Biomedical subjects

Ju Han Kim

Publications and source records attributed to Ju Han Kim.

At least 37 records · Page 2Linked to original sources

PubMed2005

Effect of anti-oxidant (carvedilol and probucol) loaded stents in a porcine coronary restenosis model.

BACKGROUND: The long-term clinical efficacy of intracoronary stenting is limited by restenosis and delivery by the stent of agents inhibiting cell cycle progression should prevent in-stent neointimal hyperplasia. Carvedilol is an antioxidant that inhibits smooth muscle cell proliferation and migration, whereas probucol is a vascular protectant and reduces stent restenosis by improving the lumen dimension at the stent placement site. METHODS AND RESULTS: BiodivYsio phosphorylcholine-coated stents were dip-coated with carvedilol (5 mg/ml) or probucol (50 mg/ml) by immersion in respective methanol solutions. Twenty-four stents (carvedilol=8, probucol=8, control=8) were placed in 12 pigs and histopathologic analysis was done 4 weeks later. Histomorphometry of the carvedilol-coated stent group compared with the control groups showed that the neointimal area decreased by 42% (1.12+/-0.55 mm2 in the carvedilol group vs 1.92+/-0.52 mm2 in the control, p=0.004) and the lumen area increased by 20% (5.15+/-0.90 mm2 vs 4.17+/-0.87 mm2, p=0.008), resulting in a 43% reduction of the percent area stenosis (18.22+/-9.6% vs 31.9+/-9.2%, p=0.002). In the probucol-coated stent group, the lumen area, neointimal area, and %area stenosis did not different significantly from the control group. There were 7.7+/-2.97% proliferating nuclear cell antigen-positive cells in the carvedilol-coated stent group compared with 17.8+/-1.45% in the control group (p=0.0001) and 15.9+/-1.91% in the probucol group (vs control, p=NS). CONCLUSIONS: The carvedilol-coated stent, but not the probucol-coated one, inhibited neointimal hyperplasia in a porcine stent restenosis model.

Animals↗

PubMed2005

Usefulness of physical maneuvers for prevention of vasovagal syncope.

BACKGROUND: It is known that approximately two-thirds of patients with vasovagal syncope have prodromal symptoms and when these start, physical maneuvers that can increase venous return may abort the syncopal attack. The aims of this study were to evaluate the effects of 3 physical maneuvers, squatting, leg-crossing with muscle tensing, and handgrip, on improving hemodynamic status, and to compare the effect of each on aborting or preventing vasovagal syncope. METHODS AND RESULTS: Of 50 patients who underwent the head-up tilt test (HUT) to evaluate syncope, 27 patients with positive HUT were classified as group I (14 men, 13 women; mean age 44.5+/-15.3 years), 23 patients with negative HUT were classified as group II (13 men, 10 women; mean age 41.2 +/-16.7 years), and 21 normal subjects were classified as group III (10 men, 11 women; mean age 28.6+/-6.3 years). The effects of the physical maneuvers were evaluated in 21 patients from group I who underwent a repeat HUT 1 week after the initial test. Leg-crossing significantly increased systolic blood pressure (SBP) in all 3 groups (8.0+/-5.8 mmHg in group I, 7.0+/-8.5 mmHg in group II, 8.7+/-5.7 mmHg in group III; p < 0.05), but not diastolic blood pressure (DBP). Squatting significantly increased SBP and DBP in all 3 groups (7.1 +/-5.1, 4.6+/-5.8 mmHg in group I, 7.8+/-5.9, 4.3+/-4.7 mmHg in group II, 6.5+/-5.0, 3.7+/-3.9 mmHg in group III; p < 0.05). However, handgrip did not exert any significant influence on the hemodynamics in any group nor did heart rate change significantly during the physical maneuvers in any group. During the repeat HUT, prodromal symptoms with hypotension developed in 13 of the 21 patients and of these 5 fainted immediately after and were not able to do the physical maneuvers. Squatting and leg-crossing aborted syncope in 7 of 8 patients, but handgrip aborted syncope in only 1 patient. CONCLUSION: Squatting and leg-crossing with muscle tensing improved the hemodynamics of normal subjects as well as those of patients with vasovagal syncope. Squatting and leg-crossing can be used as a simple and effective preventive maneuver in patients with vasovagal syncope.

Adult↗

PubMed2005

N-terminal pro-B-type natriuretic Peptide predicts significant coronary artery lesion in the unstable angina patients with normal electrocardiogram, echocardiogram, and cardiac enzymes.

BACKGROUND: Brain natriuretic peptide (BNP) and N-terminal pro-brain natriuretic peptide (NT-proBNP) are not specific for ventricular dysfunction and other cardiac processes, such as myocardial ischemia, may also cause elevation of these markers. METHODS AND RESULTS: To determine whether elevation of NT-proBNP without elevation of cardiac specific markers can predict coronary artery disease (CAD), the serum level of NT-proBNP was measured in 161 patients with unstable angina (61.0+/-8.1 years, male 54.0%) with normal ventricular function (left ventricular ejection fraction >55% and no regional wall motion abnormality by echocardiography) and normal troponin I level (<0.05 ng/ml). In these patients, levels of C-reactive protein and myoglobin were normal and none had Q wave on electrocardiographic (ECG). The NT-proBNP level was higher in patients with CAD (n=74) than in patients without CAD (n=87) (173.1+/-231.6 vs 68.1+/-62.5 pg/ml, p<0.001). At the standard cut-off point of >200 pg/ml, elevated NT-proBNP level shows high probability of CAD (odds ratio, 10.1; 95% confidence interval, 2.6-38.7, p=0.001). The NT-proBNP level positively correlated with the extent of CAD (r=0.329, p=0.001). In multivariate analysis, the NT-proBNP was an independent predictor of CAD. CONCLUSION: These results suggested that NT-proBNP is a useful screening test for CAD in the unstable angina patients with normal ECG, echocardiogram and cardiac enzyme levels.

Adult↗

PubMed2005

Elevated preprocedural high-sensitivity C-reactive protein levels are associated with neointimal hyperplasia and restenosis development after successful coronary artery stenting.

BACKGROUND: Recent data indicate that an elevated serum level of high-sensitivity C-reactive protein (hs-CRP) predicts the risk of recurrent coronary events, and that statin therapy decreases the risk of coronary events. This study assessed the relationship between the pre-procedural hs-CRP level and in-stent neointimal hyperplasia (NIH) after stenting and the effects of statins on the relationship between restenosis after stenting and the serum hs-CRP levels of patients with coronary artery disease. METHODS AND RESULTS: This study included 100 patients who underwent stent implantation for angiographically significant stenosis. Patients were divided into a normal C-reactive protein (CRP) group (<0.5 mg/dl, n=59) and elevated CRP group (>or=0.5 mg/dl, n=41). All patients underwent angiographic and intravascular ultrasound follow-up at 6 months. The baseline CRP level was 0.29+/-0.08 mg/dl in the normal CRP group and 2.90+/-2.31 mg/dl in the elevated CRP group. The NIH cross-sectional area (CSA) in the minimal lumen CSA at follow-up was significantly larger in the elevated CRP group compared with the normal CRP group (1.9+/-1.3 mm2 vs 3.0+/-1.5 mm2, p=0.001). A significant positive correlation was found between pre-interventional CRP level and NIH area (r=0.52, p<0.001). In patients with normal CRP, an association between statin therapy and restenosis was not observed. However, when the analysis was confined to patients with elevated CRP, statin therapy significantly reduced the restenosis rate (20% vs 37.5%, p=0.031). In the normal CRP group, the intra-stent neointimal area at 6 months was not different between the non-statin and statin groups (2.2+/-1.4 mm2 vs 1.8+/-1.1 mm2). However, in the elevated CRP group, statin therapy significantly decreased the neointimal area at 6-month follow-up (3.6+/-1.7 mm2 vs 2.4+/-1.3 mm2, p<0.001). CONCLUSION: Measuring the pre-interventional hs-CRP level may help predict the development of restenosis after stenting and statin therapy will significantly reduce the restenosis rate in patients with an elevated hs-CRP.

Adult↗

PubMed2005

Predictive factors of major adverse cardiac events in acute myocardial infarction patients complicated by cardiogenic shock undergoing primary percutaneous coronary intervention.

BACKGROUND: The aim of this study was to assess in-hospital mortality and major adverse cardiac events (MACE) during long-term clinical follow-up of patients who developed cardiogenic shock (CS) after acute myocardial infarction (AMI) and who underwent primary percutaneous coronary intervention (PCI). METHODS AND RESULTS: The data from 147 patients with CS after AMI (61.7 +/-10.4 years, M:F =156:99) who underwent primary PCI at Chonnam National University Hospital between January 1999 and December 2002 were analyzed: clinical characteristics, coronary angiographic findings and mortality during admission, and MACE during a 1-year clinical follow-up. Of the enrolled patients, 121 patients survived (group I, M:F =94:27) and 26 died (group II, M:F =14:12) during admission. By binary logistic regression analysis, in-hospital death was associated with low Thrombolysis In Myocardial Infarction (TIMI) flow after coronary revascularization (p=0.02, odds ratio (OR) =1.3). Eighty-nine patients (60.5%) survived without MACE during the 1-year clinical follow-up and MACE was associated with a C-reactive protein (CRP) of more than 1 mg/dl (p=0.002, OR =6.3) and low TIMI flow after coronary revascularization (p<0.001, OR =7.8). CONCLUSIONS: Primary PCI achieving TIMI 3 flow reduces in-hospital death in AMI with CS. High concentration of CRP and low TIMI flow are associated with MACE during long-term clinical follow-up.

Aged↗

PubMed2005

Long-term clinical outcomes of platelet glycoprotein IIb/IIIa inhibitor combined with low molecular weight heparin in patients with acute coronary syndrome.

BACKGROUND: Platelet activation and aggregation with resultant arterial thrombus formation play a pivotal role in the pathophysiology of acute coronary syndrome (ACS). In the present study the efficacy of tirofiban, a specific inhibitor of the platelet glycoprotein IIb/IIIa receptor, combined with heparin or low-molecular-weight heparin (dalteparin), was evaluated for the management of ACS. METHODS AND RESULTS: One hundred and sixty patients (60.9+/-11.1 years, 104 male) with unstable angina or non-ST elevation myocardial infarction and who had ST-T changes and elevated troponin were randomly assigned to 4 groups: group I (n=40: heparin alone), group II (n=40: dalteparin alone), group III (n=40: tirofiban + heparin) and group IV (n=40: tirofiban + dalteparin). The occurrence of major adverse cardiac events (MACE) was compared prospectively during a 6-month clinical follow-up. Percutaneous coronary intervention or coronary artery bypass graft was performed in 32 cases in group I, 29 in group II, 28 in group III and 31 in group IV (p=0.72). Minor bleeding complication developed in 2 patients (5.0%) in group I, 2 (5.0%) in group II, 4 (10.0%) in group III and 3 (7.5%) in group IV (p=0.78). During the follow-up MACE occurred in 10 patients (31.3%) in group I, 9 (31.0%) in group II, 4 (14.3%) in group III and 4 (12.9%) in group IV (p=0.02: Group I and II vs Group III and IV). CONCLUSIONS: Tirofiban combined with dalteparin was associated with relatively more bleeding complications in the short term, but was effective in reducing the incidence of MACE during long-term clinical follow-up in patients with ACS.

Acute Disease↗

PubMed2005

Myocardial protective effects of nicorandil during percutaneous coronary intervention in patients with unstable angina.

BACKGROUND: The purpose of the study was to prospectively evaluate the protective effect of nicorandil during percutaneous coronary intervention (PCI) in patients with unstable angina (UAP). METHODS AND RESULTS: Two hundred patients (61+/-10 year-old, male 143) diagnosed with UAP at an emergency medical center were randomly assigned to 2 groups: intravenous isosorbide dinitrate, Group I (n=100), or intravenous nicorandil, Group II (n=100). PCI was performed 12-48 h after infusion of each agent. Serum concentrations of creatine kinase-MB (CK-MB), cardiac troponin T (cTnT), and I (cTnI) were measured before and 6, 12, 24 h after PCI. Patients with non-coronary chest pain, requiring emergency coronary angiogram, temporary pacemaker or glycoprotein IIb/IIIa receptor blocker were excluded. PCI was successfully performed in 96 patients (Group I=54, 61.7+/-8.2 years, 32 males; Group II=42, 60.4+/-11.7 years, 27 males). No significant differences in clinical or coronary angiographic characteristics were observed between the 2 groups. The concentration of CK-MB was elevated in 9 patients (17%) of Group I and 6 (14%) of Group II, cTnT in 16 (30%), 6 (14%) and cTnI in 25 (46%), 9 (21%) after PCI. Elevation of any troponin was less frequent in Group II [28/54 (52%) vs 10/42 (24%) patients, p=0.01]. Major adverse coronary events during the 6-month clinical follow-up occurred in 9 (17%) of Group I and 5 patients of Group II (12%, p=NS). Follow-up echocardiography revealed lower left ventricular ejection fraction in Group I than in Group II (65.4+/-7.2% vs 71.0+/-6.7%, p=0.03). CONCLUSION: Nicorandil has a myocardial protective effect during PCI in patients with UAP.

Aged↗

PubMed2005

Impact of preinterventional arterial remodeling on in-stent neointimal hyperplasia and in-stent restenosis after coronary stent implantation.

BACKGROUND: Patterns of arterial remodeling during the course of plaque development have been shown to play an important role in both the progression of de novo atherosclerosis and in the restenotic process following coronary intervention. The aim of the present prospective study was to evaluate the effect of pre-interventional arterial remodeling on in-stent neointimal hyperplasia (NIH) and in-stent restenosis (ISR) after stenting. METHODS AND RESULTS: Pre-interventional arterial remodeling was assessed in 85 native coronary lesions by using intravascular ultrasound (IVUS). The remodeling index (RI) was 1.09+/-0.20 in the positive remodeling (PR)/intermediate remodeling (IR) group and 0.84+/-0.12 in the negative remodeling (NR) group. The plaque plus media cross sectional area (P&M CSA) at pre-intervention and NIH CSA at follow-up in the minimal lumen CSA were significantly larger in the PR/IR group (9.2+/-2.9 mm2 vs 6.2+/-1.8 mm2, 3.3+/-1.2 mm2 vs 1.5+/-0.9 mm2; p = 0.001, p = 0.001, respectively). On 3-dimensional analysis of IVUS images at follow-up, the lumen volume was significantly smaller in the PR/IR group than that in the NR group (62+/-15 mm3 vs 75 +/-20 mm3; p = 0.001), and neointima hyperplasia volume was significantly larger in the PR/IR group than that in the NR group (46+/-15 mm3 vs 26+/-10 mm3; p = 0.001). A significant positive correlation was found between pre-interventional RI and follow-up NIH CSA (r = 0.25, p = 0.022). The incidence of ISR and repeat intervention was significantly higher in the PR/IR group (30.8% vs 18.2%, 28.8% vs 15.2%; p = 0.032, 0.035, respectively). CONCLUSION: Measuring pre-interventional arterial remodeling patterns by IVUS may be helpful to stratify lesions at high-risk of ISR.

Aged↗

PubMed2005

The effects of QRS duration and pacing sites on the acute hemodynamic changes during right ventricular pacing.

BACKGROUND: Has been reported that patients exhibiting prolonged paced QRS duration tend to have more serious heart disease, and the paced QRS duration can be an effective indicator of impaired left ventricular function. However, the acute and chronic hemodynamic effects of paced QRS duration and pacing sites during right ventricular (RV) pacing remain unknown. METHODS: A total of 14 patients who underwent electrophysiologic study for paroxysmal supraventricular tachycardia were examined. RV pacing was performed at 10 different sites with cycle lengths of 600 ms and 500 ms utilizing a 6-7F deflectable quadripolar electrode catheter. Systolic, diastolic, and mean blood pressures during pacing were measured once the blood pressure was stabilized. RESULTS: During RV pacing, blood pressures (systolic/diastolic/mean) decreased. The change of post-pacing QRS duration and pre-pacing the systolic blood pressure (SBP) were greater in the group with paced QRS duration. The differences overall were greater than 140 ms. The SBP decrease during pacing was larger in the group exhibiting paced QRS duration of greater than 140 ms. The SBP decrease during pacing showed relation to QRS duration during pacing (r = 0.500, p = 0.001), the change of QRS duration post-pacing (r = 0.426, p = 0.001), and SBP during sinus rhythm (r = 0.342, p = 0.001) on linear correlation analysis. The pacing site, on the other hand, did not affect acute hemodynamic changes during pacing. CONCLUSION: Ventricular pacing of less than 40 ms at the area of paced QRS duration is recommended.

Blood Pressure↗

PubMed2005

Long-term predictive factors of major adverse cardiac events in patients with acute myocardial infarction complicated by cardiogenic shock.

BACKGROUND: Cardiogenic shock (CS) after acute myocardial infarction (AMI) develops in 5-10% of patients and it is associated with high mortality. The aim of this study is to assess the predictive factors of mortality for patients with AMI and CS. METHODS: Two hundred fifty five AMI patients with CS (the mean age was 66.0 +/- 11.0 years, M:F=156:99) out of 1268 AMI patients who admitted at Chonnam National University Hospital between July 2000 and June 2002 were analyzed according to the clinical characteristics, coronary angiographic findings and MACE during admission and for the 1-year clinical follow-up. RESULTS: Among the enrolled patients, 129 patients survived without MACE (Group I, mean age 64.2 +/- 10.6 years, M:F=76:53), and 126 patients had MACE (Group II, mean age 68.1 +/- 10.0 years, M:F = 80:46) during admission or during the 1-year follow-up period. There were significant differences in age between the Groups I and II (64.2 +/- 10.6 vs. 68.1 +/- 11.0 years, respectively, p = 0.004) and the previous MI history (0 vs. 17.4%, respectively, p<0.001). The left ventricular ejection fraction (EF) was lower in Group II (Group I vs. II: 49.1 +/- 13.0 vs. 39.1 +/- 12.9%, p < 0.001). The levels of troponin (Tn) I and C-reactive protein (CRP) were higher in Group II (Group I vs. II: 29.2 +/- 7.72 vs. 50.8 +/- 5.17 ng/dL, p = 0.017, 3.8 +/- 0.48 vs. 9.9 +/- 1.21 mg/dL, p < 0.001 respectively). Left main stem lesion (LMSL) was more common in Group II than in Group I (0.7% vs. 22.0%, respectively, p = 0.004). In-hospital death was associated with low Thrombolysis In Myocardial Infarction (TIMI) flow after coronary revascularization. CONCLUSION: Old age, a previous MI history, high Tn and CRP, low EF and LMSL are associated with higher MACE for patients with AMI and CS. Coronary revascularization with TIMI 3 flow lowers the in-hospital mortality.

Aged↗

PubMed2005

Integrating microarray gene expression object model and clinical document architecture for cancer genomics research.

Systematic integration of genomic-scale expression profiles with clinical information may facilitate cancer genomics research. MAGE-OM (Microarray Gene Expression Object Model) defines standard objects for genomic but not for clinical data. HL7 CDA (Clinical Document Architecture) is a document model for clinical information, describing syntax (generic structure) but not semantics. We designed a document template in XML Schema with additional constraints for CDA to define content semantics, enabling data model-level integration of MAGE-OM and CDA for cancer genomics research.

Gene Expression Profiling↗

PubMed2004

GOChase: correcting errors from Gene Ontology-based annotations for gene products.

SUMMARY: The Gene Ontology (GO) is a controlled biological vocabulary that provides three structured networks of terms to describe biological processes, cellular components and molecular functions. Many databases of gene products are annotated using the GO vocabularies. We found that some GO-updating operations are not easily traceable by the current biological databases and GO browsers. Consequently, numerous annotation errors arise and are propagated throughout biological databases and GO-based high-level analyses. GOChase is a set of web-based utilities to detect and correct the errors in GO-based annotations.

Database Management Systems↗

PubMed2004

Effect of abciximab-coated stent on in-stent intimal hyperplasia in human coronary arteries.

The investigators tested whether abciximab-coated stents prevent neointimal hyperplasia (NIH) formation in coronary de novo lesions. Abciximab-coated stents were compared with control stents. All patients underwent follow-up coronary angiography and intravascular ultrasound (IVUS). All stents were successfully deployed, and patients were discharged home without clinical events. At follow-up coronary angiography, the restenosis rate and late loss were 14% and 0.33 +/- 0.28 mm in the abciximab-coated stent group and 28.6% and 0.64 +/- 0.32 mm in the control stent group (p = 0.099 and p = 0.014, respectively). At follow-up IVUS, the intrastent luminal area and intrastent NIH area were 5.7 +/- 1.6 and 2.0 +/- 1.6 mm(2), respectively, in the abciximab-coated stent group and 4.2 +/- 0.8 and 3.4 +/- 1.7 mm(2), respectively, in the control stent group (p = 0.001 and p = 0.001, respectively). Abciximab-coated stents are feasible and significantly inhibit NIH, with potential therapeutic benefit in preventing stent restenosis.

Abciximab↗

PubMed2004

Increased expression of metallothionein is associated with irinotecan resistance in gastric cancer.

To gain insight into clinically relevant mechanisms of irinotecan resistance, we undertook oligonucleotide microarray analyses on paired malignant effusion samples obtained from eight gastric cancer patients treated with weekly irinotecan. Pretreatment and posttreatment (48 h) effusion samples were obtained for each patient, and the change in expression profile was compared between clinical responders and nonresponders. When differences in the expression of genes were examined using SAM (Significance Analysis of Microarrays) software, five isoforms of the metallothionein family were identified to have significantly higher signal log ratios in five nonresponders, compared with three responders. Compared with control cells, metallothionein 1X (MT1X)-transfected AGS cells showed a 1.4-fold higher irinotecan IC(50) by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay and tended to form more colonies. These findings collectively suggest that irinotecan-induced up-regulation of metallothionein might be associated with irinotecan resistance in patients with gastric cancer, although it remains to be confirmed in a larger data set.

Adult↗

PubMed2004

ArrayXPath: mapping and visualizing microarray gene-expression data with integrated biological pathway resources using Scalable Vector Graphics.

Biological pathways can provide key information on the organization of biological systems. ArrayXPath (http://www.snubi.org/software/ArrayXPath/) is a web-based service for mapping and visualizing microarray gene-expression data for integrated biological pathway resources using Scalable Vector Graphics (SVG). By integrating major bio-databases and searching pathway resources, ArrayXPath automatically maps different types of identifiers from microarray probes and pathway elements. When one inputs gene-expression clusters, ArrayXPath produces a list of the best matching pathways for each cluster. We applied Fisher's exact test and the false discovery rate (FDR) to evaluate the statistical significance of the association between a cluster and a pathway while correcting the multiple-comparison problem. ArrayXPath produces Javascript-enabled SVGs for web-enabled interactive visualization of pathways integrated with gene-expression profiles.

Cluster Analysis↗

PubMed2004

DNA microarray analysis of the correlation between gene expression patterns and acquired resistance to 5-FU/cisplatin in gastric cancer.

The mechanisms of intrinsic and/or acquired anti-cancer drug resistance have been described in in vitro resistance models, but the clinical relevance has remained undefined. We undertook a prospective study to identify correlations between gene expression and clinical resistance to 5-FU/cisplatin. We compared expression profiles from gastric cancer endoscopic biopsy specimens obtained at a chemosensitive state (partial remission after 5-FU/cisplatin) with those obtained at a refractory state (disease progression), using Affymetrix oligonucleotide microarray technology (U133A). Using 119 discriminating probes and a cross-validation approach, we were able to correctly identify the chemo-responsiveness of 7 pairs of training samples and 1 independent test pair. These exploratory data demonstrate that the gene expression profiles differ between chemosensitive and refractory state gastric cancer biopsy samples.

Adult↗

PubMed2004

ChromoViz: multimodal visualization of gene expression data onto chromosomes using scalable vector graphics.

SUMMARY: ChromoViz is an R package for the visualization of microarray gene expression data, cross-species and cross-platform comparisons, as well as non-expression genomic data obtained from public databases onto chromosomes. Chromosomal visualization format is proposed for the clear decoupling of the data layer from the procedure layer and the combined visualization of genomic data from heterogeneous data sources. Visualization with Javascript-enabled scalable vector graphics enables interactive visualization and navigation of data objects on the Web. AVAILABILITY: http://www.snubi.org/software/ChromoViz/

Chromosome Mapping↗

PubMed2004

Discovering significant and interpretable patterns from multifactorial DNA microarray data with poor replication.

MOTIVATION: Multivariate analyses are advantageous for the simultaneous testing of the separate and combined effects of many variables and of their interactions. In factorial designs with many factors and/or levels, however, sufficient replication is often prohibitively costly. Furthermore, complicated statements are often required for the biological interpretation of the higher-order interactions determined by standard statistical techniques like analysis of variance. RESULTS: Because we are usually interested in finding factor-specific effects or their interactions, we assumed that the observed expression profile of a gene is a manifestation of an underlying factor-specific generative pattern (FSGP) combined with noise. Thus, a genetic algorithm was created to find the nearest FSGP for each expression profile. We then measured the distance between each profile and the corresponding nearest FSGP. Permutation testing for the distance measures successfully identified those genes with statistically significant profiles, thus yielding straightforward biological interpretations. Association networks of genes, drugs, and cell lines were created as tripartite graphs, representing significant and interpretable relations, by using a microarray experiment of gastric-cancer cell lines with a factorial design and no replication. The proposed method may benefit the combined analysis of heterogeneous expression data from the growing public repositories.

Algorithms↗