title: Classification of protein profiles using fuzzy clustering techniques: an application in early diagnosis of oral, cervical and ovarian cancer.
abstract: Present study has brought out a comparison of PCA and fuzzy clustering techniques in classifying protein profiles (chromatogram) of homogenates of different tissue origins: Ovarian, Cervix, Oral cancers, which were acquired using HPLC-LIF (High Performance Liquid Chromatography-Laser Induced Fluorescence) method developed in our laboratory. Study includes 11 chromatogram spectra each from oral, cervical, ovarian cancers as well as healthy volunteers. Generally multivariate analysis like PCA demands clear data that is devoid of day-to-day variation, artifacts due to experimental strategies, inherent uncertainty in pumping procedure which is very common activities during HPLC-LIF experiment. Under these circumstances we demonstrate how fuzzy clustering algorithm like Gath Geva followed by Sammon mapping outperform PCA mapping in classifying various cancers from healthy spectra with classification rate up to 95 % from 60%. Methods are validated using various clustering indexes and shows promising improvement in developing optical pathology like HPLC-LIF for early detection of various cancers in all uncertain conditions with high sensitivity and specificity.
authors.affiliation: University of Copenhagen and Nordic Bioscience Imaging A/S, Herlev Hovedgade 203, 2730, Denmark. gp@nordicbioscience.com
authors.forename: Gopal
authors.initials: G
authors.lastname: Karemore
authors.forename: Jhinuk B
authors.initials: JB
authors.lastname: Mullick
authors.forename: R
authors.initials: R
authors.lastname: Sujatha
authors.forename: Mads
authors.initials: M
authors.lastname: Nielsen
authors.forename: C
authors.initials: C
authors.lastname: Santhosh
mesh_terms: D000328:Adult; D000465:Algorithms; D002851:Chromatography, High Pressure Liquid; D005260:Female; D006801:Humans; D008875:Middle Aged; D009062:Mouth Neoplasms / Q000175:diagnosis*; D010051:Ovarian Neoplasms / Q000175:diagnosis*; D025341:Principal Component Analysis; D011506:Proteins / Q000032:analysis; D013050:Spectrometry, Fluorescence; D002583:Uterine Cervical Neoplasms / Q000175:diagnosis*
chemical_list: D011506:Proteins