User: Benni

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Benni10
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Posts by Benni

<prev • 12 results • page 1 of 2 • next >
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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 5 weeks ago by Benni10 • updated 5 weeks ago by Elisabeth Gasteiger1.0k
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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 7 weeks ago by Benni10 • updated 7 weeks ago by b.nota2.2k
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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 weeks 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 9 weeks 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 9 weeks 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 4 months ago by Benni10 • updated 4 months ago by natasha.sernova2.3k
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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 4 months ago by Benni10
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Map GO Terms to Protein/Gene of E.coli
... I have a list of Proteins/Genes and I want to find out, which GO Terms (especially Cellular Component) belong to every Protein. Is there maybe a simple .csv file available online? I looked at Gene Ontology, Uniprot and EcoCyc, but I couldn´t find such a list. Alternatively there could be a online to ...
e.coli go written 5 months ago by Benni10 • updated 5 months ago by EagleEye2.7k
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Cytoscape ClusterMaker2. Use Expression Matrix, Network needed?
... I want to use the Cytoscape App ClusterMaker2 on data from an expression matrix (rows =genes, columns = conditiones). But I think I need an Network to use ClusterMaker2. How can I create a Network out of my matrix? Or is there a way to use ClusterMaker2 on an imported table? Thanks UPDATE: I found ...
clustermaker2 expression matrix cytoscape written 5 months ago by Benni10
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Cluster Protein abundance matrix only on similar expression shape to find "coexpressed" Proteins
... I have a Matrix with Proteins in the rows and conditions in the columns. The values are relative changes in the Protein abundance compared to a standard condition. E.g. 1 -> no change; 1,5 -> 50% more; 0,5 -> 50% less The values range from 0 up to 6000, but are mostly in the range around on ...
cluster protein coexpression written 5 months ago by Benni10 • updated 5 months ago by Jean-Karim Heriche7.3k

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