MutMix

Comprehensive database about mutation and miRNA expression dysregulation

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This section will explain the all parameters and results in MutMix database.


Index
MutMix Modules
Notes on query output
Notes on query input
Table headers





*Association* Using rigorous statistical methods, MutMix infers mutation-miRNA association based on genome sequencing data of mRNA genes and RNA-Seq data of miRNAs. Presumable TF→miRNA relationships are evidenced with TransmiR. A surrogate CGES expression score is summarized for all miRNAs associated with the common mutated gene, and its prognosis predictability is assessed with respect to Disease-Specific Survival or Overall Survival. Intersection of mRNA-miRNA associations can be interrogated in either a cross-gene or a cross-cancer manner.

*Mutation* Mutations are tabulated and visually displayed. The tabular representation reveals the chromosome coordinates, host gene name, protein-coding disruption, tissue-specificity, and regulatory alternations (RBP/miRNA binding). A gene-body ideogram indicates the intron-exon linear structure marked with categorized mutations. A patient-mutation oncoprint resorts to the heatmap concept to visualize the occurrence of categorized mutations in diverse genes across individual patients.

*Network* mRNA-miRNA associations are visually represented in a network, which can be updated and exported to reflect the user’s interactive parametrization. Pleiotropic and/or confluent associations are more notable in the network representation than in the tabular form. The network can be centered on select protein-coding genes (forward query) or select miRNAs (reverse query).

*Disease* Disease associations for a set of miRNAs/mRNAs undergo an enrichment analysis (over-representation analysis), and the most prominent diseases are returned in a ranked list. Visualization of the top-ranking enriched diseases is provided.









Header Meaning
Alt Alternative allele of a genomic variant
Cancer The cancer in which an association was inferred
Chr Chromosome
Class Mutation class (synonymous, nonsynomous, stopgain, etc)
Disease The disease associated with miRNA(s)
Disease_miRNAs miRNAs associated with a disease
Disease_p p-value of disease enrichment among a set of miRNAs
Disease_q q-value of disease enrichment among a set of miRNAs
DSS_beta_p p-value of miRNA-set's Disease-Specific Survival (DSS) prognosis, inferred via Beta distribution of permutation data
DSS_Cox_p p-value of miRNA-set's DSS prognosis, inferred via Cox proportional-hazards model
DSS_HR Hazard Ratio (HR) of DSS prognosis association, inferred via Cox proportional-hazards model
DSS_p p-value of single miRNA's DSS prognosis, inferred via Cox proportional-hazards model
DSS_perm_p p-value of miRNA-set's DSS prognosis, inferred via permutation data
DSS_Z Z-score of miRNA-set's DSS prognosis, inferred via permutation data
Effect Putative regulatory effect between a TF and a miRNA, per TransmiR
Expected Expected proportion of disease-associated miRNAs in a miRNA set
FDR False Discovery Rate, in miRNA dysregulation statistical test (per edgeR)
KM Plot Kaplan-Meier survival plot
LogFC Logged fold change, in miRNA dysregulation statistical test (per edgeR)
miRNA microRNA name
miRNA_NB_p p-value for mutation-associated miRNA dysregulation extensity, inferred via Negative Binomial distribution
miRNA_number number of dysregulated miRNAs associated with the mutated gene
miRNA_perm_p p-value for mutation-associated miRNA dysregulation extensity, inferred via permutation data
miRNA_Z Z-score for mutation-associated miRNA dysregulation extensity, inferred via permutation data
Mutated_gene The mutated gene (gene symbol)
Mutation_rate Proportion of patients in a cancer-type cohort who carry a mutation in the concerned gene
Observed Observed proportion of disease-associated miRNAs in a miRNA set
OS_beta_p p-value of miRNA-set's Overall Survival (OS) prognosis, inferred via Beta distribution of permutation data
OS_Cox_p p-value of miRNA-set's OS prognosis, inferred via Cox proportional-hazards model
OS_HR Hazard Ratio (HR) of OS prognosis association, inferred via Cox proportional-hazards model
OS_p p-value of single miRNA's OS prognosis, inferred via Cox proportional-hazards model
OS_perm_p p-value of miRNA-set's OS prognosis, inferred via permutation data
OS_Z Z-score of miRNA-set's OS prognosis, inferred via permutation data
Pos Chromosome coordinate position of a variant
RBP_gene Whether the mutated gene is a RNA-binding protein (RBP)
Ref Reference allele of a genomic variant
SMDB_effect The type of somatic motif per the implicated regulator, also the sector of SMDB
SMDB_motif Mutation-caused somatic motif (new form), per SMDB
SMDB_regulator The regulator (RBP, miRNA seed, or miRNA target) implicated with the somatic motif, per SMDB
SomamiR_cancer The related cancer type, per SomamiR
SomamiR_effect The effect of cancer-related somatic mutation, per SomamiR
SomamiR_extID The external ID of the implicated regulator of the somatic mutation, per SomamiR
SomamiR_miRNA The miRNA implicated with the somatic mutation, per SomamiR
TF_gene Whether the mutated gene is a Transcription Factor (TF)