Instructions

Instructions

The type of query performed on CELLX is determined by the pulldown menu underneath the Pfizer Icon.

The types of queries are:

CNV
[target] : Search for CNV alterations.
[CNV-barplot] : Plot each CNV dataset in a barchart and stripchart.
[cnv_exp] : Find genes with cnv that have statistically different expression of the selected gene.
Expression
[expression_list] : expression table for named genes and heatmap.
[RSEM-barplot] : Plot each RSEM expression dataset in a barchart, stripchart, and histogram.
[expression_stat] : Find which genes are statistically different between groups defined by expression cutoffs.
[expression_cor] : Find which genes are correlated with the selected gene(s).
[expression_plot] : 2D scatter plot of molecular features.
[expression_mut] : Find which genes are statistically different between groups defined by mutation status.
[expression_cnv] : Find which genes are statistically different between groups defined by cnv status.
[expression_IC50] : Find genes correlated or enriched between groups defined by IC50 cutoffs.
[expression_meta] : Find genes correlated or enriched between groups defined by meta data.
[expression_mirna] : Find which genes are statistically different between groups defined by mirna status.
[expression_exon]
[pca_plot] : PCA plot whole expression data *dev
Mutation
[fisher_mutation]
[meta_mutation] : Fisher test for mutation status and metadata
[mutation_exp] : Find genes with mutations that have statistically different expression of the selected gene.
[mutation_table] : create table of mutations.
[mutation_report] : Database wide survey of mutations in a gene.
[mutation_count]
[mirna_mut] : Find miRNAs that are statistically different between groups defined by mutation status.
Other
[sample_report] : List cnv and mutations present for a given sample.
[sample_search] : Search for sample names in the database.
[marker_report] : Count samples that meet the criteria for positive or negative sets of putative biomarkers.
[mirna_barplot]
[survival] : Plot survival plots (TCGA only)
[meta_heatmap]
[meta_search]
[matrix] : Output expression, CNV, and mutations in table format.
[gene_loci]
[tabledump]
[venn] : Create venn diagrams based on molecular features.
[combinations] : Find genes correlated or enriched between groups defined by combination scores.
[methyl_mut]
[meta_fisher] : Fisher test of two meta categorical fields.
[snp] : Test SNPs vs. expression levels
[slide_tab]: Show associated slide images