Questions tagged [networks]

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3
votes
2answers
232 views

help with CRCmapper

I'm using CRCmapper on my data. There are several modules in the tool. I've used exactly instructed in the usage. Commands used: ...
4
votes
1answer
69 views

Using signal peptide and the expression levels of signal recognition particle in secretome analysis

I have not found any work which investigates assessment of differences in levels of secreted proteins by taking advantage of differential expression of the genes which mediate the secretory pathway. ...
3
votes
2answers
76 views

Can gene co-expression networks be used to help identify differentially expressed genes?

In my RNAseq dataset of differentiated stem-cell lines, some samples have far fewer significantly differentially expressed genes than others. QC shows that this is because there are way fewer reads ...
6
votes
3answers
250 views

Secretome and membrane receptor profiles

I am looking the secretome profile and the membrane receptor profile for a given cell type. In my specific case, this should be the secretome and outer membrane receptor profiles of dorsal root ...
3
votes
1answer
112 views

Building network for biomarker interaction analysis

I am looking for advice on how to best approach a problem I am faced with. I have a dataset of numerous degradative biomarkers, clinical information and various other measures (from clinical trials)....
6
votes
2answers
1k views

How to select a cutoff for interaction confidence in STRINGdb?

I have a list of 100 genes that are called as hits in a genetic screening. I want to have a network of the interactions between the proteins of these 100 genes. I am using both STRINGdb web and its R ...
5
votes
1answer
651 views

What are the ways to process a list of differentially expressed genes?

We are studying six different human macrophage/dendritic cell types isolated from healthy skin. They all differ from each other in a few cell surface markers. We are interested in the characteristics ...
10
votes
4answers
725 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....
10
votes
1answer
1k views

How to manipulate protein interaction network from String database in R?

How can I manipulate protein-interaction network graph from the String database using STRINGdb bioconductor package and R? I have downloaded the whole graph for ...
6
votes
1answer
2k views

How to select a power for a scale-free topology network

In a weighted gene co-expression network analysis (using WGCNA), the soft-threshold power is recommended as a noise filtering. It consists on raising the correlation to a certain number. To decide ...

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