dag_bcell

The B cell receptor signaling pathway (BCR) converted to a DAG. In case of nodes with multiple genes, the most differentially expressed
between groups of patients defined in y1 (acute lymphocytic leukemia patients
 with BCR/ABL gene rearrangement) and y2 (acute lymphocytic leukemia patients
 with BCR/ABL gene rearrangement) matrices.
Chiaretti S., Li X., Gentleman R., Vitale A., Wang K.S., Mandelli F., Fo R., Ritz J. (2005) Gene expression
profiles of B-lineage adult acute lymphocytic leukemia reveal genetic patterns that identify lineage derivation
and distinct mechanisms of transformation. Clin Cancer Res, 11:7209-7219.
<a href="https://aacrjournals.org/clincancerres/article/11/20/7209/188537/Gene-Expression-Profiles-of-B-lineage-Adult-Acute">https://aacrjournals.org/clincancerres/article/11/20/7209/188537/Gene-Expression-Profiles-of-B-lineage-Adult-Acute</a>
Massa, M.S., Chiogna, M., Romualdi, C. (2010). Gene set analysis exploiting the topology of a pathway. BMC Systems Biology, 4:121
<a href="https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-4-121">https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-4-121</a>

Using Gaussian graphical models we propose a novel approach to
perform pathway analysis using gene expression. Given the
structure of a graph (a pathway) we introduce two statistical
tests to compare the mean and the concentration matrices between
two groups. Specifically, these tests can be performed on the
graph and on its connected components (cliques). The package is
based on the method described in Massa M.S., Chiogna M., Romualdi
C. (2010) <doi:10.1186/1752-0509-4-121>.

Gabriele Sales

topologyGSA

Gene Set Analysis Exploiting Pathway Topology

dag_bcell function

The B cell receptor signaling pathway (BCR) converted to a DAG. In case of nodes with multiple genes, the most differentially expressed
between groups of patients defined in y1 (acute lymphocytic leukemia patients
 with BCR/ABL gene rearrangement) and y2 (acute lymphocytic leukemia patients
 with BCR/ABL gene rearrangement) matrices.
Chiaretti S., Li X., Gentleman R., Vitale A., Wang K.S., Mandelli F., Fo R., Ritz J. (2005) Gene expression
profiles of B-lineage adult acute lymphocytic leukemia reveal genetic patterns that identify lineage derivation
and distinct mechanisms of transformation. Clin Cancer Res, 11:7209-7219.
<a href='https://aacrjournals.org/clincancerres/article/11/20/7209/188537/Gene-Expression-Profiles-of-B-lineage-Adult-Acute'>https://aacrjournals.org/clincancerres/article/11/20/7209/188537/Gene-Expression-Profiles-of-B-lineage-Adult-Acute</a>
Massa, M.S., Chiogna, M., Romualdi, C. (2010). Gene set analysis exploiting the topology of a pathway. BMC Systems Biology, 4:121
<a href='https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-4-121'>https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-4-121</a>

dag_bcell: DAG representation of the B cell receptor signaling pathway

Description

Arguments