Cluster analysis of serum proteins in malignant cutaneous melanoma: search for disease markers

Ragazzi, Eugenio; Vogliardi, Susanna; Allegri, Graziella; Costa, Carlo Virgilio Luigi; Lise, Mario; Róssi, Carlo; Seraglia, Roberta; Traldi, Pietro

doi:10.1002/rcm.1080

Cited by 12 publications

(12 citation statements)

References 66 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Data classification consists in placing samples into more or less homogeneous groups, in order to reveal any relationship among groups. Cluster analysis has been often used in the study of gene expression analysis7; clustering can be useful also for the study of metabolite pattern in pathological conditions 8–1112; standard hierarchical agglomerative clustering techniques were applied using average linkage or the Ward method.…”

Section: Methodsmentioning

confidence: 99%

Low molecular weight proteins in urines from healthy subjects as well as diabetic, nephropathic and diabetic‐nephropathic patients: a MALDI study

Lapolla

Seraglia²,

Molin

et al. 2009

J. Mass Spectrom.

View full text Add to dashboard Cite

Urine samples from healthy subjects as well as diabetic, nephropathic and diabetic-nephropathic patients were analyzed by matrix assisted laser desorption/ionization (MALDI) mass spectrometry in order to establish evidence of some possible differences in the peptide profile related to the pathological states. Multivariate analysis suggested the possibility of a distinction among the considered groups of patients. Some differences have been found, in particular, in the relative abundances of three ions at m/z 1912, 1219 and 2049. For these reasons, further investigation was carried out by MALDI/TOF/TOF to determine the sequence of these peptides and, consequently, to individuate their possible origin. By this approach, the peptide at m/z 1912 was found to originate from uromodulin, and its lower expression in the case of nephropathy can be well related to the pathological condition. Ions at m/z 2049 and 1219 originate from the collagen alpha-1(I) chain precursor and from the collagen alpha-5 (IV) chain precursor, respectively, and, also in this case, their different expressions can be related to the pathologies under investigation. The obtained data seem to indicate that urine is an interesting biological fluid to investigate on the peptide profile and to obtain, consequently, information on the dismetabolism activated by specific pathologies.

show abstract

Section: Methodsmentioning

confidence: 99%

Low molecular weight proteins in urines from healthy subjects as well as diabetic, nephropathic and diabetic‐nephropathic patients: a MALDI study

Lapolla

Seraglia²,

Molin

et al. 2009

J. Mass Spectrom.

View full text Add to dashboard Cite

show abstract

“…CA, used to study gene expression, 20 has been recently employed in the specific gene expression profiling of patients with rectal cancer 16 ; clustering can also be useful for the study of metabolite patterns in pathological conditions. 21 AMADA software 22 or Eisen's laboratory software (Cluster and TreeView, http://rana.lbl.gov/EisenSoftware.htm) 20 were used to obtain the hierarchical agglomerative clustering of data. Average-linkage clustering was the linkage rule; the distance was measured using Euclidean distance, Spearman or Pearson correlations.…”

Section: Multivariate Analysis Cluster Analysismentioning

confidence: 99%

Multivariate analysis approach to the plasma protein profile of patients with advanced colorectal cancer

Ragazzi

Pucciarelli

Seraglia³

et al. 2006

J. Mass Spectrom.

View full text Add to dashboard Cite

The aim of the present study was to identify the pattern of plasma protein species of interest as markers of colorectal cancer (CRC). Using matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS), the plasma protein profile was determined in nine stage IV CRC patients (study group) and nine clean-colon healthy subjects (control group). Multivariate analysis methods were employed to identify distinctive disease patterns at protein spectrum. In the study and control groups, cluster analysis (CA) on the complete MALDI-MS spectra plasma protein profile showed a distinction between CRC patients and healthy subjects, thus allowing the identification of the most discriminating ionic species. Principal component analysis (PCA) and linear discriminant analysis (LDA) yielded similar grouping results. LDA with leave-one-out cross validation achieved a correct classification rate of 89% in both the patients and the healthy subjects.

show abstract

“…The authors stated that they identified patterns of high diagnostic value; however, prospective blinded validation of these findings is missing. Instead, further studies adopted this initial approach [42,43], which is not in accordance with accepted recommendations [44].…”

Section: Clinical Proteomicsmentioning

confidence: 89%

Proteomics for biomarker discovery in malignant melanoma

Findeisen

Peccerella

Neumaier

et al. 2008

Expert Review of Dermatology

View full text Add to dashboard Cite

Cluster analysis of serum proteins in malignant cutaneous melanoma: search for disease markers

Cited by 12 publications

References 66 publications

Low molecular weight proteins in urines from healthy subjects as well as diabetic, nephropathic and diabetic‐nephropathic patients: a MALDI study

Low molecular weight proteins in urines from healthy subjects as well as diabetic, nephropathic and diabetic‐nephropathic patients: a MALDI study

Multivariate analysis approach to the plasma protein profile of patients with advanced colorectal cancer

Proteomics for biomarker discovery in malignant melanoma

Contact Info

Product

Resources

About