HisCoM-PAGE: software for hierarchical structural component models for pathway analysis of gene expression data.

Although there have been several analyses for identifying cancer-associated pathways, based on gene expression data, most of these are based on single pathway analyses, and thus do not consider correlations between pathways. In this paper, we propose a hierarchical structural component model for pathway analysis of gene expression data (HisCoM-PAGE), which accounts for the hierarchical structure of genes and pathways, as well as the correlations among pathways. Specifically, HisCoM-PAGE focuses on the survival phenotype and identifies its associated pathways. Moreover, its application to real biological data analysis of pancreatic cancer data demonstrated that HisCoM-PAGE could successfully identify pathways associated with pancreatic cancer prognosis. Simulation studies comparing the performance of HisCoM-PAGE with other competing methods such as Gene Set Enrichment Analysis (GSEA), Global Test, and Wald-type Test showed HisCoM-PAGE to have the highest power to detect causal pathways in most simulation scenarios.

Recent research has focused on incorporating biological function and pathway information into the analysis of gene expression data, partly as a means of compensating for insufficient experimental replications, low signal to noise, lack of reproducibility and/or multiple testing confounds. A Bayesian approach seems to be ideal for incorporating functional information into gene expression data analysis. In this study, we tested the feasibility of using literature derived gene relationships in a Bayesian model to analyze gene expression data. Prior distributions were constructed based on gene associations derived from the biomedical literature using Latent Semantic Indexing (LSI). The LSI model was built using more than 1 million Medline abstracts corresponding to 22,000 human and mouse genes. A key advantage of LSI is that both explicit and implicit gene relationships can be derived from the literature. Gene neighborhoods were determined using latent Gaussian Markov random fields and logistic transformation of the latent variables. We tested the procedure on a microarray dataset for interferon-stimulated genes in mouse embryonic fibroblasts. By integrating functional information from literature, Bayesian approach identified relevant genes that previously did not meet the 0.05 significance level. In comparison to a standard mixture model, spatial mixture model has more power for identifying direct and indirect interferon regulated genes. The spatial model enhanced the ranks of some genes which are known to be affected by interferon treatment, such as Nmi (NMI N-myc and STAT interactor) and ifi35 (interferon-induced protein 35). It also identified some genes that previously were ignored because of the marginal p-values, such as dpysl2, map2k1, msn, Psck5, and Il6st. Interestingly, these genes appear to be indirectly related to interferon treatment. In summary, we show that our procedure increases statistical power and produces more biologically meaningful gene lists. These results suggest that Bayesian methods which incorporate functional information from the literature may improve analysis of gene expression data.

BackgroundSerial Analysis of Gene Expression (SAGE) is a DNA sequencing-based method for large-scale gene expression profiling that provides an alternative to microarray analysis. Most analyses of SAGE data aimed at identifying co-expressed genes have been accomplished using various versions of clustering approaches that often result in a number of false positives.Principal FindingsHere we explore the use of seriation, a statistical approach for ordering sets of objects based on their similarity, for large-scale expression pattern discovery in SAGE data. For this specific task we implement a seriation heuristic we term ‘progressive construction of contigs’ that constructs local chains of related elements by sequentially rearranging margins of the correlation matrix. We apply the heuristic to the analysis of simulated and experimental SAGE data and compare our results to those obtained with a clustering algorithm developed specifically for SAGE data. We show using simulations that the performance of seriation compares favorably to that of the clustering algorithm on noisy SAGE data.ConclusionsWe explore the use of a seriation approach for visualization-based pattern discovery in SAGE data. Using both simulations and experimental data, we demonstrate that seriation is able to identify groups of co-expressed genes more accurately than a clustering algorithm developed specifically for SAGE data. Our results suggest that seriation is a useful method for the analysis of gene expression data whose applicability should be further pursued.

Background - In the NeoTRIPaPDL1 phase III trial, triple-negative breast cancer (TNBC) patients were randomized to receive nab-paclitaxel/carboplatin for 8 cycles (CT arm) with or without atezolizumab (CT/A arm). We previously reported that the majority of patients (65%) with PD-L1- at baseline converted to PD-L1+ (the majority with IC2/IC3) after the first cycle of treatment in the atezolizumab arm. Here we studied treatment associated changes in the molecular tumour features and immune microenvironment by PD-L1 expression. Methods – A total of 158 (56.4%) of patients enrolled in the NeoTRIPaPDL1 trial (76 and 82 from CT/A and CT arm, respectively) were included in this analysis by satisfying the following criteria: i) availability of a paired core biopsy at baseline and at day 1 of the second treatment cycle (D1C2); ii) evaluation of stromal TILs (sTILs) and staining for PD-L1 (Ventana SP142); iii) successful RNA-seq gene expression profiling. PD-L1 groups were defined as IC0/IC1 (<5% PD-L1low) vs IC2/IC3 (>=5% PD-L1high). Presence of different immune cell populations was quantified by gene expression profile deconvolution using ConsensusTME R package. Cancer hallmark gene set collection and custom signature activation status were estimated in each sample using singscore R package. Differences in score distribution were evaluated by 2-sided t-test. Results At baseline, both sTILs and immune cell signatures were upregulated in PD-L1high compared to PD-L1low tumours (p<0.001). No significant differences were found between the two treatment arms in the PD-L1high subpopulation. In the PD-L1low cases, both sTILs and immune related signatures were slightly downregulated in the CT/A arm (p<0.05), suggesting a modest unbalance among treatment arms with CT arm being slightly more inflamed than CT/A arm.At D1C2, PD-L1high tumours in the CT arm systematically had high sTILs (median=70%, range=30-90%), while PD-L1low tumours receiving CT/A had low sTILs in a significant proportion of cases (median=30%, range=0-90%; p<0.001). Similarly, at D1C2 several gene expression-estimated immune cell populations and immune-related signatures were upregulated in the CT arm compared to CT/A arm in PD-L1high tumours, with the weakest association observed for M2 macrophages (p=0.058). No tumour-related signatures were differentially expressed among the two treatment arms within groups with PD-L1high, suggesting that different treatment. modulate PD-L1 by engaging a different immune mileau instead of modulating tumor related features.Considering PD-L1low groups at D1C2, in the CT arm 21 tumors had >30% sTILs (n=21/69, 30.4%), while in the CT/A arm only 2 had sTILs >30% (2/27, 7.4%) (p<0.001). Analysis of gene expression data identified IFN-related signatures as the most upregulated in the CT compared to CT/A arm in PD-L1low cases at D1C2 (p<0.05). Conclusions Integrated dynamic analysis of PD-L1 expression and gene expression data highlighted significant treatment-specific changes of the immune landscape according to PD-L1 expression, when this biomarker is assessed during treatment. This indicates that the immune milieu associated with PD-L1 status is strongly dependent on the time of assessment in relationship to treatment received. Such observation may explain why in the NeoTRIP trial, baseline PD-L1 but not on-treatment PD-L1 was predictive of pCR in CT/A arm. In addition, our findings could have implications related to the use of PD-L1 as a predictive biomarker in pre-treated patients, especially when assessed early on during treatment. Citation Format: Maurizio Callari, Chiun-Sheng Huang, Daniel Egle, Begoña Bermejo, Claudio Zamagni, Matteo Dugo, Marc Thill, Antonio Anton, Marco Barreca, Stefania Russo, Eva Maria Ciruelos, Richard Greil, Stefania Zambelli, Balázs Gyorffy, Chanel Smart, Olivia Biasi, Pinuccia Valagussa, Giuseppe Viale, Luca Gianni, Giampaolo Bianchini. Immune milieu associated with PD-L1 status in TNBC is dependent on time of biomarker assessment and treatment received: A secondary analysis of the NeoTRIPaPDL1 trial [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P1-04-02.

Analysis of temporal gene expression data poses a significant challenge due to the combination of high dimensionality and low sample size. The purpose of this paper is to present a methodology for classification, modelling, and analysis of short time-series gene expression data using spiking neural networks (SNN) and to uncover temporal expression patterns for knowledge discovery. The classification is based on the NeuCube SNN model. Time-series gene expression data of mouse primary cortical neurons is examined as a case study. The results of the analysis are promising, indicating that SNN methodologies can be effectively used to model and analyse temporal gene expression data with surpassing performance over traditional machine learning algorithms. Additionally, a gene interaction network is constructed from the temporal gene activity modelled using the NeuCube architecture offering a new way of knowledge discovery. Future work will be directed towards using gene interactions networks to help guide pharmacological research for dementia.

Pathway and network approaches are valuable tools in analysis and interpretation of large complex omics data. Even in the field of rare diseases, like Rett syndrome, omics data are available, and the maximum use of such data requires sophisticated tools for comprehensive analysis and visualization of the results. Pathway analysis with differential gene expression data has proven to be extremely successful in identifying affected processes in disease conditions. In this type of analysis, pathways from different databases like WikiPathways and Reactome are used as separate, independent entities. Here, we show for the first time how these pathway models can be used and integrated into one large network using the WikiPathways RDF containing all human WikiPathways and Reactome pathways, to perform network analysis on transcriptomics data. This network was imported into the network analysis tool Cytoscape to perform active submodule analysis. Using a publicly available Rett syndrome gene expression dataset from frontal and temporal cortex, classical enrichment analysis, including pathway and Gene Ontology analysis, revealed mainly immune response, neuron specific and extracellular matrix processes. Our active module analysis provided a valuable extension of the analysis prominently showing the regulatory mechanism of MECP2, especially on DNA maintenance, cell cycle, transcription, and translation. In conclusion, using pathway models for classical enrichment and more advanced network analysis enables a more comprehensive analysis of gene expression data and provides novel results.

BackgroundMicroarrays have become extremely useful for analysing genetic phenomena, but establishing a relation between microarray analysis results (typically a list of genes) and their biological significance is often difficult. Currently, the standard approach is to map a posteriori the results onto gene networks in order to elucidate the functions perturbed at the level of pathways. However, integrating a priori knowledge of the gene networks could help in the statistical analysis of gene expression data and in their biological interpretation.ResultsWe propose a method to integrate a priori the knowledge of a gene network in the analysis of gene expression data. The approach is based on the spectral decomposition of gene expression profiles with respect to the eigenfunctions of the graph, resulting in an attenuation of the high-frequency components of the expression profiles with respect to the topology of the graph. We show how to derive unsupervised and supervised classification algorithms of expression profiles, resulting in classifiers with biological relevance. We illustrate the method with the analysis of a set of expression profiles from irradiated and non-irradiated yeast strains.ConclusionIncluding a priori knowledge of a gene network for the analysis of gene expression data leads to good classification performance and improved interpretability of the results.

Cytoscape is a bioinformatic data analysis and visualization platform that is well-suited to the analysis of gene expression data. To facilitate the analysis of yeast microarray data using Cytoscape, we constructed an interaction network (interactome) using the curated interaction data available from the Saccharomyces Genome Database (www.yeastgenome.org) and the database of yeast transcription factors at YEASTRACT (www.yeastract.com). These data were formatted and imported into Cytoscape using semi-automated methods, including Linux-based scripts, that simplified the process while minimizing the introduction of processing errors. The methods described for the construction of this yeast interactome are generally applicable to the construction of any interactome. Using Cytoscape, we illustrate the use of this interactome through the analysis of expression data from a recent yeast diauxic shift experiment. We also report and briefly describe the complex associations among transcription factors that result in the regulation of thousands of genes through coordinated changes in expression of dozens of transcription factors. These cells are thus able to sensitively regulate cellular metabolism in response to changes in genetic or environmental conditions through relatively small changes in the expression of large numbers of genes, affecting the entire yeast metabolome.

BackgroundThe primary goal of pathway analysis using transcriptome data is to find significantly perturbed pathways. However, pathway analysis is not always successful in identifying pathways that are truly relevant to the context under study. A major reason for this difficulty is that a single gene is involved in multiple pathways. In the KEGG pathway database, there are 146 genes, each of which is involved in more than 20 pathways. Thus activation of even a single gene will result in activation of many pathways. This complex relationship often makes the pathway analysis very difficult. While we need much more powerful pathway analysis methods, a readily available alternative way is to incorporate the literature information.ResultsIn this study, we propose a novel approach for prioritizing pathways by combining results from both pathway analysis tools and literature information. The basic idea is as follows. Whenever there are enough articles that provide evidence on which pathways are relevant to the context, we can be assured that the pathways are indeed related to the context, which is termed as relevance in this paper. However, if there are few or no articles reported, then we should rely on the results from the pathway analysis tools, which is termed as significance in this paper. We realized this concept as an algorithm by introducing Context Score and Impact Score and then combining the two into a single score. Our method ranked truly relevant pathways significantly higher than existing pathway analysis tools in experiments with two data sets.ConclusionsOur novel framework was implemented as ContextTRAP by utilizing two existing tools, TRAP and BEST. ContextTRAP will be a useful tool for the pathway based analysis of gene expression data since the user can specify the context of the biological experiment in a set of keywords. The web version of ContextTRAP is available at http://biohealth.snu.ac.kr/software/contextTRAP.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-016-1335-8) contains supplementary material, which is available to authorized users.

One of the key challenges in the analysis of gene expression data is how to relate the expression level of individual genes to the underlying transcriptional programs and cellular state. Here we describe T-profiler, a tool that uses the t-test to score changes in the average activity of predefined groups of genes. The gene groups are defined based on Gene Ontology categorization, ChIP-chip experiments, upstream matches to a consensus transcription factor binding motif or location on the same chromosome. If desired, an iterative procedure can be used to select a single, optimal representative from sets of overlapping gene groups. T-profiler makes it possible to interpret microarray data in a way that is both intuitive and statistically rigorous, without the need to combine experiments or choose parameters. Currently, gene expression data from Saccharomyces cerevisiae and Candida albicans are supported. Users can upload their microarray data for analysis on the web at .

【In DNA microarray studies, the number of genes far exceeds the number of samples and the gene expression measures are highly correlated. Partial least squares regression (PLSR) is one of the popular methods for dimensional reduction and known to be useful for the classifications of microarray data by several studies. In this study, we suggest a modified version of the partial least squares regression to analyze gene expression data with survival information. The method is designed as a new gene selection method using PLSR with an iterative procedure of imputing censored survival time. Mean square error of prediction criterion is used to determine the dimension of the model. To visualize the data, plot for variables superimposed with samples are used. The method is applied to two microarray data sets, both containing survival time. The results show that the proposed method works well for interpreting gene expression microarray data.】

The widespread applications in microarray technology have produced the vast quantity of publicly available gene expression datasets. However, analysis of gene expression data using biostatistics and machine learning approaches is a challenging task due to (1) high noise; (2) small sample size with high dimensionality; (3) batch effects and (4) low reproducibility of significant biomarkers. These issues reveal the complexity of gene expression data, thus significantly obstructing microarray technology in clinical applications. The integrative analysis offers an opportunity to address these issues and provides a more comprehensive understanding of the biological systems, but current methods have several limitations. This work leverages state of the art machine learning development for multiple gene expression datasets integration, classification and identification of significant biomarkers. We design a novel integrative framework, MVIAm - Multi-View based Integrative Analysis of microarray data for identifying biomarkers. It applies multiple cross-platform normalization methods to aggregate multiple datasets into a multi-view dataset and utilizes a robust learning mechanism Multi-View Self-Paced Learning (MVSPL) for gene selection in cancer classification problems. We demonstrate the capabilities of MVIAm using simulated data and studies of breast cancer and lung cancer, it can be applied flexibly and is an effective tool for facing the four challenges of gene expression data analysis. Our proposed model makes microarray integrative analysis more systematic and expands its range of applications.

Computational analysis methods including machine learning have a significant impact in the fields of genomics and medicine. High-throughput gene expression analysis methods such as microarray technology and RNA sequencing produce enormous amounts of data. Traditionally, statistical methods are used for comparative analysis of gene expression data. However, more complex analysis for classification of sample observations, or discovery of feature genes requires sophisticated computational approaches. In this review, we compile various statistical and computational tools used in analysis of expression microarray data. Even though the methods are discussed in the context of expression microarrays, they can also be applied for the analysis of RNA sequencing and quantitative proteomics datasets. We discuss the types of missing values, and the methods and approaches usually employed in their imputation. We also discuss methods of data normalization, feature selection, and feature extraction. Lastly, methods of classification and class discovery along with their evaluation parameters are described in detail. We believe that this detailed review will help the users to select appropriate methods for preprocessing and analysis of their data based on the expected outcome.

Next-generation sequencing technologies provide a revolutionary tool for generating gene expression data. Starting with a fixed RNA sample, they construct a library of millions of differentially abundant short sequence tags or "reads", which constitute a fundamentally discrete measure of the level of gene expression. A common limitation in experiments using these technologies is the low number or even absence of biological replicates, which complicates the statistical analysis of digital gene expression data. Analysis of this type of data has often been based on modified tests originally devised for analysing microarrays; both these and even de novo methods for the analysis of RNA-seq data are plagued by the common problem of low replication. We propose a novel, non-parametric Bayesian approach for the analysis of digital gene expression data. We begin with a hierarchical model for modelling over-dispersed count data and a blocked Gibbs sampling algorithm for inferring the posterior distribution of model parameters conditional on these counts. The algorithm compensates for the problem of low numbers of biological replicates by clustering together genes with tag counts that are likely sampled from a common distribution and using this augmented sample for estimating the parameters of this distribution. The number of clusters is not decided a priori, but it is inferred along with the remaining model parameters. We demonstrate the ability of this approach to model biological data with high fidelity by applying the algorithm on a public dataset obtained from cancerous and non-cancerous neural tissues.

The aim of this study was to identify key genes related to invasive ductal carcinoma (IDC) of the breast by analyzing gene expression data with bioinformatic tools. Microarray data set GSE31138 was downloaded from Gene Expression Omnibus, including 3 breast cancer tissue samples and 3 normal controls. Differentially expressed genes (DEGs) between breast cancer and normal control were screened out (FDR < 0.05 and |logFC| > 2). Coexpression between genes was examined with String, and a network was then constructed. Relevant pathways and diseases were retrieved with KOBAS. A total of 56 DEGs were obtained in the IDC of the breast compared with normal controls. A gene coexpression network including 27 pairs of genes was constructed and all the genes in the network were upregulated. Further study indicated that most of the genes in the coexpression network were enriched in ECM-receptor interaction (COL4A2, FN1, and HMMR) and nucleotide excision repair (CETN2 and PCNA) pathways, and that the most significantly related disease was autoimmune lymphoproliferative syndromes. A number of DEGs were acquired through comparative analysis of gene expression data. These findings are beneficial in promoting the understanding of the molecular mechanisms in breast cancer. More importantly, some key genes were revealed via gene coexpression network analysis, which could be potential biomarkers for IDC of the breast.