Multi omics data

[Sandhya]

I am new to Xena and have recently embarked on a journey into the realm of cancer omics data analysis. Due to my non-biological background, I find it challenging to comprehend the TCGA (The Cancer Genome Atlas) data, especially in light of a recent paper titled "A Multimodal Graph Neural Network Framework for Cancer Molecular Subtype Classification," which utilized Xena data. I am currently struggling to understand the preprocessing steps applied to TCGA data and how Xena obtained the reported results. Additionally, I am uncertain about which types (TYPE->SUBTYPE IN TCGA ) of experiments are suitable for molecular subtyping. I kindly request assistance and guidance in my research endeavors, and I am open to the possibility of someone serving as a mentor to help me acquire domain knowledge.

Iam looking for recommended resources, such as links, courses, journals, or anything that could be beneficial for my research, to gain domain knowledge in cancer data

[Mary Goldman]

Hello,

It appears that the authors of the paper you mention used data from the TCGA Pan-cancer project downloaded from Xena. We obtained this data directly from the project with no-to-minimal processing (click on a dataset here to see any wrangling steps performed by our team: https://xenabrowser.net/datapages/?cohort=TCGA%20Pan-Cancer%20(PANCAN) )

You can read more about the TCGA Pan-cancer project and how they processed their data in their flagship paper here: https://www.cell.com/cell/fulltext/S0092-8674(18)30302-7

Please let us know if you have any questions.

Best,

Mary

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Mary Goldman (she/her), Design and Outreach Engineer 

UCSC Xena

UC Santa Cruz Genomics Institute

Revealing life's code

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[SANDHYA GUBBALA]

i am unable to figure it out what are those values mens for CNV starting ending values are given what is value means how they got that and  like that i want domain knowledge of all iam literally new in cancer research and bioinformatics can you suggest me sources / course any thing   which can help me further to understand the data

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Thanks and Regards,

G Sandhya

PhD Scholar

Indian Institute of Information Technology Sri City

[Mary Goldman]

Hello,

In our tutorials we point folks to these two resources: https://www.ebi.ac.uk/training/online/courses/functional-genomics-i-introduction-and-design/what-is-functional-genomics/ and https://connect.springerpub.com/content/book/978-0-8261-6868-9/chapter/ch01

On a personal note, I have also heard good things about these resources: https://www.coursera.org/learn/introduction-genomics#syllabus and https://www.youtube.com/watch?v=yuJfie9J8S0. Additionally, I have found BioStars to be useful place to ask questions: https://www.biostars.org/