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Hypothesis Center
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EXPLORE INTEGRATED GENOTYPE AND PHENOTYPE ANALYSIS:
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The Signaling Pathways Project (SPP) is a FAIR data environment for hypothesis generation using public transcriptomic and ChIP-Seq datasets. It incorporates a powerful meta-analysis platform that surveys across millions of biocurated 'omics data points to make high-confidence connections between signaling pathways and their transcriptional targets. The site accommodates both standalone “idea-only” hypothesis generation as well as custom gene list upload. The Mouse Metabolic Phenotyping Centers (MMPC) is a National Institutes of Diabetes and Digestive and Kidney Diseases-Sponsored resource. MMPC can help researchers in finding mammalian phenotypes associated with specific gene manipulations in mouse models and vice versa. dkNET Hypothesis Center provides an integrator tool that will query across multiple sources. The integrator brings the SPP and 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 phenotypes for generating hypotheses.
*Please note that in this tutorial, we have chosen to show you an interactive module.
Explore Integrated Genotype and Phenotype Analysis
Tutorial That Has Been Selected For You:
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What hypothesis are you developing or what information are you looking for? Evidence for genes & signaling pathways that involved in my physiological events |
The hypothesis generation examples that you selected: Mouse phenotypic evidence for genes involved in regulation of glucose metabolism & transcriptomic evidence for their regulation by catalytic receptors |
Learning Goals:
Identify gene sets and signaling pathways relevant to mouse phenotypes for generating hypotheses
In Step 1, you will learn how to find genes relevant to physiological events of your interest. You will learn how to type a term, view the results and download the results.
In Step 2, you will learn how to use SPP, including how to upload the file to SPP, how to do SPP queries based on the hypothesis that you are developing or the evidence that you are looking for, and how to view the results.
Learn how to return to the main tutorial (from SPP tutorial back to the Integrator tutorial)
Learn how to use dkNET resources to search for mouse models or antibodies based on genes of interest for testing your hypothesis in the experiments.
STEP 1: Select a phenotype term listed at MMPC. In this tutorial we will be selecting abnormal glucose tolerance Phenotype Term Copied
Next, you will see a list of gene results from MMPC. The labels represent different contributors, i.e., MMPC, IMPC, or Monarch. You will then click “Download the csv file.” Please make sure that you have downloaded the csv file so that you can continue to the next part of the tutorial.
Download the results as a csv file
STEP 2: SUBMIT THE GENE SETS TO SPP TO FIND RELEVANT REGULATION NODES
To make it easier to walk through the tutorial, please launch a new window
SEARCH FOR MOUSE MODELS FOR YOUR EXPERIMENTS
Based on your results, you have explored genes and the signaling nodes regulating your biological process of interest. Now you can search for model organisms for your experiments to test your hypothesis. One way to find a mouse organism is through the dkNET’s Organism Resource Reports! You can view the results by switching between snippets view and table view. You can also use facet to refine your results. Click the resource name to view the summary report! Learn more about the dkNET Resource Reports here.
SEARCH FOR ANTIBODIES FOR YOUR EXPERIMENTS
Looking for antibodies for your experiments to test your hypothesis? You can use dkNET’s Antibody Resource Reports! The dkNET Resource Reports provides a detailed overview of individual research resources along with citation metrics from the biomedical literature, community feedback and alerts, and information about who is using the resource.
About
The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant 2U24DK097771-09.
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