Department of Computer Engineering
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Item Open Access Microarray data analysis and pathway activity inference in PATIKA(ISCB Org, 2004) Babur, Özgün; Demir, Emek; Ayaz, Aslı; Doğrusöz, Uğur; Sakarya, OnurPathway activity inference attempts to infer differential activity of cellular networks, given a qualitative state - transition model of the network and an expression profile of RNA molecules. We present an efficient algorithm for this problem, implemented as part of microarray data analysis component of PATIKA, a pathway analysis tool.Item Open Access PATIKA: An informatics infrastructure for cellular networks(ISCB Org, 2004) Aksay, Çağrı; Ayaz, Aslı; Babur, Özgün; Bilgin, C.; Çetintaş, Ahmet; Çivril, Ali; Çolak, Recep; Çözen, G.; Demir, Emek; Doğrusöz, Uğur; Erson, Zeynep; Gerdaneri, Ozan; Giral, Erhan; Güleşır, Gürcan; Nişancı, Gürkan; Sakarya, O.; Yıldırım, HilmiThe PATIKA Project aims for an informatics infrastructure to cope with the inherently complex cellular pathway data and provides software tools with sophisticated visualization technology around a central database using an extensive ontology and data integration mechanisms. It also features advanced database querying, microarray data analysis, and automatic layout components.Item Open Access PATIKAweb: a Web service for querying, visualizing and analyzing a graph-based pathway database(ISCB Org, 2005-06) Aksay, Çağrı; Arık, Fatma; Ataer, Esra; Ayaz, Aslı; Babur, Özgün; Belviranlı, Mehmet E.; Çetintaş, Ahmet; Çolak, Recep; Çözen, G.; Demir, Emek; Dilek, Alptuğ; Doğrusöz, Uğur; Giral, Erhan; Kaya, Engin; Küçük, Evren; Tekin, A. S.; Yıldırım, Hilmi; Erson, ZeynepPATIKAweb provides a Web service for retrieving and analyzing biological pathways in PATIKA database, which currently contains data integrated from popular public pathway databases like Reactome. It features a user-friendly interface, dynamic visualization, advanced graph-theoretic queries for extracting biologically important phenomena and exporting facilities to various exchange formats.