What type of cell do I have

Question

[thomasbalvert]

Hello everyone.

I'm doing a school assignment. I've got some mRNA and I have found 35 genes. How can I know from which celltype these genes are?

Hope you can help me!

[Manvendra Singh]

I am sorry, I am just trying to be funny, you can also give the same answer who ever had asked you

These genes are from same cell type, where you got your mRNA from. :)

Answer 1

[Ram]

kanwarjag is right. Unless the assignment has been designed to contain one or more genes that map only to a specific gene in a specific organism (which is highly unlikely), finding which cell line they originate from is difficult. There are too many false positives and false negatives to sort through and there is no way to ensure you have the right result at the end.

Answer 2

[russhh]

is this a thought experiment, or do schools in the Netherlands really do RNASeq experiments?

Suppose these are from human tissue and you had a panel of tissues that had been assayed for those same 35 genes under the same conditions, I'd say you could compare the similarity between the expression level in your mystery set to the tissue panel and identify some candidate tissues that your celltype might be most similar to. You'd have to do more experiments though

Answer 3

[onuralp]

Most genes are ubiquitously expressed across different cell types. However, their expression pattern may vary depending on a number of factors, which can be used to identify cell type or tissue specific features of genes.

There are some sequence features (e.g., alternative splicing) that can be informative about tissue specificity. However, I do not see any point why you would be asked for a school project to develop a computational method to infer tissue specificity based on sequence features, because it is not trivial.

What you can do is to compare the expression profiles of genes in your list to a previously assessed expression profiles across a number of tissues, and then calculate the probability that the expression profile resembles the profiles from the "reference" panel. You can read up on how to calculate similarity between two expression profiles. Based on some reasonable cut off, you can determine the tissue or cell type (if available) from which the measurement is likely to come from.

Answer 4

[kanwarjag]

I will be surprised if you can find out with this information. You may like to check with your instructor what exactly is needed and then search around or talk to your classmates.