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PubMed2026

Integrated methylome and transcriptome analysis provides insight into DNA methylation-mediated networks in sexual dimorphism of Vernicia montana.

BACKGROUND: Sexual dimorphism is fundamental to reproduction in dioecious plants and is regulated by both genetic and epigenetic mechanisms. DNA methylation is a central epigenetic mark known to influence phenotypic variation in plants. However, its specific role in shaping sexual dimorphism in dioecious trees remains poorly understood. To address this question, we performed integrated genome-wide DNA methylome and transcriptome analyses of four tissue types in the dioecious tung tree (Vernicia montana), including male and female flower buds and their corresponding leaves. RESULTS: Our analysis revealed distinct DNA methylation patterns between male and female tissues. Notably, the coordination between DNA methylation reprogramming and transcriptional regulation appeared to be more strongly associated with reproductive development than with vegetative growth in V. montana. We identified a set of sex-biased genes that may reflect different reproductive strategies between the sexes. Further analysis identified several key transcription factors (TFs) potentially associated with promoter differentially methylated regions (DMRs), including flowering-time regulators (e.g., FRS5, REM16, and VRN1) and TFs involved in hormone signaling pathways such as jasmonic acid, auxin, and salicylic acid signaling. Cis-regulatory element analysis showed that some promoter DMRs overlapped with hormone response elements related to abscisic acid, auxin, and gibberellin. Co-expression network analysis further revealed potential regulatory correlations among promoter DMR-mediated TFs, hormone-responsive pathways, and key floral development regulators. CONCLUSIONS: Collectively, our results suggest that interactions among DNA methylation, transcriptional regulation, and hormone-responsive pathways may contribute to the establishment of sexual dimorphism in V. montana. This study provides the first integrated view of these regulatory layers in V. montana and supports a species-specific regulatory framework for understanding the epigenetic basis of sexual dimorphism in this economically important dioecious tree. The proposed framework is based on multi-omics analyses and warrants further validation through targeted functional studies.

DNA Methylation↗
PubMed2005

Transcriptome analysis in the midgut of the earthworm (Eisenia andrei) using expressed sequence tags.

In order to gain insight into the expression profiles of the earthworm midgut, we analyzed 1106 expressed sequence tags (ESTs) derived from the earthworm midgut cDNA library. Among the 1106 ESTs analyzed, 557 (50.4%) ESTs showed significant similarity to known genes and represented 229 unique genes of which 166 ESTs were singletons and 63 ESTs manifest as two or more ESTs. While 552 ESTs (49.9%) were sequenced only once, 230 ESTs (20.8%) appeared two to five times and 324 ESTs (29.3%) were sequenced more than five times. Considering this redundancy of expression, it is likely that the gene expression profile of the earthworm midgut would be polarized. The expression of globin-related proteins, including ferritin and linker chain, and fibrinolytic enzymes appeared to account for 10.1% and 4.7% of the total ESTs analyzed in this study, respectively. This suggests that the prime functions of the midgut in the earthworm would be associated with protein hydrolysis as well as globin formation. Among the recognized protein-coding genes, the gene category involved in protein synthesis appeared to be the largest one accounting for 15.6% of the expression in the midgut, followed by gene categories associated with energy (11.2%), homeostasis (10.8%), metabolism (3.6%), cytoskeleton (2.5%), and protein fate (1.4%). With regard to functional aspects, the most abundantly expressed genes were associated with respiratory pigment (10.1%), cellular respiration (8.6%), and fibrin hydrolysis (4.7%). In addition, we were able to identify novel ESTs in the earthworm, which were related to the innate immune system, including destabilase, a possible antagonist of transglutaminase.

Animals↗
PubMed2004

Transcriptome analysis of early chondrogenesis in ATDC5 cells induced by bone morphogenetic protein 4.

We performed serial analysis of gene expression (SAGE) profiling in mouse chondrogenic ATDC5 cells before and 6 h after the onset of chondrogenesis induced by BMP4. A total of 43,656 SAGE tags (21,875 and 21,781 tags from the uninduced and induced libraries, respectively) were analyzed. Our analysis predicted that 139 transcripts were differentially represented in the two libraries (p < 0.05), including 72 downregulated and 67 upregulated transcripts. Ninety-five of them matched single UniGene entries (77 known genes and 18 ESTs), while 12 tags corresponded to potentially novel genes. Surprisingly, many of these known genes have never been implicated in chondrogenic differentiation. Interestingly, we found that a significant fraction of these genes formed physical linkage groups. This suggests that the transcriptional control by BMP signaling is in part targeted to genes in certain chromosomal domains. Together, our results provide novel insights into molecular events regulated by BMP signaling in chondrogenesis.

Animals↗
PubMed2026

Stage-Independent Real-Time Subtype Classification and Comprehensive Biopsy Profiling of Urothelial Carcinomas by the Lund Taxonomy System.

Bladder cancer is a heterogeneous malignancy with diverse clinical outcomes, and conventional pathological assessment alone is insufficient to capture its underlying biology. Gene expression profiling can stratify tumors into molecular subtypes with prognostic and predictive potential, but the reliability of transcriptomic classification and its clinical utility remains to be established. The translational/observational UROSCANSEQ study (ISRCTN15459149) prospectively evaluates RNA-based Lund Taxonomy (LundTax) molecular subtype classification in a clinical setting. Among 784 consecutive biopsies collected between 2018 and 2022, RNA sequencing was successful for 90% of all biopsies, encompassing 662 bladder cancer patients with a stage distribution of 48% Ta, 27% T1, 24% &#x2265;T2, and 1% CIS. We demonstrate that the LundTax subtype classification algorithm, applied to individual samples, accurately identifies cancer cell phenotypes with characteristic gene and protein expression patterns in a manner robust to RNA quality, data preprocessing strategies, and batch effects, supporting its clinical feasibility across both non-muscle-invasive and muscle-invasive disease. We further extend the LundTax framework by incorporating single-sample molecular risk scores reflecting tumor grade, proliferation, and progression risk, as well as tumor microenvironment signatures. Both risk scores and overall immune and stromal content in biopsies were significantly associated with an increased risk of clinical progression in noninvasive disease. In a separate analysis of the relative cellular composition of the tumor microenvironment, however, only the fraction of natural killer cells remained significant. Together, the expanded LundTax system provides a comprehensive molecular portrait of individual tumor biopsies. By explicitly separating cancer cell-intrinsic phenotypes, prognostic indexes, and microenvironmental signals, the framework minimizes biological confounding and establishes a strong foundation for future studies evaluating clinical outcomes and treatment responses.

Humans↗
PubMed2006

Expression profiling and mutant analysis reveals complex regulatory networks involved in Arabidopsis response to Botrytis infection.

The expression profiles of Botrytis-inoculated Arabidopsis plants were studied to determine the nature of the defense transcriptome and to identify genes involved in host responses to the pathogen. Normally resistant Arabidopsis wild-type plants were compared with coi1, ein2, and nahG plants that are defective in various defense responses and/or show increased susceptibility to Botrytis. In wild-type plants, the expression of 621 genes representing approximately 0.48% of the Arabidopsis transcriptome was induced greater than or equal to twofold after infection. Of these 621 Botrytis-induced genes (BIGs), 462 were induced at or before 36 h post-inoculation, and may be involved in resistance to the pathogen. The expression of 181 BIGs was dependent on a functional COI1 gene required for jasmonate signaling, whereas the expression of 63 and 80 BIGs were dependent on ethylene (ET) signaling or salicylic acid accumulation, respectively, based on results from ein2 and nahG plants. BIGs encode diverse regulatory and structural proteins implicated in pathogen defense and abiotic and oxidative-stress responses. Thirty BIGs encode putative DNA-binding proteins that belong to ET response, zinc-finger, MYB, WRKY, and HD-ZIP family transcription-factor proteins. Fourteen BIGs were studied in detail to determine their role in resistance to Botrytis. T-DNA insertion alleles of ZFAR1 (At2G40140), the gene encoding a putative zinc-finger protein with ankyrin-repeat domains, showed increased local susceptibility to Botrytis and sensitivity to germination in the presence of abscisic acid (ABA), supporting the role of ABA in mediating responses to Botrytis infection. In addition, two independent T-DNA insertion alleles in the WRKY70 gene showed increased susceptibility to Botrytis. The transcriptional activation of genes involved in plant hormone signaling and synthesis, removal of reactive oxygen species, and defense and abiotic-stress responses, coupled with the susceptibility of the wrky70 and zfar1 mutants, highlights the complex genetic network underlying defense responses to Botrytis in Arabidopsis.

Ankyrin Repeat↗
PubMed2005

Experimental trial for diagnosis of pancreatic ductal carcinoma based on gene expression profiles of pancreatic ductal cells.

Pancreatic ductal carcinoma (PDC) remains one of the most intractable human malignancies, mainly because of the lack of sensitive detection methods. Although gene expression profiling by DNA microarray analysis is a promising tool for the development of such detection systems, a simple comparison of pancreatic tissues may yield misleading data that reflect only differences in cellular composition. To directly compare PDC cells with normal pancreatic ductal cells, we purified MUC1-positive epithelial cells from the pancreatic juices of 25 individuals with a normal pancreas and 24 patients with PDC. The gene expression profiles of these 49 specimens were determined with DNA microarrays containing >44 000 probe sets. Application of both Welch's analysis of variance and effect size-based selection to the expression data resulted in the identification of 21 probe sets corresponding to 20 genes whose expression was highly associated with clinical diagnosis. Furthermore, correspondence analysis and 3-D projection with these probe sets resulted in separation of the transcriptomes of pancreatic ductal cells into distinct but overlapping spaces corresponding to the two clinical classes. To establish an accurate transcriptome-based diagnosis system for PDC, we applied supervised class prediction algorithms to our large data set. With the expression profiles of only five predictor genes, the weighted vote method diagnosed the class of samples with an accuracy of 81.6%. Microarray analysis with purified pancreatic ductal cells has thus provided a basis for the development of a sensitive method for the detection of PDC.

Carcinoma, Pancreatic Ductal↗
PubMed2004

Transcriptome of uropathogenic Escherichia coli during urinary tract infection.

A uropathogenic Escherichia coli strain CFT073-specific DNA microarray that includes each open reading frame was used to analyze the transcriptome of CFT073 bacteria isolated directly from the urine of infected CBA/J mice. The in vivo expression profiles were compared to that of E. coli CFT073 grown statically to exponential phase in rich medium, revealing the strategies this pathogen uses in vivo for colonization, growth, and survival in the urinary tract environment. The most highly expressed genes overall in vivo encoded translational machinery, indicating that the bacteria were in a rapid growth state despite specific nutrient limitations. Expression of type 1 fimbriae, a virulence factor involved in adherence, was highly upregulated in vivo. Five iron acquisition systems were all highly upregulated during urinary tract infection, as were genes responsible for capsular polysaccharide and lipopolysaccharide synthesis, drug resistance, and microcin secretion. Surprisingly, other fimbrial genes, such as pap and foc/sfa, and genes involved in motility and chemotaxis were downregulated in vivo. E. coli CFT073 grown in human urine resulted in the upregulation of iron acquisition, capsule, and microcin secretion genes, thus partially mimicking growth in vivo. On the basis of gene expression levels, the urinary tract appears to be nitrogen and iron limiting, of high osmolarity, and of moderate oxygenation. This study represents the first assessment of any E. coli pathotype's transcriptome in vivo and provides specific insights into the mechanisms necessary for urinary tract pathogenesis.

Animals↗
PubMed2025

Dual genetic loci and flavonoid metabolism orchestrate fruiting body coloration in Flammulina filiformis: a multi-omic roadmap for fungal pigmentation.

BACKGROUND: The fruiting bodies of macrofungi exhibit diverse coloration, traditionally attributed to melanin and carotenoid biosynthesis. This study is the first to reveal that flavonoids, rather than these classical pigments, are the predominant contributors to yellow pigmentation in the Flammulina filiformis. OBJECTIVE: To uncover the genetic basis and key regulatory genes involved in pigment formation in F. filiformis fruiting bodies, and to establish a model framework for studying color genetics in macrofungi. METHODS: Metabolomic profiling was conducted on yellow and white F. filiformis fruiting bodies to identify key pigment components. A segregating population was constructed, followed by integrated multi-omics analyses-including bulk segregant analysis (BSA), genome-wide association study (GWAS), and transcriptomics-to map regulatory loci and candidate genes. Functional roles were validated via genetic transformation and protein structural modeling. RESULTS: Flavonoid accumulation was identified as the biochemical hallmark of pigmented fruiting bodies. Genetic analysis revealed a dual regulatory mechanism: a qualitative locus governing pigmentation presence and a quantitative trait determining color intensity. Combined BSA and GWAS pinpointed a major locus, Ffcrs, within a recombination-suppressed region. Transcriptomic analysis identified two key regulators, Ffakr (a transcriptional activator) and Ffpal (encoding phenylalanine ammonia-lyase). Functional verification via transformation, structural modeling, and metabolite profiling in transgenic lines confirmed their essential roles in flavonoid biosynthesis and pigmentation. CONCLUSION: This study uncovers a flavonoid-based pigmentation mechanism in F. filiformis and elucidates a complex genetic architecture shaped by both qualitative and quantitative loci, providing a new paradigm for understanding pigment formation in macrofungi. The identified regulatory factors establish a molecular foundation for the precise manipulation of economically important pigmentation traits in edible mushroom.

Flavonoids↗
PubMed2026

Epigenetic alterations of AKT1 orchestrate a metabolic reprogramming in advanced lipedema: translational insights from an integrated multi-omics study.

BACKGROUND: lipedema is a chronic, progressive adipose disorder predominantly affecting women, characterized by painful, symmetrical subcutaneous fat accumulation, and typically resistant to lifestyle interventions. The pathophysiology of advanced-stage lipedema remains poorly defined, and no validated biomarkers or targeted therapies are currently available. METHODS: in this observational study, we applied a comprehensive multi-omics approach to dissect the molecular and metabolic alterations underlying late-stage lipedema. RESULTS: Genome-wide DNA methylation profiling identified over 5,000 differentially methylated CpG sites affecting genes involved in receptor tyrosine kinase signaling, phospho-metabolism, and immune pathways. Transcriptomic analysis revealed profound downregulation of mitochondrial functions, including oxidative phosphorylation, the TCA cycle, and fatty acid &#x3b2;-oxidation, alongside disruption of the sirtuin pathway and extracellular matrix remodeling. Integrative analysis pinpointed AKT1 as a central regulatory node: its promoter region was hypomethylated, correlating with increased gene expression and protein phosphorylation. Metabolomic profiling confirmed AKT1-linked metabolic dysregulation, including altered levels of L-arginine, NADP+, ATP, guanosine, glycerol, and glutamate, indicating impaired redox balance and energy metabolism. Trans-omic network analysis positioned AKT1 at the intersection of multiple dysregulated pathways, suggesting its key role in advanced-stage lipedema. CONCLUSIONS: the consistent enhancing of AKT pathway signaling across omic layers highlights its potential not only as a biomarker for disease stratification but also as a putative druggable target for therapeutic intervention. These findings offer new mechanistic insights into lipedema pathophysiology and provide a rationale for future personalized treatment strategies guided by AKT1-centric molecular profiling.

Proto-Oncogene Proteins c-akt↗
PubMed2003

Global gene expression profiling in the study of multiple myeloma.

Multiple myeloma (MM) is a rare but uniformly fatal malignancy of antibody-secreting plasma cells. Although several key molecular events in disease initiation or progression have been confirmed (eg, FGFR3/MMSET activation) or implicated (eg, chromosome 13 deletion), the mechanisms of MM development remain enigmatic. Although it is generally indistinguishable morphologically, MM importantly exhibits a tremendous degree of variability in its clinical course, with some patients surviving only months and others for many years. However, measures of current laboratory parameters can account for no more than 20% of this outcome variability. Furthermore, the means by which current drugs impart their anti-MM effect are mostly unknown. The development of serious comorbidities, such as osteopenia and/or focal lytic lesions of bone, is also poorly understood. Finally, very little knowledge exists concerning the molecular triggers for the conversion of benign monoclonal gammopathy of undetermined significance (MGUS) to overt MM. Given that abnormal gene expression lies at the heart of most if not all cancers, high-throughput global gene expression profiling has become a powerful tool for investigating the molecular biology and clinical behaviors Here I discuss recent progress made in addressing many of these issues through the molecular dissection of the transcriptome of normal plasma cells, MGUS, and MM.

Antineoplastic Agents↗
PubMed2003

Gene expression profile of Campylobacter jejuni in response to growth temperature variation.

The foodborne pathogen Campylobacter jejuni is the primary causative agent of gastroenteritis in humans. In the present study a whole genome microarray of C. jejuni was constructed and validated. These DNA microarrays were used to measure changes in transcription levels over time, as C. jejuni cells responded to a temperature increase from 37 to 42 degrees C. Approximately 20% of the C. jejuni genes were significantly up- or downregulated over a 50-min period after the temperature increase. The global change in C. jejuni transcriptome was found to be essentially transient, with only a small subset of genes still differentially expressed after 50 min. A substantial number of genes with a downregulated coexpression pattern were found to encode for ribosomal proteins. This suggests a short growth arrest upon temperature stress, allowing the bacteria to reshuffle their energy toward survival and adaptation to the new growth temperature. Genes encoding chaperones, chaperonins, and heat shock proteins displayed the most dramatic and rapid upregulation immediately after the temperature change. Interestingly, genes encoding proteins involved in membrane structure modification were differentially expressed, either up- or downregulated, suggesting a different protein membrane makeup at the two different growth temperatures. Overall, these data provide new insights into the primary response of C. jejuni to surmount a sudden temperature upshift, allowing the bacterium to survive and adapt its transcriptome to a new steady state.

Bacterial Proteins↗
PubMed2025

CD40 transcriptomic expression patterns across malignancies: implications for clinical trials of CD40 agonists.

BACKGROUND: CD40 is a T-cell co-stimulatory receptor targeted by next-generation immunotherapies. We conducted a pan-cancer transcriptome analysis of CD40, its ligand, and related immune markers to evaluate co-expression patterns and clinical outcomes. METHODS: We analyzed transcriptome data for CD40, its ligand, and other common checkpoints and co-stimulators (PD-1, PD-L1, PD-L2, CTLA-4, LAG-3, ICOS, CD27, CD28, OX40, and GITR). RNA expression was classified as high (75-100th percentile), moderate (25-74th), or low (0-24th) against a reference population of 735 previously tested solid tumors. RESULTS: Of 514 patients, 114 (22%) showed high, 247 (48%) moderate, and 153 (30%) low CD40 RNA expression. High CD40 expression was most frequent in liver and bile duct (42%), pancreatic (42%), and ovarian (40%) cancers. Both high CD40 and low-moderate CD40 ligand expression-potentially conducive to CD40 agonist therapy-was most frequent in ovarian (33%) and pancreatic (24%) cancer. In both UCSD (N&#x2009;=&#x2009;514) and TCGA (N&#x2009;=&#x2009;10,953) cohorts, high CD40 expression significantly correlated with high CD28 and GITR. High CD40 RNA levels were not prognostic for overall survival (OS) from metastatic disease (P&#x2009;=&#x2009;0.2) (n&#x2009;=&#x2009;272 immune checkpoint inhibitor (ICI)-na&#xef;ve patients). High CD40 expression correlated with longer OS from immunotherapy initiation (n&#x2009;=&#x2009;217 ICI-treated patients; P&#x2009;=&#x2009;0.04, univariable analysis), but not multivariable analysis, suggesting it may not be an independent predictive biomarker. CONCLUSION: High CD40 expression correlated with liver and bile duct, pancreatic, and ovarian cancers, as well as with CD28 and GITR transcripts. Immune marker co-expression in individual patients merits further exploration for the development of CD40-based and other immunotherapy interventions.

Humans↗
PubMed2026

Genome-wide analysis of the plant-specific PLATZ gene family in Taraxacum kok-saghyz and its roles in response to drought and salt tolerance.

Abiotic stress severely limits plant growth and productivity. Taraxacum kok-saghyz Rodin (TKS), known for its environmental resilience, represents a valuable resource for identifying stress-tolerant genes to improve stress-adaptive crops. Plant AT-rich protein and zinc-binding protein (PLATZ) transcription factors serve as core regulators of plant growth, developmental processes, and adaptive responses to various stress conditions; however, they remain uncharacterized in TKS. Here, we identified 10 TksPLATZ genes through a whole-genome analysis. Phylogenetically, these genes were grouped into five distinct evolutionary branches. Promoter sequence analysis revealed multiple types of cis-acting regulatory elements that are connected with hormonal signal responses and environmental stress adaptation. Integrated analysis of transcriptome datasets and RT-qPCR validation demonstrated that TksPLATZ genes display tissue-specific expression profiles and show distinct responsive patterns to drought and salt stress treatments. Among them, TksPLATZ1, TksPLATZ2 and TksPLATZ7 were markedly induced under both stressors and were selected for further functional study. We demonstrated that TksPLATZ1, TksPLATZ2 and TksPLATZ7 localize to the cell nucleus and act as transcriptional activators and repressors, respectively. Phenotypic data from overexpression experiments in plants confirm that heterologous expression of TksPLATZ1, TksPLATZ2, and TksPLATZ7 enhances the tolerance of Arabidopsis to salt and osmotic stress. These findings provide valuable genetic resources for improving plant tolerance to environmental stresses.

Salt Tolerance↗
PubMed2025

Single-cell analysis of dup15q syndrome reveals developmental and postnatal molecular changes in autism.

Duplication 15q (dup15q) syndrome is a leading genetic cause of autism spectrum disorder, offering a key model for studying autism-related mechanisms. Using single-cell and single-nucleus RNA sequencing of cortical organoids from dup15q patient-derived iPSCs and post-mortem brain samples, we identify increased glycolysis, disrupted layer-specific marker expression, and aberrant morphology in deep-layer neurons during fetal-stage organoid development. In adolescent-adult postmortem brains, upper-layer neurons exhibit heightened transcriptional burden related to synaptic signaling, a pattern shared with idiopathic autism. Using spatial transcriptomics, we confirm these cell-type-specific disruptions in brain tissue. By gene co-expression network analysis, we reveal disease-associated modules that are well preserved between postmortem and organoid samples, suggesting metabolic dysregulation that may lead to altered neuron projection, synaptic dysfunction, and neuron hyperexcitability in dup15q syndrome.

Humans↗
PubMed2026

In silico analysis of SH3BP2 genomic alterations and expression profiles in CRC.

AIM: Colorectal cancer (CRC) is a widespread health issue that attains high mortality. The adaptor protein SH3BP2 amplification results in metabolic changes, oxidative stress, NK cell activity, and inflammation. The NK cells are capable of destroying tumor cells without prior activation, help prevent metastasis, and have prognostic value. Targeting SH3BP2 to regulate NK cell activity in the TME could enhance CRC-based immunotherapy. MATERIALS AND METHODS: The cancer hallmark tool helps in understanding SH3BP2&#xa0;hallmark annotation. Utilizing the STRING tool and the KEGG pathway, protein functional enrichment and PPI networking were analyzed. TIMER 2.0 was used for immune cell infiltration correlation analysis, and UALCAN was used for CPTAC-based protein expression profiling. RESULTS AND CONCLUSIONS: The GEO (GSE9348) dataset showed SH3BP2 is upregulated in CRC (log2 fold change&#x2009;=&#x2009;1.18). GEO, TCGA, and cBioPortal revealed SH3BP2 alterations in CRC cases, potentially aiding immune evasion. Mutations in SH3BP2 influence cancer growth, suppressing tumors or promoting them by activating NF-&#x3ba;B and affecting immune responses through WNT/&#x3b2;-catenin, PI3K, MAPK, and JAK-STAT pathways. Overall, SH3BP2 plays a key role in cancer growth and immune regulation, making it a promising target for CRC therapy. Further experimental validation is needed to demonstrate its diagnostic and therapeutic potency.

Humans↗
PubMed2005

Clusters of adjacent and similarly expressed genes across normal human tissues complicate comparative transcriptomic discovery.

Transcriptomic techniques are valuable tools with which to validate genetic and biological hypotheses and are now widely available for research. However, with the exception of tumor biology, comparative genomics analyses have been difficult to use as discovery engines to describe biologically relevant expression changes. We propose that physical proximity of human genes correlates with similar mRNA expression, so that increased expression might include a disease-relevant gene and many other genes in the adjacent region. To increase the efficiency of combining susceptibility gene mapping and interpretation of transcriptomics, we developed a method to identify clusters of adjacent and similarly expressed genes. Gene expression profiles for 28,945 genes across 101 normal human tissues were obtained from the Gene Logic BioExpress system. The expression similarity for genes in sliding-windows was measured using average pair-wise Pearson correlation coefficients. We identified 187 clusters (p < 10e-4) of co-regulated genes, including 2648 genes, or 9.1% of all genes considered and termed these "clusters of adjacent and similarly expressed genes" (CASEGs). Genes in 15 (8.2%) of these clusters demonstrate a significant co-expression enrichment (p < 10e-10). This study demonstrates the coordinate expression of neighboring genes and provides a comprehensive view of expression-based compartmentalization of the human genome, which can be overlaid on genetic susceptibility gene maps.

Gene Expression Profiling↗
PubMed2026

Predicting gene-specific regulation with transcriptomic and epigenetic single-cell data.

MOTIVATION: Analysis of single cell ATAC-seq and RNA-seq data has allowed to gain unprecedented insights into gene regulation by allowing to define cell type-specific regulatory regions and their effects on gene expression. While powerful, such analysis is challenging due to the inherent sparsity of single cell data. RESULTS: We present a new approach, MetaFR, to learn gene-specific models that link open-chromatin variation from scATAC-seq data to gene expression from scRNA-seq. Using efficient regression trees, we illustrate that accurate expression prediction models can be learned on the single-cell or meta-cell level. Validation was done using fine-mapped eQTLs. Meta-cell models were found to outperform single-cell models for most genes. Comparison to the SOTA method SCARlink revealed advantages of MetaFR in terms of runtime and prediction performance. MetaFR thus allows time-efficient analysis and obtains reliable models of gene expression prediction, which can be used to study gene regulation in any organism for which scRNA-seq and scATAC-seq data is available. AVAILABILITY AND IMPLEMENTATION: MetaFR is available under https://github.com/SchulzLab/MetaFR.

Single-Cell Analysis↗