Count matrices plotting

Question

[NIkita]

Hi there! I am new in bioinformatics (dummy) and i have 13 count matrices from this article (https://diabetesjournals.org/diabetes/article/69/10/2157/16135/Integrated-Skin-Transcriptomics-and-Serum) and i need to highlight the IL33 and IL1RL1 genes expression. How should i parse these txt files? In the internet guides i have only found how to parse mtx or csv files. As i understood, i should read these files by pandas and than remake them into another format. Maybe you can advice me some nice tutorials? AI cant help me :( Thank you! dataset link: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE143735

Answer 1

[Mensur Dlakic]

Don't know if there is an automated way of doing it, but you can always import these counts files into Excel. They are tab-delimited files and at least on a PC they import directly. Once you open them, search for ENSG00000137033 (IL33) and ENSG00000115602 (IL1RL1). Numbers on the far-right (7th column) contain counts for each of these genes.

[NIkita]

Thanks for the reply! One man said my this is bulk data. Is he right?

[GenoMax]

Based on the GEO link you included above that is correct.

Bulk RNA-seq analysis revealed extracellular matrix (ECM) related genes up-regulated in Healers, including MMP2 as well as implication of IFNy and IL13 as upstream regulators.

[NIkita]

Thanks a lot!