A Galaxy Implementation of Next-Generation Clustered Heatmaps for Interactive Exploration of Molecular Profiling Data

Clustered heatmaps are the most frequently used graphics for visualization of molecular profiling data in biology. However, they are generally rendered as static, or only modestly interactive, images. We have now used recent advances in web technologies to produce interactive "next-generation" clustered heatmaps (NG-CHM) that enable extreme zooming and navigation without loss of resolution. NG-CHMs also provide link-outs to additional information sources and include other features that facilitate deep exploration of the biology behind the image. Here, we describe an implementation of the NG-CHM system in the Galaxy bioinformatics platform. We illustrate the algorithm and available computational tool using RNA-seq data from The Cancer Genome Atlas program's Kidney Clear Cell Carcinoma project. Cancer Res; 77(21); e23-26. ©2017 AACR.

Abstract 2979: A web portal of ‘next-generation’ clustered heat maps for user-friendly, interactive exploration of patterns in TCGA data

The Cancer Genome Atlas (TCGA) program is generating comprehensive molecular profiles of more than 30 clinical tumor types, the first 12 of which have been incorporated into a “Pan-Cancer12” project. One bioinformatic challenge is statistical analysis of the resulting profiles; a second is the visual detective work necessary to explore individual genes, pathways and patterns in the data. For that type of detective work, we introduced CHMs in the early 1990s for pharmacogenomic analysis (1) and later for integrated visualization of genomic, transcriptomic, proteomic, pharmacological, and functional data (2). As the ubiquitous first-order way of visualizing omic data, CHMs have appeared in many thousands of publications (3-9), including all of the major publications by the TCGA Research Network. However, a major limitation is that they have been static or only modestly interactive graphics. We have now developed “next-generation” clustered heat maps (NG-CHMs), which use a Google-maps-like tiling technology for extreme zooming and navigation without loss of resolution. NG-CHMs provide pathway and gene ontology information, re-coloring on the fly, tools for reproducibility, high-resolution graphics output, a statistical toolbox, and link-outs to public sources of information on genes, proteins, pathways and drugs. The result is a visually rich, dynamic environment for exploration of the masses of data produced by TCGA. The compendium of TCGA Pan-Cancer NG-CHMs currently includes 667 maps as an initial set, but the numbers will soon rise into the thousands as more data types, tumour types and algorithms are incorporated (at web portal http://bioinformatics.mdanderson.org/TCGA/NGCHMPortal/). As an illustrative example, NG-CHMs proved pivotal as a tool for discovering and analyzing molecular target themes common to multiple types of gynecological cancers and themes that distinguish them from each other.

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Supported in part by NCI Grant No. U24CA143883, by a gift from the Mary K. Chapman Foundation, and by a grant from the Michael and Susan Dell Foundation honoring Lorraine Dell.

Note: This abstract was not presented at the meeting.

Citation Format: John N. Weinstein, Rehan Akbani, David W. Kane, James M. Melott, Tod D. Casasent, Rong Yao, Paul L. Roebuck, Gordon B. Mills, Michael C. Ryan, Christopher Wakefield, Bradley M. Broom. A web portal of ‘next-generation’ clustered heat maps for user-friendly, interactive exploration of patterns in TCGA data. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2979. doi:10.1158/1538-7445.AM2015-2979

Abstract 5132: Interactively exploring patterns in TCGA data: a web-based compendium of ‘next-generation’ clustered heat maps

Each of the 5 TCGA marker paper published in Nature to date has included at least one clustered heat map (CHM). We introduced CHMs in the early 1990’s for pharmacogenomic analysis (1) and later for integrated visualization of genomic, transcriptomic, proteomic, pharmacological, and functional data (1). As the ubiquitous first-order way of visualizing omic data, CHMs have appeared in many thousands of publications (3–9), including those from TCGA. We have elsewhere summarized their limitations (10).

One such limitation is that CHMs are generally static images. We therefore initiated the next-generation CHM (NG-CHM) project, using an image-tiling technology similar to that in Google Maps for navigation and extreme drill-down without loss of resolution. Once the CHM has been zoomed sufficiently, labels (e.g., gene, protein, or drug names) appear on the image's axes. Clicking on a label produces a menu of link-outs (e.g., to GeneCards, Google, PubMed). For gene vs. gene maps, each pixel can represent a color-coded Pearson correlation coefficient. Clicking on the pixel pulls up the corresponding data scattergram, bootstrap statistics, literature references, or pathway relationships. Strong usability features include floating windows, flexible search tools, cluster selection tools, customizable re-coloring of the CHM, and high-quality PDF's suitable for publication. NG-CHMs are a major resource for exploratory analysis and visualization in multiple projects of TCGA and other large-scale molecular profiling programs. Explore interactive versions for TCGA breast, colorectal, lung squamous, and glioblastoma data at http://bioinformatics.mdanderson.org/main/TCGA/NGCHM.

Supported in part by NCI Grant No. U24CA143883, by a gift from the Mary K. Chapman Foundation, and by a grant from the Michael and Susan Dell Foundation honoring Lorraine Dell.

Citation Format: John N. Weinstein, David W. Kane, Rehan Akbani, Deepti Dodda, Lam Nguyen, Michael C. Ryan, Chris Wakefield, Bradley M. Broom. Interactively exploring patterns in TCGA data: a web-based compendium of ‘next-generation’ clustered heat maps. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5132. doi:10.1158/1538-7445.AM2013-5132

VennMaster: area-proportional Euler diagrams for functional GO analysis of microarrays

Background

Microarray experiments generate vast amounts of data. The functional context of differentially expressed genes can be assessed by querying the Gene Ontology (GO) database via GoMiner. Directed acyclic graph representations, which are used to depict GO categories enriched with differentially expressed genes, are difficult to interpret and, depending on the particular analysis, may not be well suited for formulating new hypotheses. Additional graphical methods are therefore needed to augment the GO graphical representation.

Results

We present an alternative visualization approach, area-proportional Euler diagrams, showing set relationships with semi-quantitative size information in a single diagram to support biological hypothesis formulation. The cardinalities of sets and intersection sets are represented by area-proportional Euler diagrams and their corresponding graphical (circular or polygonal) intersection areas. Optimally proportional representations are obtained using swarm and evolutionary optimization algorithms.

Conclusion

VennMaster's area-proportional Euler diagrams effectively structure and visualize the results of a GO analysis by indicating to what extent flagged genes are shared by different categories. In addition to reducing the complexity of the output, the visualizations facilitate generation of novel hypotheses from the analysis of seemingly unrelated categories that share differentially expressed genes.

AffyProbeMiner: a web resource for computing or retrieving accurately redefined Affymetrix probe sets

MOTIVATION

Affymetrix microarrays are widely used to measure global expression of mRNA transcripts. That technology is based on the concept of a probe set. Individual probes within a probe set were originally designated by Affymetrix to hybridize with the same unique mRNA transcript. Because of increasing accuracy in knowledge of genomic sequences, however, a substantial number of the manufacturer's original probe groupings and mappings are now known to be inaccurate and must be corrected. Otherwise, analysis and interpretation of an Affymetrix microarray experiment will be in error.

RESULTS

AffyProbeMiner is a computationally efficient platform-independent tool that uses all RefSeq mature RNA protein coding transcripts and validated complete coding sequences in GenBank to (1) regroup the individual probes into consistent probe sets and (2) remap the probe sets to the correct sets of mRNA transcripts. The individual probes are grouped into probe sets that are 'transcript-consistent' in that they hybridize to the same mRNA transcript (or transcripts) and, therefore, measure the same entity (or entities). About 65.6% of the probe sets on the HG-U133A chip were affected by the remapping. Pre-computed regrouped and remapped probe sets for many Affymetrix microarrays are made freely available at the AffyProbeMiner web site. Alternatively, we provide a web service that enables the user to perform the remapping for any type of short-oligo commercial or custom array that has an Affymetrix-format Chip Definition File (CDF). Important features that differentiate AffyProbeMiner from other approaches are flexibility in the handling of splice variants, computational efficiency, extensibility, customizability and user-friendliness of the interface.

AVAILABILITY

The web interface and software (GPL open source license), are publicly-accessible at http://discover.nci.nih.gov/affyprobeminer.

Cancers as wounds that do not heal: differences and similarities between renal regeneration/repair and renal cell carcinoma

Cancers have been described as wounds that do not heal, suggesting that the two share common features. By comparing microarray data from a model of renal regeneration and repair (RRR) with reported gene expression in renal cell carcinoma (RCC), we asked whether those two processes do, in fact, share molecular features and regulatory mechanisms. The majority (77%) of the genes expressed in RRR and RCC were concordantly regulated, whereas only 23% were discordant (i.e., changed in opposite directions). The orchestrated processes of regeneration, involving cell proliferation and immune response, were reflected in the concordant genes. The discordant gene signature revealed processes (e.g., morphogenesis and glycolysis) and pathways (e.g., hypoxia-inducible factor and insulin-like growth factor-I) that reflect the intrinsic pathologic nature of RCC. This is the first study that compares gene expression patterns in RCC and RRR. It does so, in particular, with relation to the hypothesis that RCC resembles the wound healing processes seen in RRR. However, careful attention to the genes that are regulated in the discordant direction provides new insights into the critical differences between renal carcinogenesis and wound healing. The observations reported here provide a conceptual framework for further efforts to understand the biology and to develop more effective diagnostic biomarkers and therapeutic strategies for renal tumors and renal ischemia.

Agile methods in biomedical software development: a multi-site experience report

BACKGROUND

Agile is an iterative approach to software development that relies on strong collaboration and automation to keep pace with dynamic environments. We have successfully used agile development approaches to create and maintain biomedical software, including software for bioinformatics. This paper reports on a qualitative study of our experiences using these methods.

RESULTS

We have found that agile methods are well suited to the exploratory and iterative nature of scientific inquiry. They provide a robust framework for reproducing scientific results and for developing clinical support systems. The agile development approach also provides a model for collaboration between software engineers and researchers. We present our experience using agile methodologies in projects at six different biomedical software development organizations. The organizations include academic, commercial and government development teams, and included both bioinformatics and clinical support applications. We found that agile practices were a match for the needs of our biomedical projects and contributed to the success of our organizations.

CONCLUSION

We found that the agile development approach was a good fit for our organizations, and that these practices should be applicable and valuable to other biomedical software development efforts. Although we found differences in how agile methods were used, we were also able to identify a set of core practices that were common to all of the groups, and that could be a focus for others seeking to adopt these methods.

High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID)

BACKGROUND

We previously developed GoMiner, an application that organizes lists of 'interesting' genes (for example, under-and overexpressed genes from a microarray experiment) for biological interpretation in the context of the Gene Ontology. The original version of GoMiner was oriented toward visualization and interpretation of the results from a single microarray (or other high-throughput experimental platform), using a graphical user interface. Although that version can be used to examine the results from a number of microarrays one at a time, that is a rather tedious task, and original GoMiner includes no apparatus for obtaining a global picture of results from an experiment that consists of multiple microarrays. We wanted to provide a computational resource that automates the analysis of multiple microarrays and then integrates the results across all of them in useful exportable output files and visualizations.

RESULTS

We now introduce a new tool, High-Throughput GoMiner, that has those capabilities and a number of others: It (i) efficiently performs the computationally-intensive task of automated batch processing of an arbitrary number of microarrays, (ii) produces a human-or computer-readable report that rank-orders the multiple microarray results according to the number of significant GO categories, (iii) integrates the multiple microarray results by providing organized, global clustered image map visualizations of the relationships of significant GO categories, (iv) provides a fast form of 'false discovery rate' multiple comparisons calculation, and (v) provides annotations and visualizations for relating transcription factor binding sites to genes and GO categories.

CONCLUSION

High-Throughput GoMiner achieves the desired goal of providing a computational resource that automates the analysis of multiple microarrays and integrates results across all of the microarrays. For illustration, we show an application of this new tool to the interpretation of altered gene expression patterns in Common Variable Immune Deficiency (CVID). High-Throughput GoMiner will be useful in a wide range of applications, including the study of time-courses, evaluation of multiple drug treatments, comparison of multiple gene knock-outs or knock-downs, and screening of large numbers of chemical derivatives generated from a promising lead compound.

Practical applications of usability theory to electronic data collection for clinical trials

Pharmaceutical and device companies are more frequently considering and using electronic data collection (EDC) to collect patient-reported outcomes such as satisfaction and quality of life for clinical trials. The transition from paper-and-pencil data collection to EDC is not without risks. The unique context of clinical trials presents challenges that, if not addressed, can lead to expensive mistakes. The advantages inherent to EDC can easily be cancelled out without careful attention to the characteristics of the clinical setting. This paper provides an overview of EDC issues specific to clinical trials and health care settings. In particular, it evaluates usability issues associated with methods of EDC and suggests strategies to minimize potential problems. Lessons learned from usability testing in the unique setting of the clinical trial can be applied to other projects to decrease costs, enhance the quality of the data, and minimize time to analysis.

Mistaken identifiers: gene name errors can be introduced inadvertently when using Excel in bioinformatics

Background

When processing microarray data sets, we recently noticed that some gene names were being changed inadvertently to non-gene names.

Results

A little detective work traced the problem to default date format conversions and floating-point format conversions in the very useful Excel program package. The date conversions affect at least 30 gene names; the floating-point conversions affect at least 2,000 if Riken identifiers are included. These conversions are irreversible; the original gene names cannot be recovered.

Conclusions

Users of Excel for analyses involving gene names should be aware of this problem, which can cause genes, including medically important ones, to be lost from view and which has contaminated even carefully curated public databases. We provide work-arounds and scripts for circumventing the problem.

Development of gene ontology tool for biological interpretation of genomic and proteomic data

We have designed and developed a Gene Ontology based navigation tool, GoMiner, which organizes lists of interesting genes from a microarray or a protein array experiment for biological interpretation. It provides quantitative and statistical output files and useful visualization (e.g., a tree-like structure) to map the list of genes to its biological functional categories. It also provides links to other resources such as pubmed, locuslink, and biological molecular interaction map and signaling pathway packages.

GoMiner: a resource for biological interpretation of genomic and proteomic data

We have developed GoMiner, a program package that organizes lists of 'interesting' genes (for example, under- and overexpressed genes from a microarray experiment) for biological interpretation in the context of the Gene Ontology. GoMiner provides quantitative and statistical output files and two useful visualizations. The first is a tree-like structure analogous to that in the AmiGO browser and the second is a compact, dynamically interactive 'directed acyclic graph'. Genes displayed in GoMiner are linked to major public bioinformatics resources.

Exercise-induced pulmonary vasoconstriction during combined blockade of nitric oxide synthase and beta adrenergic receptors

We studied the effects of inhibition of nitric oxide (NO) (endothelium-derived relaxation factor) synthase in combination with alpha and beta adrenergic receptor blockade on pulmonary vascular tone during exercise. In paired studies, we exercised sheep on a treadmill at a speed of 4 mph, and measured blood flow and pressures across the pulmonary circulation with and without inhibition of NO synthase (N omega-nitro-L-arginine 20 mg/kg intravenous [i.v.]), alpha receptor blockade (phentolamine 5 mg i.v.), beta receptor blockade (propranolol 1 mg i.v.), and combined alpha and beta receptor blockade. Activation of both types of adrenergic receptors occurs with exercise, and because increased release in NO is hypothesized to occur during exercise, these studies were designed to determine the magnitude of effect and interactions of these competing dilator and constrictor influences. We found that inhibition of NO synthase raised pulmonary vascular resistance (PVR) at rest and that, although a reduction in PVR occurred with exercise from this new baseline, vasoconstriction persisted. Combined beta blockade and NO synthase inhibition unmasked unopposed alpha vasoconstriction; PVR rose at rest and continued to rise with exercise; and mean pulmonary arterial pressures approached very high levels, 43.8 +/- 4.4 cmH2O. Using a distal wedged pulmonary artery catheter technique, most of the vasoconstriction was found to be in vessels upstream from small pulmonary veins. During exercise in sheep there appears to be a high degree of alpha and beta adrenergic-mediated tone in the pulmonary circulation. Endogenous production of NO actively dilates pulmonary vessels at rest and opposes potent alpha-mediated pulmonary vasoconstriction during exercise.

Adrenergic modulation of the pulmonary circulation during strenuous exercise in sheep

In paired experiments, we exercised sheep at a constant rate of 4 mph on a treadmill and measured the hemodynamic effects of alpha receptor blockade (phentolamine 5 mg intravenously), beta receptor blockade (propranolol 1 mg intravenously), and combined alpha and beta receptor blockade. Beta blockade increased pulmonary vascular resistance (PVR) at rest and during steady-state exercise compared with control runs. PVR decreased slightly at rest with alpha blockade, but it was not different during exercise from that of control runs. Combined alpha and beta blockade restored PVR to that of control runs, showing that the vasoconstrictor effect of beta blockade was due to unopposed alpha receptor activation. In all sheep an early rapid decrease in PVR within the first 20 s of the onset of exercise was followed by a smaller, slower change over the next 40 to 240 s. The early decrease in PVR was unaffected by either alpha or beta receptor blockade, suggesting that it was due to recruitment of nonmuscular microvessels. We conclude that alpha and beta receptor activation occurs during exercise but that the net vasoactive effect is neutral. The changes in PVR during normal exercise are a combination of rapid recruitment of microvessels followed by slower vasodilation of resistance vessels.

Clinical footscald and footrot in a New Zealand Romney flock: phenotypic and genetic parameters

Phenotypic and genetic parameters for clinical footscald and footrot were investigated in a pedigree flock of New Zealand Romney sheep inspected during outbreaks over six years. At inspections, each sheep's overall status with regard to footscald and footrot was summarized on a combined severity scale (Rating). Sheep were also categorized in terms of two binomial variables specifying the presence or absence of footscald or footrot (FI) and the presence or absence of footrot only (FR). A trinomial variable specified no infection, infection limited to footscald, or footrot with or without footscald (FSR), all variables being derived from the Rating value. Notwithstanding marked annual variations in prevalence of FI, F1 prevalence increased with age among ewes, and a higher prevalence of FI among male than female lambs was noted. Birth rank, birth date and dam's age had no significant effect on Rating in lambs. Repeatability of ewe Rating over successive annual inspections was low. Heritabilities of Rating, FI, FR and FSR, estimated by half-sib analyses were 0.14, 0.28, 0.17 and 0.25, respectively. Heritability of Rating estimated from dam-offspring regression was 0.12. Production traits did not appear to be genetically associated with liability to footrot. Selection of the top 5% of progenytested sires for breeding could be expected to reduce the prevalence of FI by approximately 45% per generation.

Failure of copper or vitamin D supplements to affect the dental condition of young sheep on two Wairarapa farms

Regular injections of copper or vitamin D had no overall effect on growth rate, fleece weight, or the amount of wear of the central incisor teeth of sheep on two Wairarapa farms over 26 months. The greatest amount of tooth wear occurred during the period when soil ingestion (measured by acid-insoluble residue, titanium or aluminium in the faeces) was also greatest. Various indicators of copper, calcium or nutritional status were measured in the blood of control sheep and those receiving vitamin D or copper. At no sampling time was there a significant difference for any of these between groups on either farm. Pasture samples were analysed regularly for calcium, cobalt, copper, magnesium, manganese, molybdenum, phosphorus, sulphur, zinc and percentage ash. At most times values were, on the basis of existing criteria, considered normal. Although the pasture calcium/phosphorus ratio fell below one on several occasions this did not result in a change in plasma calcium or phosphorus levels. On the basis of criteria established for pen-fed sheep, dietary available copper levels on both farms were considered low for much of the time. However, liver and blood copper values were adequate at alI times.

Mycobacterium asiaticum as a potential pulmonary pathogen for humans. A clinical and bacteriologic review of five cases

Mycobacterium asiaticum was isolated from pulmonary material from 5 persons residing in Queensland, Australia. All patients had repeated positive specimens, but the organism was considered responsible for pulmonary mycobacteriosis in only 2 of them. This is the first report of disease caused by M. asiaticum. Clinical, bacteriologic, and epidemiologic details are presented.

Mycobacterium haemophilum causing lymphadenitis in an otherwise healthy child

Suppurating submandibular lymphadenitis in an otherwise healthy infant was caused by Mycobacterium haemophilum, A fastidious organism which requires media supplemented with ferric ammonium citrate or haemoglobin for its growth. It is recommended that material from superficial lesions and lymph nodes collected for mycobacteriological investigations be cultured on media known to support growth of M. haemophilum.