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Tutorial Listing

Filter by Resource:

Evidence for signaling nodes that regulate my biological process of interest [1 Use Case]
  • Transcriptomic evidence for regulation of human cell cycle genes by FGF receptor signaling 

    This tutorial can assist you in finding evidence for cell cycle genes that are regulated by human FGF receptors.

    SPP is a hypothesis generation platform that allows users to repurpose millions of biocurated 'omics data points to make high-confidence connections between signaling pathway nodes and transcriptional targets in their biological system of interest.

    Resources Used:   Signaling Pathways Project (RRID:SCR_018412); 



Evidence for signaling nodes that regulate my gene set of interest [1 Use Case]
  • Transcriptomic evidence for regulation of a mouse gene set by members of the E3 ubiquitin ligases 

    This tutorial can assist you in finding evidence for genes that are regulated by E3 ubiquitin ligases.

    SPP is a hypothesis generation platform that allows users to repurpose millions of biocurated 'omics data points to make high-confidence connections between signaling pathway nodes and transcriptional targets in their biological system of interest.

    Resources Used:   Signaling Pathways Project (RRID:SCR_018412); 



Evidence for target genes of my signaling node of interest [2 Use Cases]
  • Transcriptomic evidence for human genes that are most transcriptionally responsive to insulin receptor signaling 

    This tutorial can assist you in finding evidence for human genes that are most transcriptionally responsive to insulin receptor signaling.

    SPP is a hypothesis generation platform that allows users to repurpose millions of biocurated 'omics data points to make high-confidence connections between signaling pathway nodes and transcriptional targets in their biological system of interest.

    Resources Used:   Signaling Pathways Project (RRID:SCR_018412); 



  • ChIP-Seq evidence for regulation of a human gene set by E2F/FOX transcription factors 

    This tutorial can assist you in finding evidence for human genes that are regulated by E2F/FOX transcription factors.

    SPP is a hypothesis generation platform that allows users to repurpose millions of biocurated 'omics data points to make high-confidence connections between signaling pathway nodes and transcriptional targets in their biological system of interest.

    Resources Used:   Signaling Pathways Project (RRID:SCR_018412); 



Evidence for physiological processes in which my gene of interest is involved [1 Use Case]
  • Mouse phenotypic evidence for physiological processes regulated by Agap2 

    This tutorial can assist you in finding mammalian phenotypes that are associated with Agap2 KO manipulations in mouse models. The MMPC is a National Institutes of Health-Sponsored resource that provides experimental testing services to scientists studying diabetes, obesity, diabetic complications, and other metabolic diseases in mice.

    Resources Used:   National Mouse Metabolic Phenotyping Centers (RRID:SCR_008997); 



Evidence for genes involved in my physiological process of interest [1 Use Case]
  • Mouse phenotypic evidence for genes involved in regulation of body weight 

    This tutorial can assist you in finding experimental datasets are relevant to increased body weight in mouse. The MMPC is a National Institutes of Health-Sponsored resource that provides experimental testing services to scientists studying diabetes, obesity, diabetic complications, and other metabolic diseases in mice.

    Resources Used:   National Mouse Metabolic Phenotyping Centers (RRID:SCR_008997); 



Evidence for genes & signaling pathways that involved in my physiological events [2 Use Cases]
  • Mouse phenotypic evidence for genes involved in regulation of glucose metabolism & transcriptomic evidence for their regulation by catalytic receptors 

    This tutorial can assist you in finding evidence for gene sets and signaling pathways that are involved in regulation of glucose tolerance.

    dkNET Hypothesis Center creates an integrator tool that brings the Signaling Pathways Project (SPP) and The Mouse Metabolic Phenotyping Centers (MMPC) together to connect cellular signaling pathways and gene expression with physiological phenotypes. This one-of-a-kind tool makes it easier for researchers to find gene sets and signaling pathways relevant to mouse and human phenotypes for generating hypotheses.

    Resources Used:   Signaling Pathways Project (RRID:SCR_018412);  National Mouse Metabolic Phenotyping Centers (RRID:SCR_008997); 




  • Mouse phenotypic evidence for genes involved in regulation of insulin levels & ChIP-Seq evidence for their regulation by histone acetyltranserases 

    This tutorial can assist you in finding evidence for gene sets and signaling pathways that are involved in regulating circulating insulin level.

    dkNET Hypothesis Center creates an integrator tool that brings the Signaling Pathways Project (SPP) and The Mouse Metabolic Phenotyping Centers (MMPC) together to connect cellular signaling pathways and gene expression with physiological phenotypes. This one-of-a-kind tool makes it easier for researchers to find gene sets and signaling pathways relevant to mouse and human phenotypes for generating hypotheses.

    Resources Used:   Signaling Pathways Project (RRID:SCR_018412);  National Mouse Metabolic Phenotyping Centers (RRID:SCR_008997); 




Data related to my disease of interest [1 Use Case]
  • Type 1 Diabetes datasets 

    This tutorial can assist you in finding Type 1 Diabetes datasets.

    HIRN Resource Browser is a collection of T1D research resources including T1D datasets submitted by HIRN investigators and curators. HIRN datasets include genomics, metabolomics, epigenomics, cellomics, transcriptomics, and proteomics datasets.

    Resources Used:   Human Islet Research Network (HIRN) (RRID:SCR_014393); 



Volcano plot visualization displaying human or mouse signatures for a gene of interest [2 Use Cases]
  • Volcano plot visualization displaying human signatures for human gene ATK1 

    This tutorial can assist you in finding the volcano plot visualization displaying human signatures for ATK1.

    Appyters are a collection of web-based software applications that enable users to execute bioinformatics workflows without coding. The Gene Centric GEO Reverse Search (GCGRS) Appyter features an interactive volcano plot that visualizes signatures that maximally up- or down-regulate the input gene in the species of interest, as well as full tabulated results for download. The GCGRS Appyter serves as a hypothesis generation tool for retrospective analyses of RNA-seq data for drug repurposing efforts and many other applications.

    Resources Used:   Appyters (RRID:SCR_021245); 



  • Volcano plot visualization displaying human Type 2 Diabetes transcriptomics signatures for human gene TCF7L2 

    This tutorial can assist you in finding the Volcano plot visualization displaying human Type 2 Diabetes transcriptomics signatures for human gene TCF7L2.

    Appyters are a collection of web-based software applications that enable users to execute bioinformatics workflows without coding. The Gene Expression T2D Signatures Appyter features an interactive volcano plot that visualizes signatures that maximally up- or down-regulate the input gene in the species of interest, as well as full tabulated results for download. The Gene Expression T2D Signatures Appyter serves as a hypothesis generation tool for retrospective analyses of RNA-seq data for drug repurposing efforts and many other applications.

    Resources Used:   Appyters (RRID:SCR_021245); 



Human genetic and genomic information linked to a phenotype or disease [1 Use Case]
  • Human genetic and genomic information linked to type 1 diabetes and related traits 

    This tutorial can assist you in finding the Human genetic and genomic information linked to type 1 diabetes and related traits.

    The Type 1 Diabetes Knowledge Portal (T1DKP) enables browsing, searching, and analysis of human genetic information linked to type 1 diabetes and related traits.​ T1DKP integrates and visualizes genetic and genomic data relevant to T1D and its complications in order to spark insights into the molecular bases of disease risk and progression. The T1DKP aggregates three types of data: genetic associations, epigenomic annotations, and results from bioinformatic methods. The T1DKP resource provides researchers access to integrated and distilled genome-wide data, allowing researchers to explore genomic regions that are linked to T1D risk and to generate hypotheses about causal genes and pathways.

    Resources Used:   Type 1 Diabetes Knowledge Portal (RRID:SCR_020936); 



Evidence for a variant or a gene that is likely to be pathogenic in human diseases [1 Use Case]
  • Pathogenic evidence in human diseases for the mouse gene Acat1 

    This tutorial can assist you in finding “Pathogenic evidence in human diseases for the mouse gene Acat1”

    MARRVEL is a web tool to search multiple public variant databases simultaneously and provide a unified interface to facilitate the search process. It is used for integration of human and model organism genetic resources to facilitate functional annotation of the human genome. It is used for analysis of human genes and variants by cross-disciplinary integration of records available in public databases to facilitate clinical diagnosis and basic research.

    Resources Used:   MARRVEL (RRID:SCR_016871);