README Supplemetary File 2 nSolver_differential_expression_analysis_results

Author(s) AND their Email addresses
James Pestka,, pestka@msu.edu
Abby Benninghoff, abby.benninghoff@usu.edu

Title of Your Dataset or Journal article:
Mapping of Dynamic Transcriptome Changes Associated with Silica-Triggered Autoimmune Pathogenesis in the Lupus-Prone NZBWF1 Mouse.  Supplementary File 2 Ð nSolver differential expression analysis results. 

Description (short description of your dataset; indicate it is supporting an article):
Microsoft Excel document with output from nSolver for differential expression analyses for pairwise comparisons noted by each named sheet.  This data set is supporting material for a journal article.

Comments


Supplementary file 2 column definitions.
Gene symbol
Official gene symbol for Mus musculus
Log2 fold change
Average log2 fold change calculated for comparison indicated by name of spreadsheet tab
std error (log2)
Log2 standard error of the calculated average log2 fold change
lower confidence limit
Upper 95% confidence limit of the average log2 fold change
upper confidence limit
Lower 95% confidence limit of the average log2 fold change
Linear fold change
Average linear fold change calculated for comparison indicated by name of spreadsheet tab
lower confidence limit (linear)
Upper 95% confidence limit of the average linear fold change
upper confidence limit (linear)
Lower 95% confidence limit of the average linear fold change
P-value
Unadjusted P-value
BH.p.value
False discovery rate adjusted P-value using the Benjamini-Hochberg method
method
Differential expression test method, where ÒwaldÓ indicates the mixture negative binomial model, Òlm.nbÓ indicates the simplified negative binomial model, and ÒloglinearÓ indicates the log-linear model.
Gene.sets
Gene sets or pathways to which the indicated gene belongs within the annotated Nanostring probe set


Discipline: Toxicology
Keywords:
autoimmunity, NanoString, lung, systemic lupus erythematosus, silica, transcriptome

Journal:  Frontiers in Immunology


Volume, Issue, Date (year is fine that is all you have): 2019  (expected)

Embargo:  3 months embargo*