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gene expression omnibus geo datasets  (Biotechnology Information)

 
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    Biotechnology Information gene expression omnibus geo datasets
    Gene Expression Omnibus Geo Datasets, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/gene+expression+datasets/expression+gene+omnibus+%E2%80%A2/pmc13197572-24-8-26
    Average 86 stars, based on 1 article reviews
    gene expression omnibus geo datasets - by Bioz Stars, 2026-11
    86/100 stars

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    Gene Expression:

    Article Title: Tumor necrosis factor alpha-induced protein 3: A key biomarker for response to ursodeoxycholic acid in primary biliary cholangitis
    Article Snippet: .. Following a systematic review, three gene expression datasets ( GSE93170 , GSE119600 and GSE159676 ) were selected from the National Center for Biotechnology Information GEO database. ..

    Article Title: Multi-cohort analysis identifies a blood-based immune transcriptomic signature for early lung cancer detection
    Article Snippet: .. We downloaded 241 gene expression datasets (Supplementary Data ) from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) and European Bioinformatics Institute (EBI) ArrayExpress, consisting of 22,773 samples derived from whole blood or peripheral blood mononuclear cells (PBMCs) from 251 independent cohorts. ..

    Article Title: Systems immunology of transcriptional responses to viral infection identifies conserved antiviral pathways across macaques and humans
    Article Snippet: .. We utilized human gene expression data collected and processed from our other studies., , This included 47 gene expression datasets from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO), Sequence Read Archive (SRA), ArrayExpress, and European Nucleotide Archive (ENA), consisting of 5,345 samples derived from whole blood or peripheral blood mononuclear cells (PBMCs) ( ). ..

    Article Title: TLR2-PI3K/Akt mediated microbe-mimetic priming boosts the therapeutic paracrine function of GelMA-Encapsulated MSCs for diabetic wound regeneration
    Article Snippet: .. Gene expression datasets ( GSE158613 and GSE158614 , Mus musculus) were retrieved from the National Center for Biotechnology Information (NCBI) database ( https://www.ncbi.nlm.nih.gov ) [ ]. .. Besides, for RNA-seq analysis, MSCs pretreated with PGN and LTA for 6 h, followed by RNA extraction and sequencing on an Illumina HiSeq 4000 platform (LC-Bio Technologies) according to the manufacturer's protocols.

    Article Title: Gene expression clock: an unsupervised deep learning approach for predicting circadian rhythmicity from whole genome expression
    Article Snippet: .. There is a vast amount of gene expression datasets in the National Center for Biotechnology Information Gene Expression Omnibus (GEO). ..

    Article Title: Identification of CDK2 as a key apoptotic gene for predicting cervical cancer prognosis using bioinformatics and machine learning
    Article Snippet: .. Methods: Gene expression datasets were obtained from the National Center for Biotechnology Information Gene Expression Omnibus (GEO) and the Cancer Genome Atlas (TCGA), with GSE192897 used as the training set. ..

    Article Title: Systems immunology of transcriptional responses to viral infection identifies conserved antiviral pathways across macaques and humans
    Article Snippet: .. Non-human primate dataset collection and preprocessing Wedownloaded 21 gene expression datasets (either microarray or RNA-seq) from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO), Sequence Read Archive (SRA) or shared by collaborators, consisting of 743 samples derived from whole blood or peripheral blood mononuclear cells (PBMCs) (Tables 1 and S1). ..

    Article Title: BNIPL is a promising biomarker of laryngeal cancer: novel insights from bioinformatics analysis and experimental validation
    Article Snippet: .. The gene expression datasets of LC-related genes were downloaded from GEO of National Center for Biotechnology Information ( https://www.ncbi.nih.gov/geo/ ). ..

    Derivative Assay:

    Article Title: Multi-cohort analysis identifies a blood-based immune transcriptomic signature for early lung cancer detection
    Article Snippet: .. We downloaded 241 gene expression datasets (Supplementary Data ) from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) and European Bioinformatics Institute (EBI) ArrayExpress, consisting of 22,773 samples derived from whole blood or peripheral blood mononuclear cells (PBMCs) from 251 independent cohorts. ..

    Article Title: Systems immunology of transcriptional responses to viral infection identifies conserved antiviral pathways across macaques and humans
    Article Snippet: .. We utilized human gene expression data collected and processed from our other studies., , This included 47 gene expression datasets from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO), Sequence Read Archive (SRA), ArrayExpress, and European Nucleotide Archive (ENA), consisting of 5,345 samples derived from whole blood or peripheral blood mononuclear cells (PBMCs) ( ). ..

    Article Title: Systems immunology of transcriptional responses to viral infection identifies conserved antiviral pathways across macaques and humans
    Article Snippet: .. Non-human primate dataset collection and preprocessing Wedownloaded 21 gene expression datasets (either microarray or RNA-seq) from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO), Sequence Read Archive (SRA) or shared by collaborators, consisting of 743 samples derived from whole blood or peripheral blood mononuclear cells (PBMCs) (Tables 1 and S1). ..

    Sequencing:

    Article Title: Systems immunology of transcriptional responses to viral infection identifies conserved antiviral pathways across macaques and humans
    Article Snippet: .. We utilized human gene expression data collected and processed from our other studies., , This included 47 gene expression datasets from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO), Sequence Read Archive (SRA), ArrayExpress, and European Nucleotide Archive (ENA), consisting of 5,345 samples derived from whole blood or peripheral blood mononuclear cells (PBMCs) ( ). ..

    Article Title: Systems immunology of transcriptional responses to viral infection identifies conserved antiviral pathways across macaques and humans
    Article Snippet: .. Non-human primate dataset collection and preprocessing Wedownloaded 21 gene expression datasets (either microarray or RNA-seq) from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO), Sequence Read Archive (SRA) or shared by collaborators, consisting of 743 samples derived from whole blood or peripheral blood mononuclear cells (PBMCs) (Tables 1 and S1). ..

    Microarray:

    Article Title: Systems immunology of transcriptional responses to viral infection identifies conserved antiviral pathways across macaques and humans
    Article Snippet: .. Non-human primate dataset collection and preprocessing Wedownloaded 21 gene expression datasets (either microarray or RNA-seq) from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO), Sequence Read Archive (SRA) or shared by collaborators, consisting of 743 samples derived from whole blood or peripheral blood mononuclear cells (PBMCs) (Tables 1 and S1). ..

    RNA Sequencing:

    Article Title: Systems immunology of transcriptional responses to viral infection identifies conserved antiviral pathways across macaques and humans
    Article Snippet: .. Non-human primate dataset collection and preprocessing Wedownloaded 21 gene expression datasets (either microarray or RNA-seq) from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO), Sequence Read Archive (SRA) or shared by collaborators, consisting of 743 samples derived from whole blood or peripheral blood mononuclear cells (PBMCs) (Tables 1 and S1). ..



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    PER2 integrates <t>circadian</t> and transcriptional signals at the mouse Esr1 promoter. ( A ) Time-course <t>expression</t> profiles of Esr1 and Per2 mRNA showing circadian oscillations in multiple mouse tissues. Wild-type mice were entrained to 12-h light:12-h dark cycles for one week, then released into constant darkness. Tissues (white adipose tissue, liver, and kidney) were collected at 2 h intervals for 48 h mRNA expression levels (normalized counts) are plotted against circadian time (CT). Fitted cosine curves (blue for Esr1 , red for Per2 ) show that both <t>genes</t> oscillate with similar periodicity across tissues, with tissue-specific phase relationships. ( B ) Quantitative circadian parameters (period, phase, amplitude, and baseline expression) determined by meta2d analysis of data shown in panel A. Upper table. Circadian periods for Esr1 and Per2 in each tissue show remarkable similarity (white adipose: ∼24.2 h for both; liver: ∼23.8 h Esr1 , ∼23.5 h Per2 ; kidney: ∼24.1 h for both). Lower table. Phase analysis reveals tissue-specific phase relationships: Esr1 leads Per2 by 2–4 h in white adipose tissue and kidney, while lagging by ∼1–2 h in liver. P-values (p < 0.01) confirm statistically significant rhythmicity for both genes in all tissues. ( C ) Per2 and Esr1 circadian rhythms are abolished in Per1 −/− / Per2 −/− double knockout mice. Liver expression data from wild-type and Per1/2 dKO mice ( GSE171975 ) show that in wild-type liver, both Per2 and Esr1 exhibit robust circadian oscillations (period ∼23 h, p < 0.01). In contrast, both genes completely lose rhythmicity in Per1/2 dKO liver tissue, with expression remaining flat across all time points. Importantly, basal transcript levels are maintained despite loss of oscillation, demonstrating that Esr1 transcription per se does not require functional PER proteins, but rather that circadian modulation of expression requires clock function. ( D ) Pou2f1 and Brca1 transcripts show no circadian rhythmicity at the mRNA level. Upper panel: Pou2f1 expression remains relatively constant across the circadian cycle in both wild-type and Per1/2 dKO liver, with no statistically significant oscillations. Lower panel: Brca1 expression similarly lacks circadian rhythmicity in both genotypes. These non-rhythmic expression patterns contrast sharply with the robust oscillations observed for Per2 and Esr1 , suggesting that constitutively expressed POU2F1(OCT-1) and BRCA1 serve as stable scaffolding factors that cooperate with rhythmically expressed PER2 to impose circadian control on Esr1 transcription. ( E ) Meta2d analysis results for Brca1 and Pou2f1 showing circadian parameters and statistical assessment. p-values confirm the absence of significant circadian rhythmicity (p > 0.01) for both genes in both wild-type and Per1/2 dKO animals. ( F ) Direct temporal comparison of Per2 and Esr1 oscillations in wild-type and Per1/2 dKO liver. Per2 (red) and Esr1 (blue) expression from GSE171975 are plotted together to visualize their temporal relationship.
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    PER2 integrates <t>circadian</t> and transcriptional signals at the mouse Esr1 promoter. ( A ) Time-course <t>expression</t> profiles of Esr1 and Per2 mRNA showing circadian oscillations in multiple mouse tissues. Wild-type mice were entrained to 12-h light:12-h dark cycles for one week, then released into constant darkness. Tissues (white adipose tissue, liver, and kidney) were collected at 2 h intervals for 48 h mRNA expression levels (normalized counts) are plotted against circadian time (CT). Fitted cosine curves (blue for Esr1 , red for Per2 ) show that both <t>genes</t> oscillate with similar periodicity across tissues, with tissue-specific phase relationships. ( B ) Quantitative circadian parameters (period, phase, amplitude, and baseline expression) determined by meta2d analysis of data shown in panel A. Upper table. Circadian periods for Esr1 and Per2 in each tissue show remarkable similarity (white adipose: ∼24.2 h for both; liver: ∼23.8 h Esr1 , ∼23.5 h Per2 ; kidney: ∼24.1 h for both). Lower table. Phase analysis reveals tissue-specific phase relationships: Esr1 leads Per2 by 2–4 h in white adipose tissue and kidney, while lagging by ∼1–2 h in liver. P-values (p < 0.01) confirm statistically significant rhythmicity for both genes in all tissues. ( C ) Per2 and Esr1 circadian rhythms are abolished in Per1 −/− / Per2 −/− double knockout mice. Liver expression data from wild-type and Per1/2 dKO mice ( GSE171975 ) show that in wild-type liver, both Per2 and Esr1 exhibit robust circadian oscillations (period ∼23 h, p < 0.01). In contrast, both genes completely lose rhythmicity in Per1/2 dKO liver tissue, with expression remaining flat across all time points. Importantly, basal transcript levels are maintained despite loss of oscillation, demonstrating that Esr1 transcription per se does not require functional PER proteins, but rather that circadian modulation of expression requires clock function. ( D ) Pou2f1 and Brca1 transcripts show no circadian rhythmicity at the mRNA level. Upper panel: Pou2f1 expression remains relatively constant across the circadian cycle in both wild-type and Per1/2 dKO liver, with no statistically significant oscillations. Lower panel: Brca1 expression similarly lacks circadian rhythmicity in both genotypes. These non-rhythmic expression patterns contrast sharply with the robust oscillations observed for Per2 and Esr1 , suggesting that constitutively expressed POU2F1(OCT-1) and BRCA1 serve as stable scaffolding factors that cooperate with rhythmically expressed PER2 to impose circadian control on Esr1 transcription. ( E ) Meta2d analysis results for Brca1 and Pou2f1 showing circadian parameters and statistical assessment. p-values confirm the absence of significant circadian rhythmicity (p > 0.01) for both genes in both wild-type and Per1/2 dKO animals. ( F ) Direct temporal comparison of Per2 and Esr1 oscillations in wild-type and Per1/2 dKO liver. Per2 (red) and Esr1 (blue) expression from GSE171975 are plotted together to visualize their temporal relationship.
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    PER2 integrates <t>circadian</t> and transcriptional signals at the mouse Esr1 promoter. ( A ) Time-course <t>expression</t> profiles of Esr1 and Per2 mRNA showing circadian oscillations in multiple mouse tissues. Wild-type mice were entrained to 12-h light:12-h dark cycles for one week, then released into constant darkness. Tissues (white adipose tissue, liver, and kidney) were collected at 2 h intervals for 48 h mRNA expression levels (normalized counts) are plotted against circadian time (CT). Fitted cosine curves (blue for Esr1 , red for Per2 ) show that both <t>genes</t> oscillate with similar periodicity across tissues, with tissue-specific phase relationships. ( B ) Quantitative circadian parameters (period, phase, amplitude, and baseline expression) determined by meta2d analysis of data shown in panel A. Upper table. Circadian periods for Esr1 and Per2 in each tissue show remarkable similarity (white adipose: ∼24.2 h for both; liver: ∼23.8 h Esr1 , ∼23.5 h Per2 ; kidney: ∼24.1 h for both). Lower table. Phase analysis reveals tissue-specific phase relationships: Esr1 leads Per2 by 2–4 h in white adipose tissue and kidney, while lagging by ∼1–2 h in liver. P-values (p < 0.01) confirm statistically significant rhythmicity for both genes in all tissues. ( C ) Per2 and Esr1 circadian rhythms are abolished in Per1 −/− / Per2 −/− double knockout mice. Liver expression data from wild-type and Per1/2 dKO mice ( GSE171975 ) show that in wild-type liver, both Per2 and Esr1 exhibit robust circadian oscillations (period ∼23 h, p < 0.01). In contrast, both genes completely lose rhythmicity in Per1/2 dKO liver tissue, with expression remaining flat across all time points. Importantly, basal transcript levels are maintained despite loss of oscillation, demonstrating that Esr1 transcription per se does not require functional PER proteins, but rather that circadian modulation of expression requires clock function. ( D ) Pou2f1 and Brca1 transcripts show no circadian rhythmicity at the mRNA level. Upper panel: Pou2f1 expression remains relatively constant across the circadian cycle in both wild-type and Per1/2 dKO liver, with no statistically significant oscillations. Lower panel: Brca1 expression similarly lacks circadian rhythmicity in both genotypes. These non-rhythmic expression patterns contrast sharply with the robust oscillations observed for Per2 and Esr1 , suggesting that constitutively expressed POU2F1(OCT-1) and BRCA1 serve as stable scaffolding factors that cooperate with rhythmically expressed PER2 to impose circadian control on Esr1 transcription. ( E ) Meta2d analysis results for Brca1 and Pou2f1 showing circadian parameters and statistical assessment. p-values confirm the absence of significant circadian rhythmicity (p > 0.01) for both genes in both wild-type and Per1/2 dKO animals. ( F ) Direct temporal comparison of Per2 and Esr1 oscillations in wild-type and Per1/2 dKO liver. Per2 (red) and Esr1 (blue) expression from GSE171975 are plotted together to visualize their temporal relationship.
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    PER2 integrates circadian and transcriptional signals at the mouse Esr1 promoter. ( A ) Time-course expression profiles of Esr1 and Per2 mRNA showing circadian oscillations in multiple mouse tissues. Wild-type mice were entrained to 12-h light:12-h dark cycles for one week, then released into constant darkness. Tissues (white adipose tissue, liver, and kidney) were collected at 2 h intervals for 48 h mRNA expression levels (normalized counts) are plotted against circadian time (CT). Fitted cosine curves (blue for Esr1 , red for Per2 ) show that both genes oscillate with similar periodicity across tissues, with tissue-specific phase relationships. ( B ) Quantitative circadian parameters (period, phase, amplitude, and baseline expression) determined by meta2d analysis of data shown in panel A. Upper table. Circadian periods for Esr1 and Per2 in each tissue show remarkable similarity (white adipose: ∼24.2 h for both; liver: ∼23.8 h Esr1 , ∼23.5 h Per2 ; kidney: ∼24.1 h for both). Lower table. Phase analysis reveals tissue-specific phase relationships: Esr1 leads Per2 by 2–4 h in white adipose tissue and kidney, while lagging by ∼1–2 h in liver. P-values (p < 0.01) confirm statistically significant rhythmicity for both genes in all tissues. ( C ) Per2 and Esr1 circadian rhythms are abolished in Per1 −/− / Per2 −/− double knockout mice. Liver expression data from wild-type and Per1/2 dKO mice ( GSE171975 ) show that in wild-type liver, both Per2 and Esr1 exhibit robust circadian oscillations (period ∼23 h, p < 0.01). In contrast, both genes completely lose rhythmicity in Per1/2 dKO liver tissue, with expression remaining flat across all time points. Importantly, basal transcript levels are maintained despite loss of oscillation, demonstrating that Esr1 transcription per se does not require functional PER proteins, but rather that circadian modulation of expression requires clock function. ( D ) Pou2f1 and Brca1 transcripts show no circadian rhythmicity at the mRNA level. Upper panel: Pou2f1 expression remains relatively constant across the circadian cycle in both wild-type and Per1/2 dKO liver, with no statistically significant oscillations. Lower panel: Brca1 expression similarly lacks circadian rhythmicity in both genotypes. These non-rhythmic expression patterns contrast sharply with the robust oscillations observed for Per2 and Esr1 , suggesting that constitutively expressed POU2F1(OCT-1) and BRCA1 serve as stable scaffolding factors that cooperate with rhythmically expressed PER2 to impose circadian control on Esr1 transcription. ( E ) Meta2d analysis results for Brca1 and Pou2f1 showing circadian parameters and statistical assessment. p-values confirm the absence of significant circadian rhythmicity (p > 0.01) for both genes in both wild-type and Per1/2 dKO animals. ( F ) Direct temporal comparison of Per2 and Esr1 oscillations in wild-type and Per1/2 dKO liver. Per2 (red) and Esr1 (blue) expression from GSE171975 are plotted together to visualize their temporal relationship.

    Journal: Neurobiology of Sleep and Circadian Rhythms

    Article Title: The PER2:BRCA1:POU2F1(OCT-1) ternary complex represents a multi-component scaffold model for circadian gene regulation

    doi: 10.1016/j.nbscr.2025.100141

    Figure Lengend Snippet: PER2 integrates circadian and transcriptional signals at the mouse Esr1 promoter. ( A ) Time-course expression profiles of Esr1 and Per2 mRNA showing circadian oscillations in multiple mouse tissues. Wild-type mice were entrained to 12-h light:12-h dark cycles for one week, then released into constant darkness. Tissues (white adipose tissue, liver, and kidney) were collected at 2 h intervals for 48 h mRNA expression levels (normalized counts) are plotted against circadian time (CT). Fitted cosine curves (blue for Esr1 , red for Per2 ) show that both genes oscillate with similar periodicity across tissues, with tissue-specific phase relationships. ( B ) Quantitative circadian parameters (period, phase, amplitude, and baseline expression) determined by meta2d analysis of data shown in panel A. Upper table. Circadian periods for Esr1 and Per2 in each tissue show remarkable similarity (white adipose: ∼24.2 h for both; liver: ∼23.8 h Esr1 , ∼23.5 h Per2 ; kidney: ∼24.1 h for both). Lower table. Phase analysis reveals tissue-specific phase relationships: Esr1 leads Per2 by 2–4 h in white adipose tissue and kidney, while lagging by ∼1–2 h in liver. P-values (p < 0.01) confirm statistically significant rhythmicity for both genes in all tissues. ( C ) Per2 and Esr1 circadian rhythms are abolished in Per1 −/− / Per2 −/− double knockout mice. Liver expression data from wild-type and Per1/2 dKO mice ( GSE171975 ) show that in wild-type liver, both Per2 and Esr1 exhibit robust circadian oscillations (period ∼23 h, p < 0.01). In contrast, both genes completely lose rhythmicity in Per1/2 dKO liver tissue, with expression remaining flat across all time points. Importantly, basal transcript levels are maintained despite loss of oscillation, demonstrating that Esr1 transcription per se does not require functional PER proteins, but rather that circadian modulation of expression requires clock function. ( D ) Pou2f1 and Brca1 transcripts show no circadian rhythmicity at the mRNA level. Upper panel: Pou2f1 expression remains relatively constant across the circadian cycle in both wild-type and Per1/2 dKO liver, with no statistically significant oscillations. Lower panel: Brca1 expression similarly lacks circadian rhythmicity in both genotypes. These non-rhythmic expression patterns contrast sharply with the robust oscillations observed for Per2 and Esr1 , suggesting that constitutively expressed POU2F1(OCT-1) and BRCA1 serve as stable scaffolding factors that cooperate with rhythmically expressed PER2 to impose circadian control on Esr1 transcription. ( E ) Meta2d analysis results for Brca1 and Pou2f1 showing circadian parameters and statistical assessment. p-values confirm the absence of significant circadian rhythmicity (p > 0.01) for both genes in both wild-type and Per1/2 dKO animals. ( F ) Direct temporal comparison of Per2 and Esr1 oscillations in wild-type and Per1/2 dKO liver. Per2 (red) and Esr1 (blue) expression from GSE171975 are plotted together to visualize their temporal relationship.

    Article Snippet: Circadian gene expression datasets were obtained from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database.

    Techniques: Expressing, Double Knockout, Functional Assay, Scaffolding, Control, Comparison