Questions tagged [data-mining]

Initial process of data analysis often used to define the hypothesis for subsequent analysis

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How to investigate the correlation between transcript and protein abundance?

Our study shows that gene A knockout will down-regulate cell cycle-related genes in some cell lines. My aim is to understand whether cell cycle-related genes are down regulated on the transcriptional ...
Wang Ming's user avatar
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Is there a way antiSMASH can be used to screen a large number of genomes just for one type of biosynthetic gene cluster?

When we use antismash command with the genome sequence file as follows: antismash GCA_002095535.1_ASM209553v1_genomic.gbff it screens the genome for all the ...
snap_v's user avatar
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RNA-seq gene/transcript read counts database for Mouse

Is there any RNAseq gene/transcript read count database for the mouse? I already know about ARCHS4, looking for some other source. Thank you
Priya's user avatar
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Are these standard species abbreviations and how to look up others?

Reactome uses a three letter code for each species which are listed below. Are the letter codes used by Reactome a standard? If so is there a web page or download file that can validate the code and ...
Guy Coder's user avatar
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Viral Load and Antiretroviral Therapy Dataset

My project is on Mathematical Modeling of the relationship between viral load and antiretroviral therapy. Its purely an academic investigation which is exploratory in nature. Question I am seeking a ...
Obinoscopy's user avatar
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How do I get the gene order from genbank file using gene names?

I have a list of gene names which I know are present in a genbank file. I want to order these genes based on the order of their presence in the genbank. This should also account for whether they are ...
AudileF's user avatar
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How to measure or assign hydrophobicity score values to individual amino acids of a PDB structure?

I want measure the hydrophobicity of each amino acid within a PDB structure file. Since I have the PDB file I want to consider the 3D information, rather than sequence-only measures such as GRAVY. I ...
Aalawlx's user avatar
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2 votes
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Is there a way to retrieve ENSEMBL IDs from a search query?

I would like to be able to batch download FASTA files from ENSEMBL. I normally would use the API to download them from the ENSEMBL gene IDs. However, the IDs aren't ones I know, only ones I would get ...
TW93's user avatar
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Minfi returning incorrect beta values

UPDATE: I found the solution. I was using normalized values and GEO was using raw beta values. I'm trying to link GEOquery and minfi. Specifically I want to obtain beta values from the idat files ...
Ezra Bekele's user avatar
2 votes
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Using data mining of papers in order to derive genomic connections [closed]

Are there any examples of researchers data mining articles and papers (e.g., from pubmed or google scholar) in order to derive relations between genes and diseases?
0x90's user avatar
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