Clustering miRNAs-genes pairs in similar pattern expression

Source: R/targets.R

Clustering miRNAs-genes pairs

isoNetwork(
  mirna_rse,
  gene_rse,
  summarize = NULL,
  target = NULL,
  org = NULL,
  enrich = NULL,
  genename = "ENSEMBL",
  min_cor = -0.6,
  min_fc = 0.5
)

Arguments

mirna_rse

SummarizedExperiment with miRNA information. See details.
gene_rse

SummarizedExperiment with gene information. See details.
summarize

Character column name in colData(rse) to use to group samples and compare betweem miRNA/gene expression.
target

Matrix with miRNAs (columns) and genes (rows) target prediction (1 if it is a target, 0 if not).
org

AnnotationDb obejct. For example:(org.Mm.eg.db)
enrich

The output of clusterProfiler of similar functions.
genename

Character keytype of the gene names in gene_rse object.
min_cor

Numeric cutoff to consider a miRNA to regulate a target.
min_fc

Numeric cutoff to consider as the minimum log2FoldChange between groups to be considered in the analysis.

Value

list with network information

Details

This function will correlate miRNA and gene expression data using a specific metadata variable to group samples and detect pattern of expression that will be annotated with GO terms. mirna_rse and gene_rse can be created using the following code:

mi_rse = SummarizedExperiment(assays=SimpleList(norm=mirna_matrix), colData, metadata=list(sign=mirna_keep))

where, mirna_matrix is the normalized counts expression, colData is the metadata information and mirna_keep the list of miRNAs to be used by this function.

Examples

# library(org.Mm.eg.db)
# library(clusterProfiler)
data(isoExample)
# ego <- enrichGO(row.names(assay(gene_ex_rse, "norm")),
#                 org.Mm.eg.db, "ENSEMBL", ont = "BP")
data <- isoNetwork(mirna_ex_rse, gene_ex_rse, 
                   summarize = "group", target = ma_ex,
                   enrich = ego)

#> Number of mirnas 20 with these columns:A201_Day0A200_Day0A196_Day0A167_Day1A165_Day1A63_Day1A172_Day2A70_Day2A69_Day2A178_Day3A75_Day3A74_Day3A181_Day7A180_Day7A80_Day7A189_Day14A85_Day14A84_Day14
#> Number of genes 25 with these columns:control_1control_2control_3day1_1day1_2day1_3day2_1day2_2day2_3day3_1day3_2day3_3day7_1day7_2day7_3day14_1day14_2day14_3
#> Number of mirnas 20 with these columns:controlday1day2day3day7day14
#> Number of mirnas 25 with these columns:controlday1day2day3day7day14
#> Dimmension of cor matrix: 20 25 
#> Working with 18 genes.
#> Warning: `distinct_()` is deprecated as of dplyr 0.7.0.
#> Please use `distinct()` instead.
#> See vignette('programming') for more help
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_warnings()` to see where this warning was generated.
#> Working with 18 genes after filtering: minc > 0
#> Joining, by = "merge"
#> Joining, by = "merge"
#> geom_path: Each group consists of only one observation. Do you need to adjust
#> the group aesthetic?
#> geom_path: Each group consists of only one observation. Do you need to adjust
#> the group aesthetic?
#> geom_path: Each group consists of only one observation. Do you need to adjust
#> the group aesthetic?
#> geom_path: Each group consists of only one observation. Do you need to adjust
#> the group aesthetic?
#> geom_path: Each group consists of only one observation. Do you need to adjust
#> the group aesthetic?
#> geom_path: Each group consists of only one observation. Do you need to adjust
#> the group aesthetic?
#> geom_path: Each group consists of only one observation. Do you need to adjust
#> the group aesthetic?
#> geom_path: Each group consists of only one observation. Do you need to adjust
#> the group aesthetic?
#> geom_path: Each group consists of only one observation. Do you need to adjust
#> the group aesthetic?
#> cell-matrix adhesion
#> cell-substrate adhesion
#> regulation of cell-substrate adhesion
#> regulation of cell-matrix adhesion
#> positive regulation of cell-substrate adhesion
#> cell-substrate junction assembly
#> regulation of focal adhesion assembly
#> regulation of cell-substrate junction assembly
#> regulation of adherens junction organization
#> positive regulation of cell adhesion
#> cell-substrate adherens junction assembly
#> focal adhesion assembly
#> regulation of cell junction assembly
#> adherens junction assembly
#> positive regulation of cell-matrix adhesion
#> adherens junction organization
#> cell junction assembly
#> cell junction organization
#> cell-cell junction organization
#> regulation of ERK1 and ERK2 cascade
#> ERK1 and ERK2 cascade
#> epithelial cell proliferation
#> regulation of cellular response to growth factor stimulus
#> positive regulation of focal adhesion assembly
#> positive regulation of adherens junction organization
#> angiogenesis
#> positive regulation of cell junction assembly
#> substrate adhesion-dependent cell spreading
#> positive regulation of ERK1 and ERK2 cascade
#> extracellular matrix organization
#> extracellular structure organization
#> wound healing
#> endothelial cell proliferation
#> positive regulation of cell projection organization
#> regulation of protein secretion
#> response to wounding
#> positive regulation of vascular endothelial growth factor receptor signaling pathway
#> positive regulation of cell migration
#> positive regulation of cell motility
#> regulation of peptide secretion
#> negative regulation of wound healing
#> positive regulation of cellular component movement
#> regulation of actin cytoskeleton organization
#> positive regulation of locomotion
#> positive regulation of neuron projection development
#> negative regulation of response to wounding
#> regulation of epithelial cell proliferation
#> regulation of actin filament-based process
#> regulation of hematopoietic progenitor cell differentiation
#> integrin-mediated signaling pathway
#> regulation of cell-cell adhesion
#> regulation of vascular endothelial growth factor receptor signaling pathway
#> negative regulation of endothelial cell apoptotic process
#> positive regulation of neuron differentiation
#> developmental growth involved in morphogenesis
#> endothelium development
#> positive regulation of protein secretion
#> cellular response to vascular endothelial growth factor stimulus
#> regulation of cytoskeleton organization
#> blood circulation
#> circulatory system process
#> regulation of cell morphogenesis
#> positive regulation of MAPK cascade
#> positive regulation of cellular component biogenesis
#> skeletal system development
#> positive regulation of peptide secretion
#> regulation of homeostatic process
#> regulation of wound healing
#> renal system development
#> vascular endothelial growth factor receptor signaling pathway
#> positive regulation of angiogenesis
#> regulation of cell morphogenesis involved in differentiation
#> negative regulation of epithelial cell apoptotic process
#> regulation of endothelial cell apoptotic process
#> negative regulation of blood coagulation
#> negative regulation of hemostasis
#> peptidyl-tyrosine phosphorylation
#> peptidyl-tyrosine modification
#> negative regulation of coagulation
#> endothelial cell apoptotic process
#> positive regulation of vasculature development
#> positive regulation of cell morphogenesis involved in differentiation
#> negative regulation of cell-substrate adhesion
#> regulation of body fluid levels
#> urogenital system development
#> ameboidal-type cell migration
#> regulation of cytokine secretion
#> regulation of response to wounding
#> anatomical structure homeostasis
#> blood coagulation
#> hemostasis
#> regulation of epithelial cell migration
#> coagulation
#> response to follicle-stimulating hormone
#> epithelial tube morphogenesis
#> cytokine secretion
#> response to hypoxia
#> positive regulation of endothelial cell migration
#> post-embryonic camera-type eye development
#> response to decreased oxygen levels
#> sprouting angiogenesis
#> tissue homeostasis
#> positive regulation of secretion by cell
#> regulation of epithelial cell apoptotic process
#> tube morphogenesis
#> surfactant homeostasis
#> negative regulation of substrate adhesion-dependent cell spreading
#> regulation of vasculogenesis
#> positive regulation of cell-cell adhesion
#> developmental cell growth
#> cellular response to gonadotropin stimulus
#> positive regulation of endothelial cell chemotaxis
#> positive regulation of axonogenesis
#> positive regulation of secretion
#> response to gonadotropin
#> calcium-mediated signaling using intracellular calcium source
#> chemical homeostasis within a tissue
#> regulation of blood coagulation
#> regulation of hemostasis
#> epithelial cell migration
#> regulation of angiogenesis
#> epithelium migration
#> vasculogenesis
#> skeletal system morphogenesis
#> tissue migration
#> regulation of coagulation
#> response to oxygen levels
#> negative regulation of cell adhesion
#> positive regulation of hydrolase activity
#> negative regulation of extrinsic apoptotic signaling pathway
#> regulation of endothelial cell proliferation
#> epithelial cell apoptotic process
#> regulation of endothelial cell chemotaxis
#> regulation of vasculature development
#> endothelial cell differentiation
#> kidney development
#> positive regulation of protein transport
#> retinal ganglion cell axon guidance
#> fibrinolysis
#> regulation of extent of cell growth
#> negative regulation of response to external stimulus
#> post-embryonic animal organ development
#> positive regulation of epithelial cell migration
#> vascular endothelial growth factor signaling pathway
#> phosphatidylinositol 3-kinase signaling
#> positive regulation of cytokine secretion
#> regulation of GTPase activity
#> regulation of endothelial cell migration
#> plasminogen activation
#> leukocyte migration
#> positive regulation of positive chemotaxis
#> positive regulation of chemotaxis
#> smooth muscle tissue development
#> regulation of positive chemotaxis
#> trabecula formation
#> peptidyl-serine phosphorylation
#> lymph vessel development
#> monocyte differentiation
#> embryonic hemopoiesis
#> endothelial cell chemotaxis
#> mononuclear cell differentiation
#> regulation of cell shape
#> phosphatidylinositol-mediated signaling
#> nephron development
#> negative regulation of cell development
#> protein kinase C signaling
#> multicellular organismal homeostasis
#> inositol lipid-mediated signaling
#> peptidyl-serine modification
#> negative regulation of cell-matrix adhesion
#> positive regulation of interleukin-10 production
#> regulation of peptidyl-serine phosphorylation
#> ephrin receptor signaling pathway
#> regulation of cellular component size
#> calcium-mediated signaling
#> hematopoietic progenitor cell differentiation
#> regulation of endothelial cell differentiation
#> endothelial cell migration
#> cell migration involved in sprouting angiogenesis
#> positive regulation of mesenchymal cell proliferation
#> positive regulation of cytokine production involved in immune response
#> myeloid cell homeostasis
#> neuron projection extension
#> regulation of hemopoiesis
#> neuron death
#> regulation of extrinsic apoptotic signaling pathway
#> regulation of axonogenesis
#> neural crest cell migration
#> branching involved in blood vessel morphogenesis
#> positive chemotaxis
#> regulation of cell size
#> ossification
#> positive regulation of cell growth
#> regulation of cell growth
#> regulation of chemotaxis
#> regulation of mesenchymal cell proliferation
#> branching morphogenesis of an epithelial tube
#> zymogen activation
#> regulation of chondrocyte differentiation
#> mesenchymal cell differentiation
#> regulation of interleukin-10 production
#> regulation of substrate adhesion-dependent cell spreading
#> vascular process in circulatory system
#> cell adhesion mediated by integrin
#> positive regulation of axon extension
#> positive regulation of developmental growth
#> positive regulation of cytoskeleton organization
#> stem cell differentiation
#> muscle tissue development
#> interleukin-10 production
#> regulation of organ morphogenesis
#> negative regulation of cytokine secretion
#> trabecula morphogenesis
#> axon development
#> peptidyl-tyrosine autophosphorylation
#> mesenchymal cell proliferation
#> positive regulation of smooth muscle cell migration
#> regulation of peptide hormone secretion
#> negative regulation of apoptotic signaling pathway
#> second-messenger-mediated signaling
#> lung development
#> morphogenesis of a branching epithelium
#> peptide cross-linking
#> lung alveolus development
#> respiratory tube development
#> negative regulation of neuron death
#> regulation of blood circulation
#> embryonic organ development
#> regulation of ossification
#> extrinsic apoptotic signaling pathway
#> regulation of cytokine production involved in immune response
#> regulation of cartilage development
#> regulation of peptidyl-tyrosine phosphorylation
#> regulation of cardiac muscle contraction
#> morphogenesis of a branching structure
#> ovarian follicle development
#> neural crest cell development
#> positive regulation of phosphatidylinositol 3-kinase signaling
#> mesenchyme development
#> positive regulation of fibroblast proliferation
#> muscle fiber development
#> smooth muscle cell differentiation
#> positive regulation of endothelial cell proliferation
#> artery morphogenesis
#> ureteric bud morphogenesis
#> protein autophosphorylation
#> reactive oxygen species metabolic process
#> mesonephric tubule morphogenesis
#> respiratory system development
#> mesenchymal cell development
#> stem cell development
#> cellular response to interleukin-1
#> cell chemotaxis
#> neural crest cell differentiation
#> peptide hormone secretion
#> positive regulation of response to external stimulus
#> cytokine production involved in immune response
#> regulation of striated muscle contraction
#> nephron tubule morphogenesis
#> blood vessel endothelial cell migration
#> regulation of calcium-mediated signaling
#> nephron epithelium morphogenesis
#> positive regulation of production of molecular mediator of immune response
#> regulation of smooth muscle cell migration
#> nephron morphogenesis
#> negative regulation of cell morphogenesis involved in differentiation
#> positive regulation of blood circulation
#> response to retinoic acid
#> regulation of hormone secretion
#> gliogenesis
#> renal tubule morphogenesis
#> positive regulation of growth
#> metanephros development
#> regulation of phosphatidylinositol 3-kinase signaling
#> smooth muscle cell migration
#> response to interleukin-1
#> cellular response to hypoxia
#> actin cytoskeleton reorganization
#> positive regulation of protein kinase B signaling
#> sensory organ morphogenesis
#> homeostasis of number of cells
#> platelet activation
#> cellular response to decreased oxygen levels
#> ovulation cycle process
#> regulation of axon extension
#> membrane depolarization
#> kidney morphogenesis
#> nephron tubule development
#> chondrocyte differentiation
#> artery development
#> cellular response to oxygen levels
#> muscle cell migration
#> positive regulation of ossification
#> ovulation cycle
#> renal tubule development
#> ureteric bud development
#> mesonephric epithelium development
#> mesonephric tubule development
#> regulation of fibroblast proliferation
#> mesonephros development
#> fibroblast proliferation
#> odontogenesis
#> nephron epithelium development
#> positive regulation of transmembrane receptor protein serine/threonine kinase signaling pathway
#> hormone secretion
#> regulation of neuron death
#> transmembrane receptor protein serine/threonine kinase signaling pathway
#> female gonad development
#> positive regulation of peptide hormone secretion
#> response to acid chemical
#> hormone transport
#> positive regulation of peptidyl-serine phosphorylation
#> development of primary female sexual characteristics
#> regulation of calcium ion import
#> regulation of morphogenesis of an epithelium
#> regulation of developmental growth
#> regulation of receptor activity
#> erythrocyte differentiation
#> axon extension
#> cardiac muscle contraction
#> cellular response to glucose stimulus
#> adaptive immune response
#> regulation of production of molecular mediator of immune response
#> cellular response to hexose stimulus
#> memory
#> digestive tract development
#> cellular response to monosaccharide stimulus
#> regulation of protein complex assembly
#> positive regulation of cytokine production
#> erythrocyte homeostasis
#> cellular response to carbohydrate stimulus
#> negative regulation of cellular response to growth factor stimulus
#> regulation of membrane potential
#> calcium ion transport
#> negative regulation of protein secretion
#> camera-type eye morphogenesis
#> regulation of apoptotic signaling pathway
#> negative regulation of epithelial cell proliferation
#> cellular glucose homeostasis
#> regulation of epithelial cell differentiation
#> digestive system development
#> stem cell proliferation
#> post-embryonic development
#> regulation of protein kinase B signaling
#> negative regulation of peptide secretion
#> regulation of osteoblast differentiation
#> kidney epithelium development
#> nail development
#> cardiac muscle fiber development
#> primitive hemopoiesis
#> vascular smooth muscle cell development
#> regulation of interleukin-2 secretion
#> negative regulation of protein localization to cell surface
#> negative regulation of protein phosphorylation
#> cytosolic calcium ion transport
#> female sex differentiation
#> cellular calcium ion homeostasis
#> regulation of muscle contraction
#> muscle cell differentiation
#> positive regulation of stress-activated MAPK cascade
#> positive regulation of hormone secretion
#> positive regulation of stress-activated protein kinase signaling cascade
#> neutrophil apoptotic process
#> blood vessel endothelial cell proliferation involved in sprouting angiogenesis
#> regulation of skeletal muscle contraction
#> positive regulation of heterotypic cell-cell adhesion
#> post-embryonic animal organ morphogenesis
#> positive regulation of collateral sprouting
#> venous blood vessel morphogenesis
#> positive regulation of mitochondrial depolarization
#> bone trabecula formation
#> response to forskolin
#> cellular response to forskolin
#> negative regulation of neuron migration
#> transforming growth factor beta receptor signaling pathway
#> axonogenesis
#> positive regulation of kinase activity
#> calcium ion homeostasis
#> dendrite morphogenesis
#> regulation of microtubule cytoskeleton organization
#> endocardium development
#> positive regulation of odontogenesis
#> response to mercury ion
#> retina vasculature morphogenesis in camera-type eye
#> regulation of transcription from RNA polymerase II promoter in response to hypoxia
#> interleukin-2 secretion
#> regulation of cellular response to vascular endothelial growth factor stimulus
#> divalent metal ion transport
#> cellular divalent inorganic cation homeostasis
#> divalent inorganic cation transport
#> striated muscle contraction
#> reproductive structure development
#> regulation of tube diameter
#> regulation of blood vessel diameter
#> response to glucose
#> reproductive system development
#> signal release
#> mast cell chemotaxis
#> negative regulation of keratinocyte proliferation
#> regulation of cardiac muscle contraction by calcium ion signaling
#> cranial nerve structural organization
#> hepatocyte growth factor receptor signaling pathway
#> regulation of neurotransmitter uptake
#> establishment of blood-brain barrier
#> regulation of cellular response to hypoxia
#> positive regulation of membrane depolarization
#> response to hexose
#> negative regulation of phosphorylation
#> response to monosaccharide
#> cell-cell adhesion via plasma-membrane adhesion molecules
isoPlotNet(data, minGenes = 5)