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WebGIVI: a web-based gene enrichment analysis and visualization tool
BMC Bioinformatics volume 18, Article number: 237 (2017)
A major challenge of high throughput transcriptome studies is presenting the data to researchers in an interpretable format. In many cases, the outputs of such studies are gene lists which are then examined for enriched biological concepts. One approach to help the researcher interpret large gene datasets is to associate genes and informative terms (iTerm) that are obtained from the biomedical literature using the eGIFT text-mining system. However, examining large lists of iTerm and gene pairs is a daunting task.
WebGIVI provides an interactive and integrated network graph of gene and iTerms that allows filtering, sorting, and grouping, which can aid biologists in developing hypothesis based on the input gene lists. In addition, WebGIVI can visualize hundreds of nodes and generate a high-resolution image that is important for most of research publications. The source code can be freely downloaded at https://github.com/sunliang3361/WebGIVI. The WebGIVI tutorial is available at http://raven.anr.udel.edu/webgivi/tutorial.php.
High-throughput technologies provide biologists with large lists of genes or proteins when they compare expression data between two biological states (e.g., normal tissue vs. cancer tissue). Grouping enriched genes to known biological processes and pathways is a common strategy for understanding the biology that underlies the differences between the two states. Approaches include GO enrichment analysis such as DAVID [1, 2], GOEAST  and Gorilla , and pathway analysis such as KEGG  and Reactome .
eGIFT  uses a text-mining method to identify informative terms (iTerms) for individual genes. iTerms are not limited to gene ontology (GO) terms; they also capture more detailed biological knowledge. Consequently, eGIFT provides a finer grained interpretation of gene lists than GO analysis. The current gene analysis results of eGIFT provide users with a list of ranked iTerms and their associated genes in a tabular format. A graphic representation of these gene and iTerm relations would allow biologists to better interpret their input gene lists or gene-iTerm pair lists. This often captures the biological concept enriched in the input data.
Interactive WebGIVI provides an integrated graph to help users generate biological hypotheses. A database of rate-limiting genes, identified by text mining and manually verified, was also integrated into WebGIVI. All genes encoding rate-limiting products are colored in the visualization. Expression data that is uploaded to WebGIVI can also be color-coded according to expression levels in two different biological states. These features are accomplished by using PHP, Cytoscape.js and D3.js to generate a powerful and interactive web based visualization tool that implements gene enrichment analysis and gene and iTerms visualization.
The flow chart of the data processing is depicted in Fig. 1. Currently, WebGIVI accepts multiple input data formats including: NCBI Entrez gene ID, UniProt , or Ensemble  Gene IDs. Prior to accessing WebGIVI, the user will have identified genes of interest in their biological system. The WebGIVI input list is used to retrieve the gene symbols and iTerms through an eGIFT API. In the retrieved list of gene symbol-iTerm pairs, the first column contains the gene symbols, and the second column contains the gene-associated iTerms. Interactive WebGIVI also supports uploading and visualization of any two-column tab separated data. For instance, gene symbols and related pathways data can be visualized.
WebGIVI has three major functions:
Visualization. Interactive table visualization includes sorting and deleting functions that help users reduce the graph to only iTerms and genes of interest. GUI functions in the Concept Map visualization include switching, filtering, sorting, searching, grouping and saving the data in tab delimited text files or as high-resolution images.
Integration of Rate-limiting and Expression Data. Rate limiting gene products determine the flow rate of metabolites or signal through pathways. We have identified 150 rate limiting gene products via text-mining of primary literature and biochemistry textbooks. This list was manually verified (CJS), and integrated into WebGIVI.
When a user enters an expression data list, genes that encode a rate limiting gene product are colored when visualizing gene:iTerm pair in the concept map. If such genes are differentially regulated they are likely have a significant impact on the overall rate of metabolite or signal flow through their respective pathways. Furthermore, to emphasize certain features of their data, users can upload expression files that highlight nodes that they consider informative.
Link-out Functions. Nodes and edges provide link outs to gene specific, iTerms or gene:iTerm pairs via the NCBI, UniPROT, or eGIFT database. For example, gene-iTerm pairs link to eGIFT sentence web page, which contain sentences with the gene and iTerm highlighted in the text.
Results and discussion
Data filtering functions
Sorting Functions: eGIFT uses a precomputed text-mining database that has extracted all gene associated informative terms (iTerm) from PubMed abstracts. After submitting a gene list to WebGIVI, a table is returned to the user containing the iTerms associated with the input genes. By hovering over an iTerm, the user can see the genes associated with that iTerm. The default list is sorted based on the Fisher’s exact test p-value, but the user can choose to sort based on alphabetical order, the gene ontology group (process, function, compartment or unclassified) to which the iTerm has been classified or the frequency of appearance of each iTerm.
Editing Functions: Not all iTerms are informative in all use cases, but could be important to others. For example, ‘in situ hybridization’ is an irrelevant iTerm to our use case scenario but will be interesting to researchers who might want to apply this experimental method to their own work. However, some iTerms are highly likely to be non-informative. To remove such iTerms a “blacklist” has been developed that includes terms such as “some cell” or “10 fold” that are typically non-informative to the general WebGIVI user. Since the developers of WebGIVI cannot be certain that a given iTerm is irrelevant to all users, the returned iTerm list includes the blacklisted terms; a checkbox is provided that allows the user to hide any terms that are included in the blacklist. It is also beneficial to the user to also be able to filter out irrelevant iTerms in the context of their study, and only save iTerms of direct relevance. Once data is submitted on WebGIVI’s homepage, the returned list will allow the user to delete iTerms from the results table using deleting functions. If the user prefers, they can choose not to prefilter but visualize data in Concept Map or Cytoscape directly.
A biological use case scenario
We used the Sun et al. white-leghorn hepatocellular (LMH) cell heat stress dataset , which is a RNA-Seq study of LMH cells under heat stress. This study identified a total of 235 up-regulated and 578 down-regulated genes. Figure 2 shows a completed WebGIVI submission page with a portion of the regulated genes from the LMH study (Additional file 1). In this case we used Entrez gene identification numbers. Following submission, an iTerm list (Fig. 3) is returned that can be sorted alphabetically, by frequency, Gene Ontology categories, or by p-value as determined by the Fisher’s exact test. In this case the list is sorted by p-value. Hovering over an iTerm will show the corresponding p-value, along with the genes from the list associated with that iTerm. One can choose to display iTerms that have been blacklisted by checking the “Include blacklisted items”. You can also select irrelevant iTerms by right clicking and delete them using the remove options. Users can view the output in either Cytoscape (Fig. 4) or as a Concept Map (Fig. 5) by selecting the appropriate buttons. The default mode in Cytoscape generates a force graph (Fig. 4a) and clicking on an edge connecting a gene product to an iTerm pops up a window that allows the user to connect to either NCBI or eGIFT (Fig. 4b). Additional view modes include tree or circle that are accessible by the Layout button.
While Cytoscape can be useful for small graphs, the Concept map view is generally easier to use for larger input data sets. In the default view, gene symbols are displayed in a column at the center of the view, while iTerms are displayed as a wheel around the gene symbols (Fig. 5). If necessary, additional layers are automatically added to display more gene:iTerm relations. Several attributes are visible in the Concept Map view. In this case we have uploaded a file indicating how the gene was regulated by heat stress using the Load Expression File button. Genes highlighted in yellow are enriched under heat stress while those in green are enriched in the control (thermoneutral) samples. In addition, genes encoding rate limiting gene products are indicated by a blue rectangle added to the symbol.
In the concept map view users can right click to select either genes or iTerms. Selecting one will create a gene:iTerm edge (Fig. 6) then clicking on the Subset Data button will create a new concept map with just the selected gene and iTerms (Fig. 7). This is useful to allow an investigator to link genes with similar iTerms for subsequent investigation. At any point, right clicking on an active edge will open a window that can be used to connect to PubMed, UniProt or eGIFT (Fig. 8). Linking out to NCBI database will search that database with the gene and iTerm, and retrieve links to abstracts that contain those two search terms. For example when searching for a gene:iTerm pair such as HSP90AA1 and the iTerm “chaperone” the search will be in the syntax “HSP90AA1 AND chaperone” and the results will include all abstracts that include both the HSP90AA1 and chaperone. Linking to UniProt will access a search page allowing the user to view the UniProt entry for the gene product. Linking to eGIFT web pages provides users with the sentences extracted from the literature that contain the gene and iTerm pair (Fig. 9). This feature of WebGIVI greatly facilitates the user’s understanding of the gene product’s function. In addition, the PMID under a sentence links to the PubMed abstract pages from which the sentence was extracted. This further aids in placing the gene product in biological context. The ability to provide users with these sentences is a unique facet of WebGIVI functionality.
Interactive WebGIVI also provides a way to save the current view: users can export all data on the Concept Map as a two-column tab separated file, which can be resubmitted in WebGIVI to obtain the same graph. This feature allows a user to readily share the data with collaborators. Users can also export the graph as a scalable vector graphics (SVG) format, which can be transformed to high resolution image types via readily accessible image conversion web sites.
Comparison of WebGIVI, DAVID and AmiGO2 analysis
Incorporating the text-mining tool, WebGIVI, into the analysis of high-throughput transcriptome experiments complements Functional Annotation clustering provided by DAVID and GO analysis provided by AmiGO2 . DAVID is an online knowledgebase that can output a list of enriched biological concepts from an input list of gene identifiers. The site makes use of multiple resources including the Gene Ontology, the KEGG pathway database, Interpro , along with several others. Amigo2 is a product of the Gene Ontology consortium and allows users to submit gene lists and identify enriched GO terms. We chose to compare WebGIVI with DAVID and Amigo2 because these resources are easy to use and have been widely adopted by the scientific community.
Heat stress has been implicated in affecting cell cycle regulatory processes including DNA synthesis, DNA repair, cell cycle checkpoints, cell proliferation, and spindle formation. The objective was to compare the ability of DAVID, AmiGO2 and WebGIVI to identify genes affecting cell cycle regulation that are up-regulated by heat stress in the liver of chickens (Jastrebski et al. manuscript submitted). Genes whose expression was increased by heat stress were identified and submitted to Amigo2, DAVID, and WebGIVI for comparative analysis. Genes recognized by each analytical method as associated with the concept of cell cycle regulation (including cell cycle, DNA replication, DNA repair, checkpoint) were considered in this comparison of methods (see Additional file 2 for complete list of identified genes).
In combination DAVID, AMIGO2 and WebGIVI identified a total of 214 genes affecting cell cycle regulation as enriched by heat stress in the liver. WebGIVI identified the largest percentage of total genes (80%) and uniquely identified the greatest percentage of genes (30%) not recognized by either DAVID or AMIGO2 (Table 1). However, WebGIVI missed 7 genes that were captured by either DAVID or Amigo2 (Fig. 10). Taken together, this analysis indicates that multiple approaches are best for categorizing the biology embodied in gene lists, and that WebGIVI provides an important contribution to these analyses.
WebGIVI can be used to visualize not only eGIFT data, but also any two-column relationship data. For example, microRNA and target genes, kinase and substrate pairs, and protein-protein interactions could all be visualized with WebGIVI. Our tool can also be used as an extension for other tools. Compared to other visualization tools, our web-based gene iTerm visualization tool is highly customizable. Users can easily upload their own data and edit their data in the graph. No pre-installed or third party software such as Java Runtime Environment is required to visualize users’ data. While we are developing a WebGIVI blacklist of iTerms we believe are not informative, users still need to examine all iTerms and remove ones they find uninformative manually. This inability of WebGIVI to learn as user’s preferences and automatically remove iTerm provides room for future improvement. Potentially, machine-learning techniques could be applied to remove such iTerms. Future work will also integrate more bioinformatics databases such as protein kinase database and transcriptional factor database to enable the user to discover more interesting biological relationships and improve the usability of WebGIVI.
Interactive WebGIVI tool provides an integrated visualization and gene enrichment analysis tool. It helps biologists to visualize genes and iTerms online, makes sense of their biological data, and is useful to generating biological hypotheses from high throughput data.
Availability and requirements
Project name: WebGIVI: Web-based Gene and Iterm Visualization Tool
Project home page: http://raven.anr.udel.edu/webgivi/
Source code: https://github.com/sunliang3361/WebGIVI
Operation system(s): Web based, Platform independent
Other requirements: Modern Browser
License: BSD License
Any restrictions to use by non-academics: None.
White-leghorn hepatocellular cell
Scalable vector graphics
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LS thanks Allen Hubbard for his help in editing this manuscript and Andrew Bancroft for his help in creating the tutorial video.
This work was supported by NSF grants NSF DBI-1147029 to CJS and NSF DBI-1260795 to JC.
LS, CJS, JC and YZ designed the software; LS, YZ and AM wrote the codes; COT, AM and KVS provided eGIFT data. JR helped design the Cytoscape network map. All authors helped revise the paper and implement the software. LS and CJS wrote the paper. All authors have read and approve of the final version of the manuscript.
The authors declare that they have no competing interests.
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NCBI Gene Entrez ID List for the Case Scenario. This file contains NCBI gene Entrez ID list. The first column is Entrez ID, and the second column is the gene symbol. (XLSX 9 kb)
NCBI Entrez IDs for Comparison of WebGIVI, DAVID and AmiGO2. This file contains NCBI gene Entrez ID list which is identifed by WebGIVI, DAVID and AmiGO2 to be associated with the concept of cell cycle regulation. (TXT 1 kb)
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Sun, L., Zhu, Y., Mahmood, A.S.M.A. et al. WebGIVI: a web-based gene enrichment analysis and visualization tool. BMC Bioinformatics 18, 237 (2017). https://doi.org/10.1186/s12859-017-1664-2
- Gene iTerm
- Gene enrichment
- Web development