Web services for transcriptomics

Transcriptomics is part of a family of disciplines focussing on high throughput molecular biology experiments. In the case of transcriptomics, scientists study the expression of genes resulting in transcripts. These transcripts can either perform a biological function themselves or function as messenger molecules containing a copy of the genetic code, which can be used by the ribosomes as templates to synthesise proteins. Over the past decade microarray technology has become the dominant technology for performing high throughput gene expression experiments. A microarray contains short sequences (oligos or probes), which are the reverse complement of fragments of the targets (transcripts or sequences derived thereof). When genes are expressed, their transcripts (or sequences derived thereof) can hybridise to these probes. Many thousand copies of a probe are immobilised in a small region on a support. These regions are called spots and a typical microarray contains thousands or sometimes even more than a million spots. When the transcripts (or sequences derived thereof) are fluorescently labelled and it is known which spots are located where on the support, a fluorescent signal in a certain region represents expression of a certain gene. For interpretation of microarray data it is essential to make sure the oligos are specific for their targets. Hence for proper probe design one needs to know all transcripts that may be expressed and how well they can hybridise with candidate oligos. Therefore oligo design requires: 1. A complete reference genome assembly. 2. Complete annotation of the genome to know which parts may be transcribed. 3. Insight in the amount of natural variation in the genomes of different individuals. 4. Knowledge on how experimental conditions influence the ability of probes to hybridise with certain transcripts. Unfortunately such complete information does not exist, but many microarrays were designed based on incomplete data nevertheless. This can lead to a variety of problems including cross-hybridisation (non-specific binding), erroneously annotated and therefore misleading probes, missing probes and orphan probes. Fortunately the amount of information on genes and their transcripts increases rapidly. Therefore, it is possible to improve the reliability of microarray data analysis by regular updates of the probe annotation using updated databases for genomes and their annotation. Several tools have been developed for this purpose, but these either used simplistic annotation strategies or did not support our species and/ or microarray platforms of interest. Therefore, we developed OligoRAP (Oligo Re- Annotation Pipeline), which is described in chapter 2. OligoRAP was designed to take advantage of amongst others annotation provided by Ensembl, which is the largest genome annotation effort in the world. Thereby OligoRAP supports most of the major animal model organisms including farm animals like chicken and cow. In addition to support for our species and array platforms of interest OligoRAP employs a new annotation strategy combining information from genome and transcript databases in a non-redundant way to get the most complete annotation possible. In chapter 3 we compared annotation generated with 3 oligo annotation pipelines including OligoRAP and investigated the effect on functional analysis of a microarray experiment involving chickens infected with Eimeria bacteria. As an example of functional analysis we investigated if up- or downregulated genes were enriched for Terms from the Gene Ontology (GO). We discovered that small differences in annotation strategy could lead to alarmingly large differences in enriched GO terms. Therefore it is important to know, which annotation strategy works best, but it was not possible to assess this due to the lack of a good reference or benchmark dataset. There are a few limited studies investigating the hybridisation potential of imperfect alignments of oligos with potential targets, but in general such data is scarce. In addition it is difficult to compare these studies due to differences in experimental setup including different hybridisation temperatures and different probe lengths. As result we cannot determine exact thresholds for the alignments of oligos with non-targets to prevent cross-hybridisation, but from these different studies we can get an idea of the range for the thresholds that would be required for optimal target specificity. Note that in these studies experimental conditions were first optimised for an optimal signal to noise ratio for hybridisation of oligos with targets. Then these conditions were used to determine the thresholds for alignments of oligos with non-targets to prevent cross-hybridisation. Chapter 4 describes a parameter sweep using OligoRAP to explore hybridisation potential thresholds from a different perspective. Given the mouse genome thresholds were determined for the largest amount of gene specific probes. Using those thresholds we then determined thresholds for optimal signal to noise ratios. Unfortunately the annotation-based thresholds we found did not fall within the range of experimentally determined thresholds; in fact they were not even close. Hence what was experimentally determined to be optimal for the technology was not in sync with what was determined to be optimal for the mouse genome. Further research will be required to determine whether microarray technology can be modified in such a way that it is better suited for gene expression experiments. The requirement of a priori information on possible targets and the lack of sufficient knowledge on how experimental conditions influence hybridisation potential can be considered the Achiles’ heels of microarray technology. Chapter 5 is a collection of 3 application notes describing other tools that can aid in analysis of transcriptomics data. Firstly, RShell, which is a plugin for the Taverna workbench allowing users to execute statistical computations remotely on R-servers. Secondly, MADMAX services, which provide quality control and normalisation of microarray data for AffyMetrix arrays. Finally, GeneIlluminator, which is a tool to disambiguate gene symbols allowing researchers to specifically retrieve literature for their genes of interest even if the gene symbols for those genes had many synonyms and homonyms. Web services High throughput experiments like those performed in transcriptomics usually require subsequent analysis with many different tools to make biological sense of the data. Installing all these tools on a single, local computer and making them compatible so users can build analysis pipelines can be very cumbersome. Therefore distributed analysis strategies have been explored extensively over the past decades. In a distributed system providers offer remote access to tools and data via the Internet allowing users to create pipelines from modules from all over the globe. Chapter 1 provides an overview of the evolution of web services, which represent the latest breed in technology for creating distributed systems. The major advantage of web services over older technology is that web services are programming language independent, Internet communication protocol independent and operating system independent. Therefore web services are very flexible and most of them are firewall-proof. Web services play a major role in the remaining chapters of this thesis: OligoRAP is a workflow entirely made from web services and the tools described in chapter 5 all provide remote programmatic access via web service interfaces. Although web services can be used to build relatively complex workflows like OligoRAP, a lack of mainly de facto standards and of user-friendly clients has limited the use of web services to bioinformaticians. A semantic web where biologists can easily link web services into complex workflows does n