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PubMed2002

Renal transcriptomes: segmental analysis of differential expression.

BACKGROUND/AIMS: Progress accomplished by complete genomes and cDNA-sequencing projects calls for methods that fully use these resources to study gene expression patterns in characterized cell populations. However, since the number of functional genes cannot be readily inferred from the genomic sequence, it is highly desirable to make use of methods enabling to study both known and unknown genes. METHODS: The method of serial analysis of gene expression provides short diagnostic cDNA tags without bias towards known genes. In addition, the frequency of each tag in the library conveys quantitative information on gene expression. A microassay was set-up to perform serial analysis of gene expression in minute samples such as those obtained by microdissecting nephron segments. RESULTS: Studies carried out in the thick ascending limb of Henle's loop and the collecting duct of the mouse kidney provided expression data for several thousand genes. Known markers were found appropriately enriched, and several of the thick ascending limb or collecting duct specific transcripts had no database match. CONCLUSIONS: The microassay for serial analysis of gene expression makes possible large-scale quantitative measurements of mRNA levels in nephron segments. The comprehensive picture generated by analyzing both known and unknown transcripts in defined cell populations should help to discover genes with dedicated functions.

Animals↗

PubMed1999

The genexpress IMAGE knowledge base of the human muscle transcriptome: a resource of structural, functional, and positional candidate genes for muscle physiology and pathologies.

Sequence, gene mapping, and expression data corresponding to 910 genes transcribed in human skeletal muscle have been integrated to form the muscle module of the Genexpress IMAGE Knowledge Base. Based on cDNA array hybridization, a set of 14 transcripts preferentially or specifically expressed in muscle have been selected and characterized in more detail: Their pattern of expression was confirmed by Northern blot analysis; their structure was further characterized by full-insert cDNA sequencing and cDNA extension; the map location of the corresponding genes was refined by radiation hybrid mapping. Five of the 14 selected genes appear as interesting positional and functional candidate genes to study in relation with muscle physiology and/or specific orphan muscular pathologies. One example is discussed in more detail. The expression profiling data and the associated Genexpress Index2 entries for the 910 genes and the detailed characterization of the 14 selected transcripts are available from a dedicated Web server at. The database has been organized to provide the users with a working space where they can find curated, annotated, integrated data for their genes of interest. Different navigation routes to exploit the resource are discussed.

Base Sequence↗

PubMed2025

Genomic and Immune Landscape of Pancreatic Ductal Adenocarcinoma Associated with Germline Pathogenic Variants in ATM.

PURPOSE: Germline pathogenic variants (PV) in ATM increase the risk of pancreatic ductal adenocarcinoma (PDAC), but the underlying tumor biology of PDAC associated with germline PV in ATM has not been adequately explored. EXPERIMENTAL DESIGN: Whole-genome, whole-exome, and RNA sequencing were performed on PDAC tumors from 25 germline ATM PV carriers diagnosed at Mayo Clinic between 2007 and 2017. Somatic and copy-number alterations, mutational signatures, transcriptomic subtypes, and the immune landscape were evaluated. RESULTS: High-quality whole-exome and whole-genome sequencing were obtained from 21 and 15 tumors, respectively. Biallelic inactivation of ATM was observed in 87%, KRAS PV in 90%, CDKN2A homozygous loss in 60%, and TP53 alterations in <10% of these tumors. A predominant clock-like mutational signature was present in all samples. Whole-transcriptome analysis identified that the aberrantly differentiated endocrine exocrine subtype accounted for 18% of PDAC and was consistently associated with >5-year overall survival. In addition, a 28-gene expression-based signature associated with overall survival was identified and further validated in The Cancer Genome Atlas cohort. Immune landscape analysis through CODEX identified enriched CD4 T-helper cell/tumor interactions and reduced B7H3-high cell/tumor interactions in ATM PV carriers compared with noncarriers. CONCLUSIONS: The observed absence of TP53 PV and enrichment for CDKN2A alterations in ATM tumors, along with differences in the mutational signatures, transcriptomic subtypes and immune landscape, improve our understanding of the mechanistic pathways involved in PDAC development in germline ATM PV carriers and help identify potential targeted therapeutic strategies.

Humans↗

PubMed2025

Expression regulation network in papillae of sea cucumbers: Whole-transcriptome and DNA methylation datasets.

To elucidate the expression regulation network of papilla size of sea cucumbers (Apostichopus japonicus), the whole-transcriptome and DNA methylome datasets of different sizes of papillae in sea cucumbers were generated. Average clean bases of whole-transcriptome (16.35 G) and DNA methylome (28.92 G) were obtained using RNA sequencing and whole-genome bisulfite sequencing techniques. A total of 3,188 ceRNA networks were also identified including 3,081 long non-coding RNAs (lncRNA)/microRNAs (miRNA)/mRNA networks and 107 circular RNA (circRNA)/miRNA/mRNA networks. Methylome data indicate that there were 3,307 and 3,776 differentially methylated regions (DMRs) with high-level methylation as well as 3,125 and 3,016 DMRs with low-level methylation in big papillae compared to small papillae. The identified DMRs were mainly distributed in introns, promotors, or exons. The whole-transcriptome and DNA methylome datasets generated from this study not only established a robust theoretical foundation (especially from the epigenetic aspect) for elucidating expression regulation network determining papilla size in sea cucumbers but also can be a valuable resource of biomarker mining for papilla appearance-based selective breeding in sea cucumbers.

DNA Methylation↗

PubMed2004

PUNS: transcriptomic- and genomic-in silico PCR for enhanced primer design.

UNLABELLED: We developed a CGI/Perl-based web server to perform in silico polymerase chain reaction (PCR) on PCR primer sequences. The PUNS (Primer-UniGene Selectivity) server simulates PCR reactions by running BLASTN analysis on user-entered primer pairs against both the transcriptome and the genome to assess primer specificity. PUNS is particularly suited for the identification of highly selective primers for quantitative microarray validation. AVAILABILITY: Both system access and source-code are freely available at http://okeylabimac.med.utoronto.ca/PUNS.

Algorithms↗

PubMed2006

Neuronal transcriptome of Aplysia: neuronal compartments and circuitry.

Molecular analyses of Aplysia, a well-established model organism for cellular and systems neural science, have been seriously handicapped by a lack of adequate genomic information. By sequencing cDNA libraries from the central nervous system (CNS), we have identified over 175,000 expressed sequence tags (ESTs), of which 19,814 are unique neuronal gene products and represent 50%-70% of the total Aplysia neuronal transcriptome. We have characterized the transcriptome at three levels: (1) the central nervous system, (2) the elementary components of a simple behavior: the gill-withdrawal reflex-by analyzing sensory, motor, and serotonergic modulatory neurons, and (3) processes of individual neurons. In addition to increasing the amount of available gene sequences of Aplysia by two orders of magnitude, this collection represents the largest database available for any member of the Lophotrochozoa and therefore provides additional insights into evolutionary strategies used by this highly successful diversified lineage, one of the three proposed superclades of bilateral animals.

Animals↗

PubMed2026

Comparative transcriptomic analysis of the gills and hepatopancreas of freshwater-cultured Litopenaeus vannamei under chronic nitrite stress.

To investigate the differences in molecular responses between the gills and hepatopancreas of freshwater-cultured Litopenaeus vannamei under chronic nitrite stress, a 30-day chronic stress experiment was conducted with a control group and a stress group. Transcriptomic analysis of the gills and hepatopancreas was performed using Illumina sequencing; differentially expressed genes (DEGs) were identified, and GO, KEGG, GSEA, PPI, and RT-qPCR validation were carried out. The results showed that 196 DEGs (161 up-regulated and 35 down-regulated) were identified in the gills, and 287 DEGs (199 up-regulated and 88 down-regulated) in the hepatopancreas, with only 18 DEGs shared between the two tissues. DEGs in the gills were enriched in oxidoreductase activity, glycerophospholipid metabolism, and tyrosine metabolism; DEGs in the hepatopancreas were enriched in lipid transporter activity, phagosome, ECM-receptor interaction, and riboflavin metabolism. GSEA revealed significant suppression of the mTOR pathway in the gills and the Polycomb complex pathway in the hepatopancreas. PPI network analysis identified hub genes P5CS and eEF2 in the gills, and PER, TUBB1, SHMT, and TUBB4B in the hepatopancreas. RT-qPCR validation was consistent with the RNA-seq results (R2 = 0.764). This study indicates that, under chronic nitrite stress, the gill response is centered on redox regulation and inhibition of growth metabolism, whereas the hepatopancreas response primarily involves lipid transport, cytoskeletal remodeling, and phagosome activation. The two tissues synergistically adapt through fundamental biosynthetic and motor protein pathways. This research provides molecular evidence for deciphering the nitrite tolerance mechanisms in freshwater-cultured shrimp.

Animals↗

PubMed2026

A multi-modal survival prediction framework with group-based batch training and structural consistency alignment.

OBJECTIVE: Integrating whole-slide images (WSIs) with transcriptomic profiles is pivotal for enhancing cancer survival prediction. However, the intrinsic gigapixel resolution and variable sequence lengths of WSIs create a fundamental trade-off between training efficiency and the preservation of data heterogeneity in existing frameworks. Furthermore, substantial statistical and structural discrepancies between histological and genomic modalities often impede effective cross-modal alignment and fusion, thereby limiting prognostic accuracy. METHODS: We propose PRISM, an efficient multi-modal learning framework for integrating WSIs with transcriptomic profiles. To reconcile training efficiency with full data heterogeneity, PRISM first stochastically partitions variable-length WSI sequences into a main subset and a complementary residual subset, both of which are packed into fixed-length groups for batch training. The main subset is processed in the main branch, utilizing isolation masking to maintain intra-group sequence independence. Simultaneously, the residual subset is consolidated into "hyperslides" within a residual branch that leverages tailored supervision, effectively capturing inter-slide correlations. Furthermore, PRISM integrates an Informative Token Aggregation (ITA) module to reduce redundancy in WSIs and employs Cross-batch Structural Consistency Alignment (CBSCA) mechanism to enhance inter-modal structural connectivity. Finally, efficient cross-modal feature interaction is achieved through a Low-rank Bilinear Gated Fusion (LBGF) module. Code is available at https://github.com/Alisa2080/PRISM. RESULTS: Compared with existing methods, PRISM achieves the best overall C-index across five TCGA cohorts. On the larger TCGA-BRCA dataset, PRISM requires only 6 hours of training time, substantially reducing computational cost relative to strong multimodal baselines. Furthermore, comprehensive evaluations demonstrate that PRISM achieves the best overall IBS ranking and favorable time-dependent AUC performance at 1, 3, and 5 years, thereby delivering a more favorable trade-off between prognostic performance and computational efficiency. CONCLUSION: PRISM provides a favorable balance between predictive performance, calibration quality, and computational efficiency, highlighting its potential for practical deployment in multimodal survival modeling for computational pathology.

Humans↗

PubMed2006

Quantitative comparison of the HSV-1 and HSV-2 transcriptomes using DNA microarray analysis.

The genomes of human herpes virus type-1 and type-2 share a high degree of sequence identity; yet, they exhibit important differences in pathology in their natural human host as well as in animal host and cell cultures. Here, we report the comparative analysis of the time and relative abundance profiles of the transcription of each virus type (their transcriptomes) using parallel infections and microarray analysis using HSV-1 probes which hybridize with high efficiency to orthologous HSV-2 transcripts. We have confirmed that orthologous transcripts belong to the same kinetic class; however, the temporal pattern of accumulation of 4 transcripts (U(L)4, U(L)29, U(L)30, and U(L)31) differs in infections between the two virus types. Interestingly, the protein products of these transcripts are all involved in nuclear organization and viral DNA localization. We discuss the relevance of these findings and whether they may have potential roles in the pathological differences of HSV-1 and HSV-2.

Animals↗

PubMed2025

High MGMT expression identifies aggressive colorectal cancer with distinct genomic features and immune evasion properties.

INTRODUCTION: The epigenetic silencing of O6-methylguanine DNA methyltransferase (MGMT) is associated with reduced DNA repair capacity, carcinogenesis and increased sensitivity to alkylating chemotherapy. However, the biological role and clinical significance of MGMT overexpression in cancer remains poorly understood. METHODS: Using multiplexed quantitative immunofluorescence we measured the localized levels of MGMT protein, γH2AX and CD8+ T cells in multiple retrospective colorectal cancer (CRC) cohorts. Genomic and transcriptomic features of selected cases were also studied with whole exome DNA sequencing and genome-wide methylation analysis. MGMT-methylated human CRC cells SW620 were transfected with an MGMT-containing plasmid and co-cultured with allogeneic peripheral blood mononuclear cells. RESULTS: A subset of CRCs showed MGMT protein upregulation associated with lower γH2AX, reduced CD8+ tumor infiltrating lymphocytes (TILs), mismatch repair proficient (pMMR) status and shorter survival. CD8+ TILs were more distant from MGMT-expressing cells than MGMT-negative cells and the MGMT promoter methylation status did not highly correlate with MGMT protein levels in CRC. In genomic/transcriptomic analysis, high MGMT expression was associated with a lower nonsynonymous somatic mutational burden, higher transition-to-transversion mutation ratio, increased deleterious TP53 variants and distinct transcriptomic profiles. The exogenous expression of MGMT in SW620 CRC cells reduced the number of spontaneous nonsynonymous mutations, reproduced mutational features of MGMT-high CRC and limited the in vitro T-cell-mediated killing of malignant cells induced by proinflammatory cytokines in tumor/immune cell co-cultures. CONCLUSIONS: MGMT overexpression identifies a previously undescribed subset of CRCs with distinct biological and clinical properties including reduced mutagenesis, adaptive immune evasion, predominantly pMMR phenotype and aggressive clinical course. Direct, quantitative assessment of MGMT protein expression using spatially resolved analysis is more reliable than inference of MGMT expression by promoter methylation status in CRC.

Humans↗

PubMed2025

Ulmus minor response to Dutch elm disease: de novo transcriptome assembly and annotation.

Dutch elm disease (DED), caused by Ophiostoma novo-ulmi (ONU), has devastated elm populations across Europe and North America since the 20th century. In this work, a de novo transcriptome assembly of Ulmus minor in response to ONU is presented. We used two DED-resistant genotypes, MDV2.3 and VAD2, and one DED-susceptible genotype, MDV1, to capture responses to ONU at four time points post-inoculation (6, 24, 72, and 144 hours). RNA from collected samples was isolated and sequenced producing 60.88 M 100 bp paired-end reads per sample. We performed a de novo transcriptome assembly combining data from the three genotypes. The assembly was functionally annotated and validated through differential gene expression analysis of the response. This dataset provides a valuable resource for studying molecular mechanisms of DED resistance in elms, contributing to broadening our understanding of tree immunity and facilitating potential applications in functional annotation of future genome assemblies.

Transcriptome↗

PubMed2003

New trends in bioinformatics: from genome sequence to personalized medicine.

Molecular medicine requires the integration and analysis of genomic, molecular, cellular, as well as clinical data and it thus offers a remarkable set of challenges to bioinformatics. Bioinformatics nowadays has an essential role both, in deciphering genomic, transcriptomic, and proteomic data generated by high-throughput experimental technologies, and in organizing information gathered from traditional biology and medicine. The evolution of bioinformatics, which started with sequence analysis and has led to high-throughput whole genome or transcriptome annotation today, is now going to be directed towards recently emerging areas of integrative and translational genomics, and ultimately personalized medicine.Therefore considerable efforts are required to provide the necessary infrastructure for high-performance computing, sophisticated algorithms, advanced data management capabilities, and-most importantly-well trained and educated personnel to design, maintain and use these environments. This review outlines the most promising trends in bioinformatics, which may play a major role in the pursuit of future biological discoveries and medical applications.

Computational Biology↗

PubMedDate not supplied

Computational systems analysis of developmental toxicity: design, development and implementation of a Birth Defects Systems Manager (BDSM).

Birth defects and developmental disabilities remain an important public health issue worldwide. With the availability of genomic sequences from a growing number of human and model organisms and the rapid expansion of the public repositories holding large-scale gene expression datasets, a computational systems analysis of developmental toxicology can incorporate this vast digital information toward the realization of predictive models for complex disease. Here we describe the initial design, development and implementation of a Birth Defects Systems Manager (BDSM). The project was motivated by the need for a computational-bioinformatics infrastructure to manage vast digital information from functional genomics and for a new knowledge environment specifically engineered for the analysis of developmental processes and toxicities. Proof-of-concept tested BDSM using meta-analysis of gene expression data collected from different laboratories, technology platforms, and study models. The composite dataset incorporated 232 microarray comparisons of RNA samples by single or dual microarray platforms, cDNA or oligonucleotide based probes, and human or mouse sequence information. Preliminary results identified system-level features in the embryonic transcriptome as it reacted to various developmental-teratological stimuli. BDSM is open access through the worldwide web (http://systemsanalysis.louisville.edu/) and can be integrated with other bioinformatics tools and resources to advance the pace of discovery in birth defects research.

Animals↗

PubMed2025

Longitudinal Multi-Organ Transcriptomic Atlas of Salt-Induced Hypertension.

BACKGROUND: Salt-sensitive hypertension is a prevalent and clinically significant subtype of hypertension, where increased dietary salt intake elevates blood pressure and causes injury to multiple organ systems. Despite extensive research, dynamic molecular changes and conserved versus organ-specific transcriptional programs in hypertensive multi-organ damage remain poorly understood. Defining complex molecular pathways both in a temporal sequence and in an organ-specific manner is essential for developing targeted, precision therapies to mitigate hypertensive disease burden. METHODS: We generated a longitudinal multi-organ transcriptomic atlas of salt-sensitive hypertension using RNA sequencing of kidney cortex, kidney medulla, heart, and liver from Dahl salt-sensitive rats across four disease stages. A comprehensive bioinformatic analysis mapped dynamic transcriptional programs, evaluated 50 biological pathways, and defined upstream regulators. Histological and biochemical assays complemented transcriptomic analysis, while integration with human genome-wide association studies (GWAS) and compound-transcriptome analysis provided translational insights and identified candidate therapeutics. RESULTS: Salt-induced hypertension elicited both shared and tissue-specific transcriptional programs that evolved with disease progression. The kidney medulla showed robust early immune activation with metabolic suppression, while the cortex exhibited transient metabolic activation before declining and initiating immune activation. The liver and heart showed time-dependent metabolic and inflammatory remodeling. Cross-organ comparisons revealed a shared early proliferative response that converged on proinflammatory and fibrotic signatures. Upstream regulator analysis identified 79 time- and tissue-specific transcription factors associated with gene expression dynamics. GWAS integration analysis revealed endocrine signaling, ion transport, lipid metabolism, and detoxification as conserved pathways across species, underscoring the translational relevance of the model and study. Predictive compound-transcriptome analyses identified kinase inhibitors targeting phosphoinositide 3-kinase, mechanistic target of rapamycin and cyclin-dependent kinases as top candidates to counteract maladaptive transcriptional programs. CONCLUSIONS: This study defines temporal and tissue-specific transcriptomic remodeling in salt-sensitive hypertension and highlights the need for precision interventions to prevent progressive organ damage.

Journal Article↗

PubMed2006

TACT: Transcriptome Auto-annotation Conducting Tool of H-InvDB.

Transcriptome Auto-annotation Conducting Tool (TACT) is a newly developed web-based automated tool for conducting functional annotation of transcripts by the integration of sequence similarity searches and functional motif predictions. We developed the TACT system by integrating two kinds of similarity searches, FASTY and BLASTX, against protein sequence databases, UniProtKB (Swiss-Prot/TrEMBL) and RefSeq, and a unified motif prediction program, InterProScan, into the ORF-prediction pipeline originally designed for the 'H-Invitational' human transcriptome annotation project. This system successively applies these constituent programs to an mRNA sequence in order to predict the most plausible ORF and the function of the protein encoded. In this study, we applied the TACT system to 19 574 non-redundant human transcripts registered in H-InvDB and evaluated its predictive power by the degree of agreement with human-curated functional annotation in H-InvDB. As a result, the TACT system could assign functional description to 12 559 transcripts (64.2%), the remainder being hypothetical proteins. Furthermore, the overall agreement of functional annotation with H-InvDB, including those transcripts annotated as hypothetical proteins, was 83.9% (16 432/19 574). These results show that the TACT system is useful for functional annotation and that the prediction of ORFs and protein functions is highly accurate and close to the results of human curation. TACT is freely available at http://www.jbirc.aist.go.jp/tact/.

Amino Acid Motifs↗

PubMed2026

Functional characterization of the 9q34.13 locus identifies RAPGEF1 as a candidate gene modulating risk for melanoma and nevi via RAS activation.

Genome-wide association studies identified a melanoma- and nevus count-associated locus on chromosome band 9q34.13. Fine-mapping and melanocyte expression data collectively suggest two potential risk genes with opposite associations with risk: higher levels of Rap guanine nucleotide exchange factor 1 (RAPGEF1) and lower levels of uridine-cytidine kinase 1 (UCK1). Colocalization analyses and conditional transcriptome-wide association studies (TWASs) suggest multiple causal cis-regulatory sequence variants in partial linkage disequilibrium (LD) to each other. Melanocyte capture-HiC and CRISPR inhibition demonstrated regulatory interactions between fine-mapped variants and the RAPGEF1 and UCK1 promoters. Focusing on RAPGEF1, we demonstrate that RAPGEF1 expression promotes melanocyte growth and drives colony formation of human immortalized melanocytes. Following treatment with human epidermal growth factor (EGF), RAPGEF1 overexpression activated both RAP1 and RAS. Further, we show that RAPGEF1 expression is significantly enriched in melanomas that lack strongly activating RAS-MAPK pathway mutations, which suggests that RAPGEF1 may promote oncogenic RAS-MAPK pathway signaling in melanomas. Furthermore, in these tumors, we provide preliminary evidence to support the prognostic relevance of RAPGEF1 expression in individuals whose melanomas lack RAS or BRAF mutations. Together with other recent studies, these data suggest that germline variation influencing RAS activation may play a key role in nevus development and melanoma risk.

GWAS↗

PubMed2004

Using functional genomics to improve productivity in the manufacture of industrial biochemicals.

Recent developments in the field of functional genomics have been used to increase productivity in the manufacture of industrial biochemicals. Technologies like transcriptomics and proteomics have profited from the increasing number of genome sequencing projects. Meanwhile functional genomics has evolved from several isolated technologies, such as DNA chip technology and proteomics, to combined approaches that can help us to understand why organisms produce a certain product. The combination of expression studies and kinetic studies, such as carbon flux determination or metabolite measurements, has significantly improved productivity in production processes.

Bacteria↗

PubMed2006

Emerging Corynebacterium glutamicum systems biology.

Corynebacterium glutamicum is widely used for the biotechnological production of amino acids. Amino acid producing strains have been improved classically by mutagenesis and screening as well as in a rational manner using recombinant DNA technology. Metabolic flux analysis may be viewed as the first systems approach to C. glutamicum physiology since it combines isotope labeling data with metabolic network models of the biosynthetic and central metabolic pathways. However, only the complete genome sequence of C. glutamicum and post-genomics methods such as transcriptomics and proteomics have allowed characterizing metabolic and regulatory properties of this bacterium on a truly global level. Besides transcriptomics and proteomics, metabolomics and modeling approaches have now been established. Systems biology, which uses systematic genomic, proteomic and metabolomic technologies with the final aim of constructing comprehensive and predictive models of complex biological systems, is emerging for C. glutamicum. We will present current developments that advanced our insight into fundamental biology of C. glutamicum and that in the future will enable novel biotechnological applications for the improvement of amino acid production.

Amino Acids↗