Answers.Body: <p>I suggest you give <a href="https://david.ncifcrf.gov/" rel="nofollow noreferrer">DAVID</a> a try. Specifically, their <a href="https://david.ncifcrf.gov/summary.jsp" rel="nofollow noreferrer">Functional Annotation</a> tool. Just enter your list of protein IDs, and it will return groups of proteins where particular GO functions are overrepresented.</p>
  
  <p><a href="https://i.sstatic.net/kkbI7.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/kkbI7.png" alt="screenshot of the DAVID page"></a></p>
  
  <p>This should at least help you start categorizing your list into functional groups. </p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-03T05:16:18.023Z
Answers.Text: Thanks. Is there a way to analyze whether if 2 proteins belong to the same protein family or not?
Answers.UserDisplayName: Priyadarshini Thirunavukkarasu
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-03T08:53:33.633Z
Answers.Text: @PriyadarshiniThirunavukkarasu just look at the protein's annotations.
Answers.UserDisplayName: terdon
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-03-28T13:08:48.700Z
Answers.LastActivityDate: 2020-03-28T13:08:48.700Z
Answers.UserDisplayName: terdon
Body: <p>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.</p>
  
  <p>Thanks</p>
  
  <p>Priya</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-03-27T12:24:38.680Z
Comments.Text: 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?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-03-27T13:03:16.373Z
Comments.Text: @terdon I have edited the question
Comments.UserDisplayName: Priyadarshini Thirunavukkarasu
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-03-27T13:04:46.237Z
Comments.Text: Thank you! So these are human sequences? You mention OMIM, but it is better to be sure.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-03-28T09:28:06.587Z
Comments.Text: @terdon Yes I have list of protein names (not sequences) from Homo sapiens. Thanks
Comments.UserDisplayName: Priyadarshini Thirunavukkarasu
Tags: <structural-variation><gene-ontology><sequence-homology><multi-omics><paralogs>
Title: Analyzing proteins based on sequence similarity
ThreadText: # Analyzing proteins based on sequence similarity
  
  (Asked by: username_0 on 2020-03-27)
  
  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
  
  **Tags:** structural-variation, gene-ontology, sequence-homology, multi-omics, paralogs
  
  > **Comments:**
  > **username_1**: 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?  
  > **username_0**: @username_1 I have edited the question  
  > **username_1**: Thank you! So these are human sequences? You mention OMIM, but it is better to be sure.  
  > **username_0**: @username_1 Yes I have list of protein names (not sequences) from Homo sapiens. Thanks  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2020-03-28. Score: 2
  
  I suggest you give [DAVID](https://david.ncifcrf.gov/) a try. Specifically, their [Functional Annotation](https://david.ncifcrf.gov/summary.jsp) 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](https://i.sstatic.net/kkbI7.png)](https://i.sstatic.net/kkbI7.png)
  
  This should at least help you start categorizing your list into functional groups.
  
  > **Comments:**
  > **username_0**: Thanks. Is there a way to analyze whether if 2 proteins belong to the same protein family or not?  
  > **username_1**: @username_0 just look at the protein's annotations.  
  
  ---
  
  