The gene family of subtilisin-like serine proteases (subtilases) in Arabidopsis thaliana comprises 56 members, divided into six distinct subfamilies. Whereas the members of five subfamilies are similar to pyrolysins, two genes share stronger similarity to animal kexins. Mutant screens confirmed 144 T-DNA insertion lines with knockouts for 55 out of the 56 subtilases. Apart from SDD1, none of the confirmed homozygous mutants revealed any obvious visible phenotypic alteration during growth under standard conditions. Apart from this specific case, forward genetics gave us no hints about the function of the individual 54 non-characterized subtilase genes. Therefore, the main objective of our work was to overcome the shortcomings of the forward genetic approach and to infer alternative experimental approaches by using an integrative bioinformatics and biological approach. Computational analyses based on transcriptional co-expression and co-response pattern revealed at least two expression networks, suggesting that functional redundancy may exist among subtilases with limited similarity. Furthermore, two hubs were identified, which may be involved in signalling or may represent higher-order regulatory factors involved in responses to environmental cues. A particular enrichment of co-regulated genes with metabolic functions was observed for four subtilases possibly representing late responsive elements of environmental stress. The kexin homologs show stronger associations with genes of transcriptional regulation context. Based on the analyses presented here and in accordance with previously characterized subtilases, we propose three main functions of subtilases: involvement in (i) control of development, (ii) protein turnover, and (iii) action as downstream components of signalling cascades. Supplemental material is available in the Plant Subtilase Database (PSDB) (http://csbdb.mpimp-golm.mpg.de/psdb.html), as well as from the CSB.DB (http://csbdb.mpimp-golm.mpg.de).

Analyzing data to find trends, correlations, and stable patterns is an important task in many industrial applications. This paper proposes a new technique based on parallel coordinate visualization. Previous work on parallel coordinate methods has shown that they are effective only when variables that are correlated and/or show similar patterns are displayed adjacently. Although current parallel coordinate tools allow the user to manually rearrange the order of variables, this process is very time-consuming when the number of variables is large. Automated assistance is required. This paper introduces an edit-distance based technique to rearrange variables so that interesting change patterns can be easily detected visually. The Visual Miner (V-Miner) software includes both automated methods for visualizing common patterns and a query tool that enables the user to describe specific target patterns to be mined or displayed by the system. In addition, the system can filter data according to rules sets imported from other data mining tools. This feature was found very helpful in practice, because it enables decision makers to visually identify interesting rules and data segments for further analysis or data mining. This paper begins with an introduction to the proposed techniques and the V-Miner system. Next, a case study illustrates how V-Miner has been used at Motorola to guide product design and test decisions.

Analyzing data to find trends, correlations, and stable patterns is an important problem for many industrial applications. We propose a new technique based on parallel coordinates visualization. Previous work on parallel coordinates method has shown that they are effective only when variables that are correlated and/or show similar patterns are displayed adjacently. Although current parallel coordinates tools allow the user to manually rearrange the order of variables, this process is very time-consuming when the number of variables is large. Automated assistance is needed. We propose an edit-distance based technique to rearrange variables so that interesting patterns can be easily detected. Our system, V-Miner, includes both automated methods for visualizing common patterns and a query tool that enables the user to describe specific target patterns to be mined/displayed by the system. Following an overview of the system, a case study is presented to explain how Motorola engineers have used V-Miner to identify significant patterns in their product test and design data.