User: Benni

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Benni20
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2 months ago
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10 months, 3 weeks ago
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Posts by Benni

<prev • 18 results • page 1 of 2 • next >
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Data on translational efficiency of genes in e.coli?
... I´m searching for existing data on translational efficiency of genes in e.coli. The efficiency is influenced by the codon bias, the Shine-Dalgarno sequence etc.. Maybe there is simulation data or even experimental data? The best case would be a numerical value for each gene. I also search for mRNA- ...
translation e.coli written 11 weeks ago by Benni20
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Comment: C: Annotate Protein List with COG / E.coli COG table
... EcoCyc doesn´t support COG annotation. How do I get the table in .csv and not .html? ...
written 11 weeks ago by Benni20
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Annotate Protein List with COG / E.coli COG table
... I have a protein list of escherichia coli. I want to annotate this list with the COG terms. Is there an online tool for that or is there a way to get a annotated gene/protein list for e.coli? I don´t want to run a sequence blast, since there should be already a database for e.coli proteins? ...
cog written 11 weeks ago by Benni20
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E.coli RNA-seq Gene Expression Collection
... I´m searching for a gene expression matrix over different conditions based on RNA-seq data. Is there a already a collected matrix of several experiments? ...
e.coli rna-seq written 5 months ago by Benni20 • updated 5 months ago by Biostar ♦♦ 20
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Comment: C: Compare two gene co-expression networks/correlation matrizes
... Thanks for your inputs. I found "differential network analysis", which seems to be a common tool for such a problem. Can anyone recommend this? ...
written 5 months ago by Benni20
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Compare two gene co-expression networks/correlation matrizes
... Is their a way to compare two gene co-expression networks or correlation matrizes of the same genes? My idea was to just compare the pearson correlation values of the gene pairs eg. check for differences in the correlation matrix. But a pearson correlation of 0.7 could mean something different in th ...
gene network correlation written 5 months ago by Benni20 • updated 5 months ago by Jean-Karim Heriche11k
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Get the Protein-Accession - GO-ids mapping for every Protein in e.coli K12
... I only found the annotation file for e.coli from EcoCyc: "gene_association.ecocyc" But I can´t open the file. I just need a simple text file, that maps ProteinAccession to all GO-ids. SOLVED: I just renamed the file to .gaf since it already is in the .gaf format. ...
gene ontology protein go written 6 months ago by Benni20 • updated 6 months ago by Elisabeth Gasteiger1.1k
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Correlation Metric for Gen Expression Matrix that is robust against noise?
... Currently I´m using Pearson, but is there a more robust distance metric? I want to calculate the correlation between two genes over several conditions. ...
gen expression correlation written 6 months ago by Benni20 • updated 6 months ago by b.nota3.5k
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Python implementation for enrichment of terms on already annotated genes
... I have a matrix like this: 1. Column = Genes 2. Column = Cluster gene belongs to 3. Column = Annotation1 4. Column = Annotation2 5. Column = Annotation3 A new matrix would look like this: 1. Column = Cluster 2. Column = Annotation Terms and their pValue. It checks one column and one te ...
gene set enrichment written 7 months ago by Benni20
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Calculate gene-gene distance on the circular genome of e.coli
... I have a gene annotation with: Left-End-Direction, Right-End-Direction and Transcription Direction. To get the coordinate of the gene, I would take the Left- or Right-End-Direction based on the Transcription Direction. So I have the transcription start as the coordinate. But I can´t simply subtract ...
gene e.coli dna written 7 months ago by Benni20

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