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Principle Component Analysis: Gene Expression

Introduction

In this analysis a microarray gene expression dataset will be analysed, attempting to obtain an understanding on gene expression among type 2 diabetic and non-diabetic individuals between two cohorts (organ donors vs partially pancreatectomized patients).

Context

This dataset is extracted from IMIDIA Biobank project (Improving beta-cell function and identification of diagnostic biomarkers For treatment monitoring in diabetes)which was launched on February, 2010[1].

Important Informtaion:

βšͺ Source: IMIDIA biobank data πŸ”— [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE76896]

βšͺ GEO Accession Number: GSE76896

βšͺ Platform: Affymetrix Human Genome U133 Plus 2.0 Array

βšͺ Sample Details: pancreatic islet samples from organ donors and partially pancreatectomized patients

The dataset "GSE76896.ALL.csv" contains the prepared data which contain the gene id, gene expression data, disease status (T2D vs ND, where T2D is Type 2 Diabetes and ND is Non-Diabetic), sample number (GSM0000000) and cohort type (rgan donors vs partially pancreatectomized patients).

References:

[1] GmbH, A. (2021). IMIDIA - European compined excellence in diabetes research. Retrieved 3 February 2021, from https://www.imidia.org/

[2] Solimena, Michele et al. β€œSystems biology of the IMIDIA biobank from organ donors and pancreatectomised patients defines a novel transcriptomic signature of islets from individuals with type 2 diabetes.” Diabetologia vol. 61,3 (2018): 641-657. https://doi:10.1007/s00125-017-4500-3

[3] Khamis, A., Canouil, M., Siddiq, A., Crouch, H., Falchi, M., Bulow, M. V., Ehehalt, F., Marselli, L., Distler, M., Richter, D., Weitz, J., Bokvist, K., Xenarios, I., Thorens, B., Schulte, A. M., Ibberson, M., Bonnefond, A., Marchetti, P., Solimena, M., & Froguel, P. (2019). Laser capture microdissection of human pancreatic islets reveals novel eQTLs associated with type 2 diabetes. Molecular metabolism, 24, 98–107. https://doi.org/10.1016/j.molmet.2019.03.004

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