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#Task# Calculate significance of relations between random gene set of group A and B. Each group contains 500 gene sets.

HINT:

• Take only those links into account which have an higher score than 10 and only those groups which have more that 10 genes.

• Further randomize the network 222 times and save it as 'preprocessed'

• Save the results as 'Pathways_vs_Signatures.tsv'

#Input#

#!bash
BinoX -n Network.tsv -c 0.99 -i 100 -s 1234 -a Pathways.tsv -b Signatures.tsv -g 4 -o Pathways_vs_Signatures.tsv -p large -r preprocessed

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LOADING NETWORK:  
         Network.tsv                   Networkfile
                0.99                Used threshold
              335695                Imported links
                7392                Imported genes

RANDOMIZING NETWORK:
         SecondOrder                        Method
                 100                Randomizations
             3.16713  min        Expected run time

GENESET A:       289                  Pathways.tsv
GENESET B:      2392                Signatures.tsv

STATISTICAL ANALYSIS:
                   4      Min. # of genes in group
                  22     #Groups in Set A to small
                 199     #Groups in Set B to small
              441860              #tests for BinoX

WRITING RESULTS:
                        Pathways_vs_Signatures.tsv

WRITING RANDOM NETWORKFILE:
                                      preprocessed

             5.55482  min         Computation Time

When the analysis is done, BinoX will output the following files:

• file named "preprocessed*, containing information about the preprocessed network
• file named "Pathways_vs_Signatures.tsv" containing the statistical analysis

##Result##

-p is set to compact per default. If the argument is set to large it will generate the following result file:

|#1:ID|#2:NameGroupA|#3:NameGroupB|#4:p.value|#5:FDR|#6:relationType|#7:PFC|#8:id.first|#9:id.second|#10:groupSize.first|#11:groupSize.second|#12:groupLinkDegree.first|#13:groupLinkDegree.second|#14:expectedLinks|#15:sharedOriglinks|#16:sharedRndlinks| |---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---| |1|A1|B1|0.215803|0.788568|+|0.939417|0|0|161|155|25812|25766|333.302|348|73993| |2|A1|B10|0.185131|0.846836|+|0.948733|0|1|161|117|25812|21576|276.739|292|61436| |3|A1|B100|0.352901|0.629748|-|0.958564|0|2|161|44|25812|7696|98.3559|94|21835| |4|A1|B101|0.342057|0.637788|+|0.94457|0|3|161|161|25812|23871|308.536|316|68495| |5|A1|B102|0.153034|0.925865|-|0.951491|0|4|161|158|25812|34470|443.865|422|98538| |...| |..|

##Pre processed Network

Here is the output of the pre processed network file

#Download#

All described files in this section can be downloaded.

• Network.tsv
• GroupA.tsv

• GroupB.tsv

• GroupA_vs_GroupB.tsv

• preprocessed

Klick the following link to download the example files: DOWNLOAD