Examples

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 Network Miner, run these jobs and see the results!

• 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).

• 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).

• 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).

• 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).

• 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).