User: Benni

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Benni10
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Posts by Benni

<prev • 15 results • page 1 of 2 • next >
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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 4 weeks ago by Benni10 • updated 4 weeks ago by Biostar ♦♦ 10
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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 4 weeks ago by Benni10
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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 weeks ago by Benni10 • updated 5 weeks ago by Jean-Karim Heriche7.9k
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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 10 weeks ago by Benni10 • updated 10 weeks 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 12 weeks ago by Benni10 • updated 12 weeks ago by b.nota2.3k
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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 3 months ago by Benni10
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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 3 months ago by Benni10
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Using Random Forest as a supervised cluster algorithm?
... I want to cluster genes based on a expression matrix and annotation. With unsupervised learning algorithms (Hierachical, K-means,...), the clusters are only based on the correlation of the gen expression. So my idea was to supervise the learning with annotation data, which could lead to more meaning ...
cluster omics data random forest learning written 3 months ago by Benni10
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(Closed) E.coli: Does the protein mass per cell change over different conditiones?
... For the data analysis of my Proteom experiment, I´m searching for evidence/papers that investigate the change of the total Protein mass in E.coli over different conditiones. Is there a change, or is the Protein mass per cell constant? Maybe a E.coli professional can give a hint? ...
e.coli protein written 5 months ago by Benni10 • updated 5 months ago by natasha.sernova2.4k
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List of Protein Complexes and their Proteins in E.Coli
... I´m searching for a list of Protein complexes in E.coli with their involved Proteins. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4344305/#pcbi.1004107.ref013 This publication uses '285 “gold standard” protein complexes identified by EcoCyc'. So there should be a list of those Protein Complexes an ...
protein complex e.coli written 6 months ago by Benni10

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