====== Examples ======

[[http://babelomics.bioinfo.cipf.es/functional.html|{{:online_example.png}}]]


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Here there are some examples of ranked lists of genes. These examples are **available at the Network Miner web tool as online examples**. Go to [[http://babelomics.bioinfo.cipf.es/functional.html|Network Miner]], run these jobs and see the results!



==== Example 1 ====
  * Select your data -> BD-GWASplink.txt
  * Select your seed datalist (optional) -> BD-associatedgenesUniprot.txt
  * Select interactome:
        * Specie -> HSA
        * Level of confidence -> curated (ppis detected by two methods)
  * Order your list -> Ascending
  * Maximum number of external proteins -> 1
  * Select threshold of significance (p-value) -> 0.05
  * Job name: **Genome-Wide Association Study in Bipolar Disorder** 
  * Job description: Genotypic data comes from the Wellcome Trust Case Control Consortium. GWAS was performed using the basic association test of Plink toolset. Here, genes were ranked acording the adjusted p-value (BD-GWASplink.txt). Moreover, genes previously associated with Bipolar Disorder obtained from Uniprot database are used as seed genes (BD-associatedgenesUniprot.txt).


==== Example 2 ====
  * Select your data -> FA-differentialExpression-statistic.txt
  * Select your seed datalist (optional) -> Empty
  * Select interactome:
          *   Specie -> HSA
          *   Level of confidence -> all (all ppis)
  * Order your list -> Descending
  * Maximum number of external proteins -> 1
  * Select threshold of significance (p-value) -> 0.05
  * Job name: **Genes Down-regulated in Fancony Anemia**
  * Job description: Expression data comes form a recent study of the gene expression in Fancony Anemia (Vanderwerf et al. 2009; GEO:GSE16334).  Differential gene expression of control versus case samples was carried out using the Limma option in Differential expression analysis. Here, genes are ranked according the statistic (FA-differentialExpression-statistic.txt).

==== Example 3 ====
  * Select your data -> FA-differentialExpression-statistic.txt
  * Select your seed datalist (optional) -> Empty
  * Select interactome:
          *   Specie -> HSA
          *   Level of confidence -> all (all ppis)
  * Order your list -> Ascending
  * Maximum number of external proteins -> 1
  * Select threshold of significance (p-value) -> 0.05
  * Job name: **Genes Up-regulated in Fancony Anemia**
  * Job description: Expression data comes form a recent study of the gene expression in Fancony Anemia (Vanderwerf et al. 2009; GEO:GSE16334).  Differential gene expression of control versus case samples was carried out using the Limma option in Differential expression analysis. Here, genes are ranked according the statistic (FA-differentialExpression-statistic.txt).



==== Example 4 ====
  * Select your data -> K562.txt
  * Select your seed datalist (optional) -> Empty
  * Select interactome:
          *   Specie -> HSA
          *   Level of confidence -> curated (ppis detected by two methods)
  * Order your list -> Ascending
  * Maximum number of external proteins -> 1
  * Select threshold of significance (p-value) -> 0.05
  * Job name: **Essential genes in cancer cell line K562**
  * Job description: This data comes form a recent study of the gene essentiality in different cancer cells (Luo et al. 2008). Here, genes are ranked according the RIGER, which accounts gene essentiality (K562.txt).

==== Example 5 ====
  * Select your data -> JURKAT.txt
  * Select your seed datalist (optional) -> Empty
  * Select interactome:
          *   Specie -> HSA
          *   Level of confidence -> curated (ppis detected by two methods)
  * Order your list -> Ascending
  * Maximum number of external proteins -> 1
  * Select threshold of significance (p-value) -> 0.05
  * Job name: **Essential genes in cancer cell line JURKAT**
  * Job description: This data comes form a recent study of the gene essentiality in different cancer cells (Luo et al. 2008). Here, genes are ranked according the RIGER, which accounts gene essentiality (JURKAT.txt).