 leads with a maximal work load below the 60th percentile or a maximal work load below the 30th percentile regardless of the ECG reaction--occurred in 56.8%. Severe coronary lesions--defined as three vessel disease, left main stenosis or proximal left anterior descending artery stenosis as part of two vessel disease--was observed in 46.3%. Patients with a high risk exercise test response and patients with ST-depression during ST-recording had severe coronary lesions in 67% and 64% respectively. However, a high risk exercise test response occurred in 82%, while ST-depression at ambulatory monitoring was observed only in 41% of the patients with severe coronary lesions (p < 0.001). Thus, ambulatory ST-recording one month after an episode of unstable coronary artery disease in men adds no further information to a symptom limited exercise test in order to identify patients with severe coronary lesions.
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Affiliation(s)
- J E Karlsson
- Department of Cardiology, University Hospital, Linköping, Sweden
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Karlsson JE, Björkholm A, Nylander E, Ohlsson J, Swahn E, Wallentin L. ST-changes in ECG at rest or during exercise indicate a high risk of severe coronary lesions after an episode of unstable coronary artery disease. Int J Cardiol 1993; 42:47-55. [PMID: 8112905 DOI: 10.1016/0167-5273(93)90101-l] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
After an episode of unstable coronary artery disease, 190 patients performed a predischarge exercise test. A postdischarge exercise test and coronary angiography was performed by 172 patients after 1 month. A subgroup of 104 men performed both exercise tests with a computer-aided system. More sophisticated methods of evaluating the ECG reaction during exercise were not diagnostically superior to the simple identification of ST-depression of > or = 0.1 mV. ST-depression in ECG at rest indicated a 70% risk of severe coronary lesions and in such patients, the ECG reaction at exercise carried no additional diagnostic information. Stepwise multiple regression analysis showed that ST-depression and low maximal work load were the most important exercise variables for identification of severe coronary lesions. Using a combination of these parameters, the sensitivity and specificity for identification of severe coronary lesions were, respectively, 77% and 61% predischarge and 77% and 70% after 1 month.
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Affiliation(s)
- J E Karlsson
- Department of Internal Medicine, County Hospital Ryhov, Jönköping, Sweden
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