L2L: a simple tool for discovering the hidden significance in microarray expression data

Abstract

L2L is a database consisting of lists of differentially expressed genes compiled from published mammalian microarray studies, along with an easy-to-use application for mining the database with the user's own microarray data. As illustrated by re-analysis of a recent study of diabetic nephropathy, L2L identifies novel biological patterns in microarray data, providing insights into the underlying nature of biological processes and disease. L2L is available online at the authors' website [http://depts.washington.edu/l2l/].

Figure 1

L2L and the L2L microarray database. (a) The centerpiece of L2L is the L2L Microarray Database, a collection of published microarray data in the form of lists of genes that are up- or downregulated in some condition. The L2L Microarray Analysis Tool (MAT) is a program that compares those lists with a user's microarray data, and reports statistically significant overlaps. The analysis tool includes a web browser interface, but the L2L application itself can be downloaded and run directly from the command line for batch or customized analyses. Three additional sets of lists, based on the three organizing principles of Gene Ontology, can also be used with the analysis tool. (b) The L2L Microarray Database contains over 350 lists compiled from over 100 selected microarray publications. A wide variety of topics are represented, from chromatin modifications and DNA damage to the immune response and adipocyte differentiation.

Figure 2

L2L uses a simple web-based interface, and generates easy-to-navigate, annotated HTML pages as output. (a) The L2L web interface. (b) The Results summary page displays each list from the database that significantly matched the data, along with links to list annotations and Listmatch pages. (c) An example Listmatch page, which displays all of the probes on a list that match the data, with a variety of annotations and links to Probematch pages. (d) Probematch pages show all of the lists on which a probe is found, with links back to their Listmatch pages. Arrows indicate sample navigation paths between the output pages.

Figure 3

The L2L application sequentially compares each list in the database with the input data, and records the overlap between the two lists of genes. (a) Each list in the database is a list of HUGO symbols. These are first translated to the corresponding microarray probes that represent those genes. Depending on the microarray, some genes on a list are represented by multiple probes and some by none at all. (b) The program finds the intersection between the translated list of probes from the database and the user's list of probes. The results are logged and written to a raw output file. The program then proceeds to the next list in the database. (c) Once all lists in the database have been compared with the user's data, the program creates a set of HTML pages to browse the output.

Figure 4

L2L analysis of gene expression changes in diabetic nephropathy (DN). (a) Three major conclusions of Baelde et al. [36] revisited. L2L finds support for cytoskeletal dysfunction, but no evidence of reduced nucleotide metabolism. Evidence for the central thesis, reduced tissue repair capacity, is mixed. L2L found reduced expression of IGF-binding proteins, suggesting a defect in response to these growth factors. However, L2L also found a correlation between genes repressed by the serum-response and genes downregulated in DN, as well as a correlation between genes upregulated in DN and genes induced by EGF and VEGF - despite reduced expression of VEGF itself in DN kidneys. (b) Three new biological themes in DN found by L2L. 1. Interferon, TNFα, and their associated apoptotic pathways are all downregulated in DN. 2. The hypoxia response is impaired in DN. 3. Pathways associated with adipogenesis and adipocyte function are downregulated in DN. Complete results, along with descriptions and annotations for all lists, can be found on the L2L website [6]. Red or green denote reduced or increased expression, respectively, in DN or in the condition represented by a list.

Figure 5

L2L analysis of gene expression changes in two studies of the ageing human brain. Lists of differentially expressed genes from Lu et al. (ageing_brain) [61] and Blalock et al. (alzheimers_disease and alzheimers_incipient) [62] were compared with all ageing-related lists in the L2L Microarray Database, including each other (all data are available on the L2L website [6]). Numbers represent binomial p values for significance of overlap. Green denotes overlap between lists of genes upregulated with ageing; red denotes overlap between lists of genes downregulated with ageing; black denotes overlap between lists of contrary directions; yellow denotes self-self comparisons.