CrossQuery: A Web Tool for Easy Associative Querying of Transcriptome Data

Abstract

Enormous amounts of data are being generated by modern methods such as transcriptome or exome sequencing and microarray profiling. Primary analyses such as quality control, normalization, statistics and mapping are highly complex and need to be performed by specialists. Thereafter, results are handed back to biomedical researchers, who are then confronted with complicated data lists. For rather simple tasks like data filtering, sorting and cross-association there is a need for new tools which can be used by non-specialists. Here, we describe CrossQuery, a web tool that enables straight forward, simple syntax queries to be executed on transcriptome sequencing and microarray datasets. We provide deep-sequencing data sets of stem cell lines derived from the model fish Medaka and microarray data of human endothelial cells. In the example datasets provided, mRNA expression levels, gene, transcript and sample identification numbers, GO-terms and gene descriptions can be freely correlated, filtered and sorted. Queries can be saved for later reuse and results can be exported to standard formats that allow copy-and-paste to all widespread data visualization tools such as Microsoft Excel. CrossQuery enables researchers to quickly and freely work with transcriptome and microarray data sets requiring only minimal computer skills. Furthermore, CrossQuery allows growing association of multiple datasets as long as at least one common point of correlated information, such as transcript identification numbers or GO-terms, is shared between samples. For advanced users, the object-oriented plug-in and event-driven code design of both server-side and client-side scripts allow easy addition of new features, data sources and data types.

Xmrk‐induced melanoma progression is affected by Sdf1 signals through Cxcr7

“…One potential action of β‐arrestin 2 is to restrict Cxcr7 intracellular trafficking (Mahabaleshwar et al., ) and thereby to influence Sdf1 gradient response of melanoma cells. Transcriptome analyses of Xmrk‐induced tumors further support this hypothesis, as β‐arrestin 2 expression is increased in invasive and eye tumors compared to exophytic XE tumors or hyperpigmented skin (Schartl et al., ; Wagner et al., ). Further detailed studies will have to show how MAP kinase signaling in the Xmrk‐induced melanoma is altered in cxcr7 mutants, for example via RNA sequencing analyses, and how melanoma progression in vivo is altered after pigment cell‐specific β‐arrestin2 knockdown.…”

Conserved Expression Signatures between Medaka and Human Pigment Cell Tumors

“…For easy and efficient comparison of transcriptomes we employed CrossQuery [45] . It uses a MySQL database backend with prejoined data-tables, which allows very fast query-returns.…”