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PubMed2005

A comparison of methods for alignment of NMR peaks in the context of cluster analysis.

This paper compares the performance of two recently developed algorithms and methods for peak alignment of first-order NMR data of complex biological samples. The NMR spectra of such samples exhibit variations in peak position and peak shape due to variations in the sample matrix and to instrumental instabilities. The first method comprises an alignment of spectral segments with linear interpolation and shift correction to accommodate correspondence between a target and a test spectrum by a beam search or genetic algorithm. The second method is based on peak picking and needle vector representation of the NMR data with subsequent breadth-first search to establish shift corrections between the target and the test spectrum. The two proposed peak alignment methods and their respective merits are discussed for a real metabonomics application. Both alignment methods have been shown to enhance the interpretability of the resulting multivariate models, thereby increasing the prospect of detecting and following the onset of subtle biological changes reflected in the NMR data.

Algorithms↗

PubMed2003

Application of cluster analysis to the geochemistry zonation of the estuary waters in the Tinto and Odiel rivers (Huelva, Spain).

The combination of acid water from mines, industrial effluents and sea water plays a determining role in the evolutionary process of the chemical makeup of the water in the estuary of the Tinto and Odiel rivers. This estuary is in the southwest of the Iberian Peninsula and is one of the estuarine systems on the northwest coast of the Gulf of Cádiz. From the statistical treatment of data obtained by analyzing samples of water from this system, which is affected by industrial and mining pollution processes, we can see how the sampling points studied form two large groups depending on whether they receive tidal or fluvial influences. Fluvial input contributes acid water with high concentrations of heavy metal, whereas industrial effluents are responsible for the presence of phosphates, silica and other nutrients. The estuarine system of the Tinto and Odiel Rivers can be divided into three areas--the Tinto estuary, the Odiel estuary and the area of confluence--based on the physical--chemical characteristics of the water.

Cluster Analysis↗

PubMedDate not supplied

Cluster analysis of SF-36 scales as a predictor of spinal pain patients response to a multidisciplinary pain management approach beginning with epidural steroid injection.

OBJECTIVE: To investigate whether grouping of patients with back pain into similar behavioral patient profiles using SF-36 scores is predictive of outcome following 1-year treatment in a multidisciplinary spine center beginning with referral for epidural steroid injection. DESIGN: A prospective observational study was conducted on 81 consecutive patients selected for epidural steroid injections by independent physicians following common institutional criteria. Each patient completed a baseline SF-36 questionnaire as well as a numerical response pain scale. The initial SF-36 data were used to place each patient into one of three subgroups (Highly Functional, Emotional Adapters, and Dysfunctional). Follow-up SF-36 and numerical response pain scale questionnaires were completed by the patients at 1 month and 12 months following the initial epidural steroid injection. RESULTS: Results revealed significant improvement among all three patient subgroups following multidisciplinary treatment at both 1 month and 12 months. Few differences in outcome occurred among the subgroups. CONCLUSION: The SF-36-determined subgroups did not predict response to a multidisciplinary pain clinic. All three subgroups showed similar improvement following treatment.

Adult↗

PubMed1996

[Profile of primary care physicians in a health area: a cluster analysis].

OBJECTIVES: To discover characteristics of primary care doctors. To find homogeneous groups of doctors. DESIGN: A basically descriptive crossover observational study. SETTING: Primary care doctors from a health area. PARTICIPANTS: The following variables were recorded on the 99 doctors who worked in Castellon Area 03 during 1992: age, gender, fixed or temporary post, rural or urban area, MIR training, primary care model, patient load, sole employment, drugs expenditure, number of pensioners and total number of patients registered. MEASUREMENTS AND MAIN RESULTS: We found a first group of older doctors, working mainly in the old model, for whom PC was not their sole employment; another younger group without MIR training and with an average patient load; the third group was women in temporary posts with a somewhat higher drugs expenditure; the fourth was doctors working in rural areas with a very low patient load; the fifth, final and youngest group was family doctors, with an average patient load, low expenditure and a high number of patients registered. We observed highly significant differences between groups. CONCLUSIONS: Doctors' age and gender divide them into different groupings; family doctors form one group. Multivariable, descriptive methods proved useful in finding, describing and classifying doctors and centres, etc., and could be of use in resource and action planning.

Age Factors↗

PubMed1991

Cross validation of cluster analysis using immunostained multi-tissue tumour block slides.

We assayed the panel of SCLC MAbs using multi-tissue tumour block (MTTB) slides obtained from Dr. Hector Battifora (City of Hope Hospital, Duarte CA). MTTB slides contain up to 100 different formalin-fixed tumour tissue specimens and can be immunostained with as little as 50 microliters of antibody solution. In this study, the MAbs in the SCLC panel were used to stain slides from a MTTB comprised of eight normal, ten SCLC, ten squamous cell, ten adenocarcinoma and five undifferentiated lung cancer tissues. Many MAbs in the SCLC panel failed to immunostain the lung MTTB whereas many others showed significant immunoreactivity. Of those MAbs that stained SCLC tissue, none was found to be specific; these MAbs also stained NSCLC tissues or normal lung tissues. Some MAbs in the panel immunostained SCLC and NSCLC tissues, but were also reactive to normal lung tissue as well as other normal tissue specimens. A major advantage of immunostaining MTTBs with a panel of MAbs is that we were able to compare the immunoreactivity of the MAbs on a total of 128 different tissues requiring only 100 microliters of antibody solution using only two MTTB slides per MAb. Although this study was preliminary and certain technical problems in assembling the MTTB as well as optimising the immunostaining procedure for handling 98 or more MAbs simultaneously remain, the MTTB technique remains promising.

Adenocarcinoma↗

PubMed2005

Genotypes and haplotypes in the IL-1 gene cluster: analysis of two genetically and diagnostically distinct groups of Alzheimer patients.

Increased risk of Alzheimer's disease (AD) has been associated with polymorphisms in the IL-1 gene cluster, and in particular with the IL-1alpha-889 T/T genotype. However, this association is still unclear, and needs further investigation. In order to clarify the role of these polymorphisms in the complex pathogenesis of AD we examined genotype and haplotype frequencies of the two C-to-T SNPs at position -889 and -551 in the IL-1alpha and IL-1beta genes, respectively, and of the 86 bp VNTR intron-2 polymorphisms in the IL-1Ra gene. The analysis was performed in two genetically and diagnostically distinct groups of sporadic AD from Italy and the USA. In the Italian group a significant association between the IL-1alpha-889 T/T genotype and AD (OR=3.022, 95% CI: 1.001-9.119) was found, whereas no difference was found in the group from the USA. Results were also compared with previously published studies that analyzed the same IL-1 polymorphisms in AD. In both groups, the analysis of the estimated haplotypes shows that AD patients and controls who carry the IL-1beta-511 C allele, were also more frequently carriers of the IL-1Ra 1 allele (haplotypes -C-1). The total frequency of the two -C-1 haplotypes (C-C-1 plus T-C-1) was about one half of the total frequency of the eight estimated haplotypes. This was confirmed by significant linkage disequilibrium between these two loci in both the Italian and USA groups. In the Italian group a weak association of the T-C-2 haplotype with the disease (OR=1.648, 95% CI: 1.519-1.788) was also found, whereas in the USA group no difference was found. Although ours and other published data on different samples of Caucasian and non-Caucasian AD show a great heterogeneity in the frequencies of the IL-1alpha-889, the IL-1beta-511 and the IL-1Ra VNTR gene polymorphisms, we confirm the role of the IL-1alpha-889 T/T genotype as a risk factor for sporadic AD, and show the presence of an allelic association between IL-1beta C and IL-1Ra 1 alleles in both the Italian and the USA groups, confirmed by the presence of significant levels of linkage disequilibrium between these two loci.

Aged↗

PubMed2000

Building sickness syndrome in healthy and unhealthy buildings: an epidemiological and environmental assessment with cluster analysis.

OBJECTIVES: Building sickness syndrome remains poorly understood. Aetiological factors range from temperature, humidity, and air movement to internal pollutants, dust, lighting, and noise factors. The reported study was designed to investigate whether relations between symptoms of sick building syndrome and measured environmental factors existed within state of the art air conditioned buildings with satisfactory maintenance programmes expected to provide a healthy indoor environment. METHODS: Five buildings were studied, three of which were state of the art air conditioned buildings. One was a naturally ventilated control building and one a previously studied and known sick building. A questionnaire was administered to the study population to measure the presence of building related symptoms. This was followed by a detailed environmental survey in identified high and low symptom areas within each building. These areas were compared for their environmental performance. RESULTS: Two of the air conditioned buildings performed well with a low prevalence of building related symptoms. Both of these buildings out performed the naturally ventilated building for the low number of symptoms and in many of the environmental measures. One building (C), expected to perform well from a design viewpoint had a high prevalence of symptoms and behaved in a similar manner to the known sick building. Environmental indices associated with symptoms varied from building to building. Consistent associations between environmental variables were found for particulates (itchy eyes, dry throat, headache, and lethargy) across all buildings. There were persisting relations between particulates and symptoms (headache, lethargy, and dry skin) even in the building with the lowest level of symptoms and of measured airborne particulates (building B). There were also consistent findings for noise variables with low frequency noise being directly associated with symptoms (stuffy nose, itchy eyes, and dry skin) and higher frequency noise being relatively protective across all buildings. CONCLUSIONS: This is the first epidemiological study of expected state of the art, air conditioned buildings. These buildings can produce an internal environment better than that of naturally ventilated buildings for both reported symptoms and environmental variables. The factors associated with symptoms varied widely across the different buildings studied although consistent associations for symptoms were found with increased exposure to particulates and low frequency noise.

Adult↗

PubMed2004

Long-range interphase chromosome organization in Drosophila: a study using color barcoded fluorescence in situ hybridization and structural clustering analysis.

We have developed a color barcode labeling strategy for use with fluorescence in situ hybridization that enables the discrimination of multiple, identically labeled loci. Barcode labeling of chromosomes provides long-range path information and allows structural analysis at a scale and resolution beyond what was previously possible. Here, we demonstrate the use of a three-color, 13-probe barcode for the structural analysis of Drosophila chromosome 2L in blastoderm stage embryos. We observe the chromosome to be strongly polarized in the Rabl orientation and for some loci to assume defined positions relative to the nuclear envelope. Our analysis indicates packing approximately 15- to 28-fold above the 30-nm fiber, which varies along the chromosome in a pattern conserved across embryos. Using a clustering implementation based on rigid body alignment, our analysis suggests that structures within each embryo represent a single population and are effectively modeled as oriented random coils confined within nuclear boundaries. We also found an increased similarity between homologous chromosomes that have begun to pair. Chromosomes in embryos at equivalent developmental stages were found to share structural features and nuclear localization, although size-related differences that correlate with the cell cycle also were observed. The methodology and tools we describe provide a direct means for identifying developmental and cell type-specific features of higher order chromosome and nuclear organization.

Animals↗

PubMed2006

Hierarchical clustering analysis of flexible GBR 12909 dialkyl piperazine and piperidine analogs.

Pharmacophore modeling of large, drug-like molecules, such as the dopamine reuptake inhibitor GBR 12909, is complicated by their flexibility. A comprehensive hierarchical clustering study of two GBR 12909 analogs was performed to identify representative conformers for input to three-dimensional quantitative structure-activity relationship studies of closely-related analogs. Two data sets of more than 700 conformers each produced by random search conformational analysis of a piperazine and a piperidine GBR 12909 analog were studied. Several clustering studies were carried out based on different feature sets that include the important pharmacophore elements. The distance maps, the plot of the effective number of clusters versus actual number of clusters, and the novel derived clustering statistic, percentage change in the effective number of clusters, were shown to be useful in determining the appropriate clustering level. Six clusters were chosen for each analog, each representing a different region of the torsional angle space that determines the relative orientation of the pharmacophore elements. Conformers of each cluster that are representative of these regions were identified and compared for each analog. This study illustrates the utility of using hierarchical clustering for the classification of conformers of highly flexible molecules in terms of the three-dimensional spatial orientation of key pharmacophore elements.

Cluster Analysis↗

PubMed2005

A meta-clustering analysis indicates distinct pattern alteration between two series of gene expression profiles for induced ischemic tolerance in rats.

We have developed a visualization methodology, called a "cluster overlap distribution map" (CODM), for comparing the clustering results of time series gene expression profiles generated under two different conditions. Although various clustering algorithms for gene expression data have been proposed, there are few effective methods to compare clustering results for different conditions. With CODM, the utilization of three-dimensional space and color allows intuitive visualization of changes in cluster set composition, changes in the expression patterns of genes between the two conditions, and relationship with other known gene information, such as transcription factors. We applied CODM to time series gene expression profiles obtained from rat four-vessel occlusion models combined with systemic hypotension and time-matched sham control animals (with sham operation), identifying distinct pattern alteration between the two. Comparisons of dynamic changes of time series gene expression levels under different conditions are important in various fields of gene expression profiling analysis, including toxicogenomics and pharmacogenomics. CODM will be valuable for various types of analyses within these fields, because it integrates and simultaneously visualizes various types of information across clustering results.

Algorithms↗

PubMedDate not supplied

Cluster analysis of insomniacs' MMPI profiles: relation of subtypes to sleep history and treatment outcome.

The Minnesota Multiphasic Personality Inventory (MMPI) profiles of 100 insomniacs who presented for treatment at a university medical center were analyzed by a hierarchical clustering procedure. This analysis revealed two major personality types that accounted for 88% of the sample. The two types referred to as "Type 1" and "Type 2" insomniacs differed significantly in regard to sleep history questionnaire responses and responsivity to treatment. MMPI scales and sleep history questionnaire items suggested that Type 1 insomniacs were less defended, more aroused/activated, and had sleep histories characterized by more childhood sleep problems and greater difficulties with sleep-disruptive cognitions than did Type 2 patients. Further, Type 1 patients had a poorer response to behavioral treatment as measured by change in sleep-onset latency than did Type 2 patients. These results suggest that the MMPI may be useful in identifying distinctive personality subgroups among insomniacs. Treatment implications are discussed, and mechanisms underlying the group differences are considered.

Behavior Therapy↗

PubMed2000

An algebraic/graphical tool to compare ecosystems with respect to their pollution V: cluster analysis and Hasse diagrams.

In case of large data matrices comparative evaluations of objects/regions with the technique of Hasse diagrams may be troublesome due to a messy system of lines in the graphical representation. Here fuzzy clustering leads to useful simplifications because regions with slightly different pollution pattern are grouped together. However, fuzzy clustering implies to introduce a threshold value for the membership of an object to a cluster and to select the best number of clusters. Therefore many arbitrarities evolve. Within the systematic study presented here we found that some objects are very stable against variations of the threshold value and the number of cluster whereas other objects behaves different. According to their behaviour we investigated a classification of the objects. Formal Concept Analysis shows that in some cases specific pollution pattern imply the membership to one of these classes. For example objects which are characterized by high Pb-, Zn-concentration and moderate S-concentration imply a high stability against variants of the clustering process. Further implications are described in the paper.

Cadmium↗

PubMed2006

Cluster analysis of signal-intensity time course in dynamic breast MRI: does unsupervised vector quantization help to evaluate small mammographic lesions?

We examined whether neural network clustering could support the characterization of diagnostically challenging breast lesions in dynamic magnetic resonance imaging (MRI). We examined 88 patients with 92 breast lesions (51 malignant, 41 benign). Lesions were detected by mammography and classified Breast Imaging and Reporting Data System (BIRADS) III (median diameter 14 mm). MRI was performed with a dynamic T1-weighted gradient echo sequence (one precontrast and five postcontrast series). Lesions with an initial contrast enhancement >or=50% were selected with semiautomatic segmentation. For conventional analysis, we calculated the mean initial signal increase and postinitial course of all voxels included in a lesion. Secondly, all voxels within the lesions were divided into four clusters using minimal-free-energy vector quantization (VQ). With conventional analysis, maximum accuracy in detecting breast cancer was 71%. With VQ, a maximum accuracy of 75% was observed. The slight improvement using VQ was mainly achieved by an increase of sensitivity, especially in invasive lobular carcinoma and ductal carcinoma in situ (DCIS). For lesion size, a high correlation between different observers was found (R(2) = 0.98). VQ slightly improved the discrimination between malignant and benign indeterminate lesions (BIRADS III) in comparison with a standard evaluation method.

Algorithms↗

PubMed2005

Clonal relationship of tumor nodules in hepatocellular carcinoma: a hierarchical clustering analysis of comparative genomic hybridization data.

Information on the clonal relationship between tumor nodules in patients diagnosed with hepatocellular carcinoma (HCC) holds prognostic significance in the prediction of recurrence and postoperative treatment. Here, we investigated the clonal relationships in 11 focal nodules from 5 patients with HCC by comparative genomic hybridization (CGH) and spectral karyotyping. CGH analysis indicated tumor nodules in 5 (100%) of 5 cases to share similar patterns of genomic imbalances, suggesting nodules to be clonally related. This clonal relationship was further substantiated in 2 cases, where spectral karyotyping analysis indicated identical structural rearrangements between focal tumors. Few studies have attempted to differentiate multicentric growth from intrahepatic dissemination in HCC using CGH analysis; however, data interpretation remained subjective. In this study, we have extended our data to include published CGH findings on 57 nodules derived from 19 HCC cases. Simulation of CGH findings by unsupervised 2-way hierarchical clustering indicated tumor nodules in 20 (83.3%) of 24 cases to cluster concordantly, signifying a high incidence of clonal similarity. In sum, bioinformatic analysis of genomic profiles may represent a reliable research tool in analyzing clonal relationships among tumor nodules.

Adult↗

PubMed2006

DMRT gene cluster analysis in the platypus: new insights into genomic organization and regulatory regions.

We isolated and characterized a cluster of platypus DMRT genes and compared their arrangement, location, and sequence across vertebrates. The DMRT gene cluster on human 9p24.3 harbors, in order, DMRT1, DMRT3, and DMRT2, which share a DM domain. DMRT1 is highly conserved and involved in sexual development in vertebrates, and deletions in this region cause sex reversal in humans. Sequence comparisons of DMRT genes between species have been valuable in identifying exons, control regions, and conserved nongenic regions (CNGs). The addition of platypus sequences is expected to be particularly valuable, since monotremes fill a gap in the vertebrate genome coverage. We therefore isolated and fully sequenced platypus BAC clones containing DMRT3 and DMRT2 as well as DMRT1 and then generated multispecies alignments and ran prediction programs followed by experimental verification to annotate this gene cluster. We found that the three genes have 58-66% identity to their human orthologues, lie in the same order as in other vertebrates, and colocate on 1 of the 10 platypus sex chromosomes, X5. We also predict that optimal annotation of the newly sequenced platypus genome will be challenging. The analysis of platypus sequence revealed differences in structure and sequence of the DMRT gene cluster. Multispecies comparison was particularly effective for detecting CNGs, revealing several novel potential regulatory regions within DMRT3 and DMRT2 as well as DMRT1. RT-PCR indicated that platypus DMRT1 and DMRT3 are expressed specifically in the adult testis (and not ovary), but DMRT2 has a wider expression profile, as it does for other mammals. The platypus DMRT1 expression pattern, and its location on an X chromosome, suggests an involvement in monotreme sexual development.

Amino Acid Sequence↗

PubMed2002

Cluster analysis of an extensive human breast cancer cell line protein expression map database.

In the current study, the protein expression maps (PEMs) of 26 breast cancer cell lines and three cell lines derived from normal breast or benign disease tissue were visualised by high resolution two-dimensional gel electrophoresis. Analysis of this data was performed with ChiClust and ChiMap, two analytical bioinformatics tools that are described here. These tools are designed to facilitate recognition of specific patterns shared by two or more (a series) PEMs. Both tools use PEMs that were matched by an image analysis program and locally written programs to create a match table that is saved in an object relational database. The ChiClust tool uses clustering and subclustering methods to extract statistically significant protein expression patterns from a large series of PEMs. The ChiMap tool calculates a differential value (either as percentage change or a fold change) and represents these graphically. All such differentials or just those identified using ChiClust can be submitted to ChiMap. These methods are not dependent on any particular commercial image analysis program, and the whole software package gives an integrated procedure for the comparison and analysis of a series of PEMs. The ChiClust tool was used here to order the breast cell lines into groups according to biological characteristics including morphology in vitro and tumour forming ability in vivo. ChiMap was then used to highlight eight major protein feature-changes detected between breast cancer cell lines that either do or do not proliferate in nude mice. Mass spectrometry was used to identify the proteins. The possible role of these proteins in cancer is discussed.

Algorithms↗

PubMed1994

Use of cluster analysis technique for computerized recognition and prognosis of myocardial vulnerability.

Variability of factors exerting influence on arrhythmia origination leads to the appearance of polymodal distribution in sample space. Therefore, for the approximation of feature distribution, distribution mixture is used. To estimate the number of mixture components and to determine its parameters, cluster algorithm is used. The basic task of the algorithm is to identify the accumulation of vectors in the parallelepiped of their distribution. The accumulations of points are determined by testing statistical hypothesis of uniformity. On the basis of accumulations, clusters are formed and the parameters of normal mixtures of classes are estimated. Analysis of error matrix for recognition of mixture, enable to establish the parameters of the decision rule. The above algorithm was applied for recognition and prognosis of vulnerability of reentry and focal source in experiments on the right rabbit's atrium by using the electrophysiological parameters. We studied 30 cases of reentry, 36 cases of focal sources and 165-arrhythmia-free cases. As a result, we established the 7-class normal mixture which enabled a more effective (96.4%) recognition of the vulnerability types and 89.9% prognosis by features: increase in latency (theta), width of the interval of latency distribution, ratio theta/R, where R-refractory period.

Algorithms↗

PubMed2006

Microarray and gene-clustering analysis.

Human mast cells are capable of secreting a plethora of inflammatory mediators and cytokines that may play a pivotal role in innate immune and inflammatory responses. Activation of mast cells by antigen and immunoglobulin E (IgE) results in signaling, gene expression, and expression of inflammatory mediators. Although a variety of techniques have been used to evaluate mast cell biology, recent advances in molecular techniques have provided unprecedented tools to study these cells. The complimentary deoxyribonucleic acid (DNA) oligonucleotide microarray, or DNA-chip technology, allows simultaneous monitoring of gene expression, provides a format for identifying genes as well as changes in their activity on a whole genome scale, and potentially offers a global view of pathophysiologic changes. This chapter reviews the use of DNA-chip technology in studying the expression of genes (transcriptional profiling) in activated human mast cells obtained from cultured cord blood-derived mononuclear cells and comments on the use of bioinformatics on analysis of gene expression. The most powerful applications of transcriptional profiling involve identification of the common patterns of gene expression across many experiments using various gene-clustering analyses. Several techniques have been used for the analysis of gene-expression data including hierarchical clustering and self-organizing maps. In this chapter, a general laboratory protocol for array analysis currently being used in our laboratory and the use of bioinformatics is discussed. Although the focus is on Affymetrix oligonucleotide arrays, the techniques described are generally applicable to expression data generated using other array formats.

Computational Biology↗