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Using NCBI Gene database, I retrieved list of 7015 protein which are implicated in autism pathogenesis. This list includes tax-ID, organism name, symbol, aliases, map location, chromosome, genomic nucleotide accession version, start position on genomic accession, end position on genomic accession, orientation, exon count and OMIM). Among these 7015, 1144 proteins are involved in neurodevelopmental functions. I want to know that how many of these 1144 proteins are functionally similar to 7015 proteins? Is there a method to query 1144 proteins against 7015 proteins and group them based on structural similarity/ function similarity/ gene family?. Since I have large set of proteins, I am trying to understand if sub-set of proteins share similar function with this large set of proteins.

Thanks

Priya

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  • $\begingroup$ Please edit your question and tell us what kind of data you have. Are these known, annotated proteins? From what species? Do you just have a list of protein fasta sequences? Gene sequences? RNA? Do you instead have a list of protein accessions? $\endgroup$
    – terdon
    Mar 27 '20 at 12:24
  • $\begingroup$ @terdon I have edited the question $\endgroup$ Mar 27 '20 at 13:03
  • $\begingroup$ Thank you! So these are human sequences? You mention OMIM, but it is better to be sure. $\endgroup$
    – terdon
    Mar 27 '20 at 13:04
  • $\begingroup$ @terdon Yes I have list of protein names (not sequences) from Homo sapiens. Thanks $\endgroup$ Mar 28 '20 at 9:28
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I suggest you give DAVID a try. Specifically, their Functional Annotation tool. Just enter your list of protein IDs, and it will return groups of proteins where particular GO functions are overrepresented.

screenshot of the DAVID page

This should at least help you start categorizing your list into functional groups.

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  • $\begingroup$ Thanks. Is there a way to analyze whether if 2 proteins belong to the same protein family or not? $\endgroup$ Apr 3 '20 at 5:16
  • $\begingroup$ @PriyadarshiniThirunavukkarasu just look at the protein's annotations. $\endgroup$
    – terdon
    Apr 3 '20 at 8:53

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