Gene Expression File And Gene Regulatory Network

Question

[someone]

Hello, I wrote a program that receive gene expression file (.SOFT) and give Gene regulatory network (inference it)

click here to see the definition of SOFT file

click here to see samples of .SOFT file

Now my problem is how I can test my program? I could not find any website that give me gene expression file with their Gene regulatory network to use it for the test?

any help please?

Answer 1

[Sudeep]

You can check if any of the datasets from dream challenge will work for you, usually they will also make the gold standard network available after sometime. I am not an expert, but I have read in publications about people generating synthetic gene expression data with a network topology behind it, perhaps you could also look into what they are doing, may be something like this one

Answer 2

[pegahtv]

DERAM is the best one. It provides you with several artificial and real datasets. DREAM5 has 3 datasets, one artificial and 2 real. DREAM4 is artificial. The networks and the expression are available in the website.
Anoter dataset is the STATSEQ, which is provided by Alberto de la Foente. It is also artificial data.

[someone]

Thank you , but in DREAM5 I could not find network , only dataset .Could you please give me the link directly ?

[pegahtv]

http://www.nature.com/nmeth/journal/v9/n8/full/nmeth.2016.html#supplementary-information

Supplementary Data 1 (38M) contains DREAM5 network inference challenge (expression data, experiment descriptions, gene names, gold standards and evaluation scripts)

[someone]

Thank you for your help and sorry for my ignorance. It is the first time for me to deal with that. I have downloaded the file and I see many files with extension .tsv . I don’t know How I use it , I am still could not find the data with their network. I will appreciate your help. Thank you.

[pegahtv]

The network is in the directory of gold standard.
for example in DREAM5_NetworkInference_GoldStandard_Network1.tsv, the first column is the regulator, the second column is target. you can ignore the last column.
in net1_gold_standard_signed.tsv, the last column is the sign of the interaction, i.e. activation or inhibition.
in net1_expression_data.tsv, the columns are the genes, the rows are the experiments. in net1_chip_features.tsv, shows what is each experiment. for example, experiment in the line 521, gene #162 is deleted, and gene #164 is over-expressed. the last column shows the replicate. There are often two to three replicates for each experiments.

[someone]

Thank you very much Could you tell me please how I can visualize the network ? (represent as image)

[someone]

skip my previous question please , I find GeneNetWeaver That can visualize the network , but the problem is that the data of gene expression are very large , and I don't know How I can delete some data in net1_expression_data.tsv to give me a small network . GeneNetWeaver provide creating sub-network but it does not provide gene expression that related to this sub-network. Could you help me please?

[pegahtv]

It is impossible that GeneNetWeaver does not provide expression data. They have generated data for DREAM also with GeneNetWeaver. check it again.
For data of DREAM, simply choose part of the network and consider the expression of the chosen genes.

[someone]

Thank you

1-These steps that I followed: Run GeneNetWeaver => open =>DREAM5_NetworkInference_GoldStandard_Network1.tsv and after the network load I double-click on it to see the option => choose Extract subnetwork => choose 10 as size of subnetwork then Extract Then when I double-click on my subnetwork I see only these options: Rename , View , Anonymize gene names , Extract subnetwork , Generate Kinetic Model , Delete and Save as. So, I could not find how I can found the gene expression that related to that subnetwork!

2-When I tried to delete some data in net1_expression_data.tsv and then visualize it ,I got error.

I need small network with their expression data, could you do it that for me please for one file and then I do it for the reset files? Thank you very much

[pegahtv]

It is like this: you choose a set of genes, you choose the respective expression profiles from the file net1_expression_data.tsv, you choose the edges that contain only these genes from DREAM5_NetworkInference_GoldStandard_Network1.tsv, you plot the network with graphviz.
I cant check GeneNetWeaver for you. But the basic is that it takes a network from you, and it generates a NEW network for you which has a similar topology as the input network. Then, it uses differential equations to make expression data from this new network (should be the Generate Kinetic Model option that you have mentioned).
As you have both the network and the expression, why are you still trying to use GeneNetWeaver?
use Graphviz to visualize the network.
Please pay attention that only a subset of genes act as regulator. You might have several thousand genes, but only some hundred are regulators. The set of genes that you choose should be a mix of regulators and targets. The list of regulators is the first column in the gold standard. It is also saved separately in one of other files ( you can find it if u check).

[someone]

Thank you very much