Computational protocol: Leishmania proteophosphoglycans regurgitated from infected sand flies accelerate dermal wound repair and exacerbate leishmaniasis via insulin-like growth factor 1-dependent signalling

Similar protocols

Protocol publication

[…] RNAs were hybridized onto Affymetrix Mouse 430_2 GeneChips, using the Affymetrix Two-Cycle Eukaryotic Target Labelling procedure: http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf. MIAME-compliant data are available through ArrayExpress and GEO databases (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52101). Gene-level expression values were derived from the CEL file probe-level hybridization intensities using the model-based Robust Multichip Average algorithm (RMA) []. RMA performs normalization, background correction and data summarization. Pearson’s correlation coefficient were calculated and a heatmap representation was performed using the Expression Console Software. Local pooled error (LPE) tests [] were performed to identify significant differences in gene expression between different conditions. The estimated false discovery rate of this analyse was calculated using the Benjamini and Hochberg approach [] to correct for multiple comparisons. Ingenuity Pathway Analysis (IPA) software v 9.0 (http://www.ingenuity.com) was used identify canonical pathways regulated by PSG presence at 6 hours post-inoculation. Gene Ontology (GO) analysis was also performed to find gene pathways and networks enriched by PSG in the Affymetrix data set at 6 hours post-infection (http://www.geneontology.org). This service connects to the analysis tool from the PANTHER Classification System (http://pantherdb.org), which is maintained up to date with GO annotations. […]

Pipeline specifications

Software tools IPA, PANTHER
Application Protein sequence analysis
Organisms Leishmania, Toxoplasma gondii, Drosophila melanogaster, Mus musculus
Diseases Infection, Leishmaniasis, Retinopathy of Prematurity