All Questions
12 questions
-5
votes
0
answers
18
views
How to find hub genes when your input DEGs are more than 4000 because it takes so long to calculate modules
I tried extracting 250 hub genes from 4750 DEGs, but it takes too much time while calculating modules from 11 methods and coudn't proceed further.
1
vote
0
answers
15
views
Pathway enrichment analysis - minimum amount of proteins?
I have 6 proteins significantly associated with an outcome and have done a pathway enrichment analysis (PEA) with them (in both Enrichr and R with the same outcome). However, I wonder if that is too ...
- 11
2
votes
2
answers
179
views
How to get the nucleotide sequence for protein NCBI accession code, programatically?
It is a lot easier in my work to do blast searches against protein databases when I can, since I work with distantly related organisms. But sometimes, I need to work with the actual nucleotide ...
- 1,027
2
votes
2
answers
48
views
Is there a publication database or search engine offering geneID or UniProtID correlation?
Do we have a publication database or search engine that offers geneID or UniProtID correlation?
For example, I search "IPS cells" -> I want to know what genes or proteins are under active ...
- 329
0
votes
1
answer
458
views
Seurat DE t.test
I am new to the Seurat package and was looking at the tutorials on the Seurat website and am just curious to know if there is any way to perform a t.test for the expression of a specific gene between ...
- 31
2
votes
0
answers
327
views
How to get the GO information for all the human genes?
I would like to retrieve a list of all the human genes and their proteins’ functional classification.
The Gene type attribute on ensembl.org is not specific ...
- 1,447
1
vote
1
answer
191
views
From ensembl id to protein structure
Forgive me if this question is too trivial.
I have a list of ~700 Ensembl ID. I need to extract the protein structures of each Ensembl id. How can I do this?
Is there any script(python, R) so that ...
- 27
0
votes
1
answer
418
views
How to calculate Moreau-Broto autocorrelation, Moran autocorrelation, Geary autocorrelation from protein (amino acid) sequences?
I want to code Moreau-Broto autocorrelation, Moran autocorrelation, Geary autocorrelation in Python 3.6 from the scratch for amino acid sequences without using any package. Unfortunately, I have not ...
- 123
3
votes
2
answers
283
views
Why are some of the gene peptides returned by biomaRt missing an asterisk in the end?
Note: this question has also been asked on BioStars
I am getting peptides using biomaRt library in R for the gene 'BRCA1'. 27 different aminoacid sequences are returned, and 12 of those have an ...
- 305
6
votes
3
answers
106
views
Do any publicly available databases detail protein structure and functional domains?
I am interested in finding a database that takes a gene or protein name as input (possibly with the option to specify transcript) and gives information about the protein's functional domains in terms ...
- 63
4
votes
4
answers
162
views
What are the standard ways to visualize protein-protein or gene-gene interactions?
I would like to visualize this interaction list. Is there an online/web based way to do it? Is there a way to analyze the data?
Assuming I have exported the list into lines such as:
...
- 1,447
10
votes
4
answers
890
views
How can I build a protein network pathway from a gene expression quantification file?
Assume I have found the top 0.01% most frequent genes from a gene expression file.
Let's say, these are 10 genes and I want to study the protein protein interactions, the protein network and pathway....
- 1,447