Journal: International Journal of Molecular Sciences

Article Title: Genome-Wide Gene-Set Analysis Identifies Molecular Mechanisms Associated with ALS

doi: 10.3390/ijms24044021

Figure Lengend Snippet: The 24 significant gene sets that are associated with ALS, sorted by their FDR (FDR cut-off < 0.05). Each significant gene set is described by its FDR, degree i.e., number of undirected edges within the ALS enrichment network containing gene sets with FDR < 0.25, and their corresponding number of genes. The vast majority of the significant gene sets are highly popular. FDR: false discovery rate.

Article Snippet: The BioCarta mPR (membrane progesterone receptor) pathway ( p -value = 6.27 × 10 − 5 , FDR = 0.009), which involves the oocyte maturation by progesterone, is the highest ALS-associated gene set among the developmental-related gene sets, along with the immune-response BioCarta CSK pathway ( p -value = 5.02 × 10 − 5 , FDR = 0.009), covered in the previous section.

Techniques:

Journal: International Journal of Molecular Sciences

Article Title: Genome-Wide Gene-Set Analysis Identifies Molecular Mechanisms Associated with ALS

doi: 10.3390/ijms24044021

Figure Lengend Snippet: The 26 significant gene sets that are related to immune response, sorted by their FDR (FDR cut-off < 0.24 and p -value < 0.043). Each significant immune-response gene set is described by its p -value, FDR, degree, i.e., number of edges within the immune-response ALS enrichment network containing gene sets with FDR < 0.25, and their corresponding number of genes. We note that the vast majority of significant gene sets are highly popular. FDR: false discovery rate.

Article Snippet: The BioCarta mPR (membrane progesterone receptor) pathway ( p -value = 6.27 × 10 − 5 , FDR = 0.009), which involves the oocyte maturation by progesterone, is the highest ALS-associated gene set among the developmental-related gene sets, along with the immune-response BioCarta CSK pathway ( p -value = 5.02 × 10 − 5 , FDR = 0.009), covered in the previous section.

Techniques:

Journal: International Journal of Molecular Sciences

Article Title: Genome-Wide Gene-Set Analysis Identifies Molecular Mechanisms Associated with ALS

doi: 10.3390/ijms24044021

Figure Lengend Snippet: The significant first neighbors of the BioCarta mPR and Shh pathways, sorted by their FDR (FDR cut-off < 0.25 and p -value < 0.05). FDR: false discovery rate.

Article Snippet: The BioCarta mPR (membrane progesterone receptor) pathway ( p -value = 6.27 × 10 − 5 , FDR = 0.009), which involves the oocyte maturation by progesterone, is the highest ALS-associated gene set among the developmental-related gene sets, along with the immune-response BioCarta CSK pathway ( p -value = 5.02 × 10 − 5 , FDR = 0.009), covered in the previous section.

Techniques:

Journal: G3: Genes|Genomes|Genetics

Article Title: Transcriptomic Analysis Identifies Candidate Genes and Gene Sets Controlling the Response of Porcine Peripheral Blood Mononuclear Cells to Poly I:C Stimulation

doi: 10.1534/g3.116.028290

Figure Lengend Snippet: Common gene sets in response to poly I:C stimulation in Dapulian and Landrace

Article Snippet: BIOCARTA_CYTOKINE_PATHWAY , Cytokine network , 1.9291 , 1.12E-02 , 1.9777 , 1.58E-02.

Techniques: Transduction, Expressing, Ligand Binding Assay

Journal: eLife

Article Title: Mismatch repair deficiency endows tumors with a unique mutation signature and sensitivity to DNA double-strand breaks

doi: 10.7554/eLife.02725

Figure Lengend Snippet: Pathways most significantly affected by exonic indels DOI: http://dx.doi.org/10.7554/eLife.02725.031 10.7554/eLife.02725.032 Table 2—source data 1. Results of pathway enrichments, custom definition of the DSBR by HR pathway and the allelic frequencies of mutations in HR genes. DOI: http://dx.doi.org/10.7554/eLife.02725.032

Article Snippet: BioCarta (ranking by GenomeMusic) , ATR/BRCA pathway , 1 , 1.0E−16 , 15 , 3.50.

Techniques: Homologous Recombination, Non-Homologous End Joining, Activation Assay

Journal: BMC Bioinformatics

Article Title: Identification of reproducible gene expression signatures in lung adenocarcinoma

doi: 10.1186/1471-2105-14-371

Figure Lengend Snippet: Predictive performances of 16 pathways

Article Snippet: Biocarta cell cycle pathway (7) , Biocarta , 2.53E-08 , 0.0596 , 0.0012 , 0.025 , 0.1527 , 3 , 0.006.

Techniques:

Journal: BMC Bioinformatics

Article Title: Identification of reproducible gene expression signatures in lung adenocarcinoma

doi: 10.1186/1471-2105-14-371

Figure Lengend Snippet: Predictive performances estimated by the log - rank tests of the 11 pathways for five lung adenocarcinoma datasets

Article Snippet: Biocarta cell cycle pathway (7) , Biocarta , 2.53E-08 , 0.0596 , 0.0012 , 0.025 , 0.1527 , 3 , 0.006.

Techniques:

Journal: PLoS ONE

Article Title: Integrating Constitutive Gene Expression and Chemoactivity: Mining the NCI60 Anticancer Screen

doi: 10.1371/journal.pone.0044631

Figure Lengend Snippet: GSEA results for test compounds.

Article Snippet: Biocarta HCMV MAPKinase pathway , Human cytomegalovirus and map kinase pathways , 3 , 3.19E-05.

Techniques: Activity Assay, Phospho-proteomics, Infection, Membrane

Journal: BMC Bioinformatics

Article Title: g raphite - a Bioconductor package to convert pathway topology to gene network

doi: 10.1186/1471-2105-13-20

Figure Lengend Snippet: Pathway analysis performed using topologyGSA statistical test on graphite networks.

Article Snippet: 28 , nf-kb signaling pathway , 0.01 , Biocarta , , .

Techniques: Activation Assay, Migration, Infection, Binding Assay, Inhibition