Working with StarBioTrek package
2022-04-26
Contents
- Introduction
- Installation
Get data: Get pathway and network dataIntegration data: Integration between pathway and network dataPathway summary indexes: Score for each pathwayPathway cross-talk indexes: Score for pairwise pathwaysSelection of pathway cross-talk: Selection of pathway cross-talkIPPI: Driver genes for each pathwayVisualization: Gene interactions and pathways- References
Introduction
Motivation:
New technologies have made possible to identify marker gene signatures. However, gene expression-based signatures present some limitations because they do not consider metabolic role of the genes and are affected by genetic heterogeneity across patient cohorts. Considering the activity of entire pathways rather than the expression levels of individual genes can be a way to exceed these limits (Cancer Genome Atlas Research Network and others 2012).
This tool StarBioTrek presents some methodologies to measure pathway activity and cross-talk among pathways integrating also the information of network and TCGA data. New measures are under development.
Installation
To install use the code below.
Get data: Get pathway and network data
SELECT_path_species: Select the pathway database and species of interest
The user can select the pathway database and species of interest using some functions implemented in graphite (Sales G, et al. 2012)
| species | database |
|---|---|
| athaliana | kegg |
| athaliana | pathbank |
| athaliana | wikipathways |
| btaurus | kegg |
| btaurus | pathbank |
| btaurus | reactome |
| btaurus | wikipathways |
| celegans | kegg |
| celegans | pathbank |
| celegans | reactome |
| celegans | wikipathways |
| cfamiliaris | kegg |
| cfamiliaris | reactome |
| cfamiliaris | wikipathways |
| dmelanogaster | kegg |
| dmelanogaster | pathbank |
| dmelanogaster | reactome |
| dmelanogaster | wikipathways |
| drerio | kegg |
| drerio | reactome |
| drerio | wikipathways |
| ecoli | kegg |
| ecoli | pathbank |
| ecoli | wikipathways |
| ggallus | kegg |
| ggallus | reactome |
| ggallus | wikipathways |
| hsapiens | kegg |
| hsapiens | panther |
| hsapiens | pathbank |
| hsapiens | pharmgkb |
| hsapiens | reactome |
| hsapiens | smpdb |
| hsapiens | wikipathways |
| mmusculus | kegg |
| mmusculus | pathbank |
| mmusculus | reactome |
| mmusculus | wikipathways |
| rnorvegicus | kegg |
| rnorvegicus | pathbank |
| rnorvegicus | reactome |
| rnorvegicus | wikipathways |
| scerevisiae | kegg |
| scerevisiae | pathbank |
| scerevisiae | reactome |
| scerevisiae | wikipathways |
| sscrofa | kegg |
| sscrofa | reactome |
| sscrofa | wikipathways |
| xlaevis | kegg |
GetData: Searching pathway data for download
The user can easily search pathways data and their genes using the GetData function. It can download pathways from several databases and species using the following parameters:
## [1] "Querying............. Glycolysis / Gluconeogenesis 1 of 325 pathways"
## [1] "Querying............. Citrate cycle (TCA cycle) 2 of 325 pathways"
## [1] "Querying............. Pentose phosphate pathway 3 of 325 pathways"
## [1] "Querying............. Pentose and glucuronate interconversions 4 of 325 pathways"
## [1] "Querying............. Fructose and mannose metabolism 5 of 325 pathways"
## [1] "Querying............. Galactose metabolism 6 of 325 pathways"
## [1] "Querying............. Ascorbate and aldarate metabolism 7 of 325 pathways"
## [1] "Querying............. Fatty acid biosynthesis 8 of 325 pathways"
## [1] "Querying............. Fatty acid elongation 9 of 325 pathways"
## [1] "Querying............. Fatty acid degradation 10 of 325 pathways"
## [1] "Querying............. Steroid biosynthesis 11 of 325 pathways"
## [1] "Querying............. Primary bile acid biosynthesis 12 of 325 pathways"
## [1] "Querying............. Ubiquinone and other terpenoid-quinone biosynthesis 13 of 325 pathways"
## [1] "Querying............. Steroid hormone biosynthesis 14 of 325 pathways"
## [1] "Querying............. Oxidative phosphorylation 15 of 325 pathways"
## [1] "Querying............. Arginine biosynthesis 16 of 325 pathways"
## [1] "Querying............. Purine metabolism 17 of 325 pathways"
## [1] "Querying............. Caffeine metabolism 18 of 325 pathways"
## [1] "Querying............. Pyrimidine metabolism 19 of 325 pathways"
## [1] "Querying............. Alanine, aspartate and glutamate metabolism 20 of 325 pathways"
## [1] "Querying............. Glycine, serine and threonine metabolism 21 of 325 pathways"
## [1] "Querying............. Cysteine and methionine metabolism 22 of 325 pathways"
## [1] "Querying............. Valine, leucine and isoleucine degradation 23 of 325 pathways"
## [1] "Querying............. Lysine degradation 24 of 325 pathways"
## [1] "Querying............. Arginine and proline metabolism 25 of 325 pathways"
## [1] "Querying............. Histidine metabolism 26 of 325 pathways"
## [1] "Querying............. Tyrosine metabolism 27 of 325 pathways"
## [1] "Querying............. Phenylalanine metabolism 28 of 325 pathways"
## [1] "Querying............. Tryptophan metabolism 29 of 325 pathways"
## [1] "Querying............. Phenylalanine, tyrosine and tryptophan biosynthesis 30 of 325 pathways"
## [1] "Querying............. beta-Alanine metabolism 31 of 325 pathways"
## [1] "Querying............. Taurine and hypotaurine metabolism 32 of 325 pathways"
## [1] "Querying............. Phosphonate and phosphinate metabolism 33 of 325 pathways"
## [1] "Querying............. Selenocompound metabolism 34 of 325 pathways"
## [1] "Querying............. D-Amino acid metabolism 35 of 325 pathways"
## [1] "Querying............. Glutathione metabolism 36 of 325 pathways"
## [1] "Querying............. Starch and sucrose metabolism 37 of 325 pathways"
## [1] "Querying............. N-Glycan biosynthesis 38 of 325 pathways"
## [1] "Querying............. Mucin type O-glycan biosynthesis 39 of 325 pathways"
## [1] "Querying............. Various types of N-glycan biosynthesis 40 of 325 pathways"
## [1] "Querying............. Mannose type O-glycan biosynthesis 41 of 325 pathways"
## [1] "Querying............. Amino sugar and nucleotide sugar metabolism 42 of 325 pathways"
## [1] "Querying............. Glycosaminoglycan degradation 43 of 325 pathways"
## [1] "Querying............. Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate 44 of 325 pathways"
## [1] "Querying............. Glycosaminoglycan biosynthesis - heparan sulfate / heparin 45 of 325 pathways"
## [1] "Querying............. Glycerolipid metabolism 46 of 325 pathways"
## [1] "Querying............. Inositol phosphate metabolism 47 of 325 pathways"
## [1] "Querying............. Glycosylphosphatidylinositol (GPI)-anchor biosynthesis 48 of 325 pathways"
## [1] "Querying............. Glycerophospholipid metabolism 49 of 325 pathways"
## [1] "Querying............. Ether lipid metabolism 50 of 325 pathways"
## [1] "Querying............. Arachidonic acid metabolism 51 of 325 pathways"
## [1] "Querying............. Linoleic acid metabolism 52 of 325 pathways"
## [1] "Querying............. alpha-Linolenic acid metabolism 53 of 325 pathways"
## [1] "Querying............. Sphingolipid metabolism 54 of 325 pathways"
## [1] "Querying............. Glycosphingolipid biosynthesis - lacto and neolacto series 55 of 325 pathways"
## [1] "Querying............. Glycosphingolipid biosynthesis - globo and isoglobo series 56 of 325 pathways"
## [1] "Querying............. Glycosphingolipid biosynthesis - ganglio series 57 of 325 pathways"
## [1] "Querying............. Pyruvate metabolism 58 of 325 pathways"
## [1] "Querying............. Glyoxylate and dicarboxylate metabolism 59 of 325 pathways"
## [1] "Querying............. Propanoate metabolism 60 of 325 pathways"
## [1] "Querying............. Butanoate metabolism 61 of 325 pathways"
## [1] "Querying............. One carbon pool by folate 62 of 325 pathways"
## [1] "Querying............. Thiamine metabolism 63 of 325 pathways"
## [1] "Querying............. Riboflavin metabolism 64 of 325 pathways"
## [1] "Querying............. Vitamin B6 metabolism 65 of 325 pathways"
## [1] "Querying............. Nicotinate and nicotinamide metabolism 66 of 325 pathways"
## [1] "Querying............. Pantothenate and CoA biosynthesis 67 of 325 pathways"
## [1] "Querying............. Biotin metabolism 68 of 325 pathways"
## [1] "Querying............. Lipoic acid metabolism 69 of 325 pathways"
## [1] "Querying............. Folate biosynthesis 70 of 325 pathways"
## [1] "Querying............. Retinol metabolism 71 of 325 pathways"
## [1] "Querying............. Porphyrin metabolism 72 of 325 pathways"
## [1] "Querying............. Terpenoid backbone biosynthesis 73 of 325 pathways"
## [1] "Querying............. Nitrogen metabolism 74 of 325 pathways"
## [1] "Querying............. Sulfur metabolism 75 of 325 pathways"
## [1] "Querying............. Aminoacyl-tRNA biosynthesis 76 of 325 pathways"
## [1] "Querying............. Metabolism of xenobiotics by cytochrome P450 77 of 325 pathways"
## [1] "Querying............. Drug metabolism - cytochrome P450 78 of 325 pathways"
## [1] "Querying............. Drug metabolism - other enzymes 79 of 325 pathways"
## [1] "Querying............. Biosynthesis of unsaturated fatty acids 80 of 325 pathways"
## [1] "Querying............. Metabolic pathways 81 of 325 pathways"
## [1] "Querying............. Carbon metabolism 82 of 325 pathways"
## [1] "Querying............. 2-Oxocarboxylic acid metabolism 83 of 325 pathways"
## [1] "Querying............. Fatty acid metabolism 84 of 325 pathways"
## [1] "Querying............. Biosynthesis of amino acids 85 of 325 pathways"
## [1] "Querying............. Nucleotide metabolism 86 of 325 pathways"
## [1] "Querying............. Biosynthesis of cofactors 87 of 325 pathways"
## [1] "Querying............. Biosynthesis of nucleotide sugars 88 of 325 pathways"
## [1] "Querying............. EGFR tyrosine kinase inhibitor resistance 89 of 325 pathways"
## [1] "Querying............. Endocrine resistance 90 of 325 pathways"
## [1] "Querying............. Antifolate resistance 91 of 325 pathways"
## [1] "Querying............. Platinum drug resistance 92 of 325 pathways"
## [1] "Querying............. mRNA surveillance pathway 93 of 325 pathways"
## [1] "Querying............. RNA degradation 94 of 325 pathways"
## [1] "Querying............. Viral life cycle - HIV-1 95 of 325 pathways"
## [1] "Querying............. PPAR signaling pathway 96 of 325 pathways"
## [1] "Querying............. Homologous recombination 97 of 325 pathways"
## [1] "Querying............. Fanconi anemia pathway 98 of 325 pathways"
## [1] "Querying............. MAPK signaling pathway 99 of 325 pathways"
## [1] "Querying............. ErbB signaling pathway 100 of 325 pathways"
## [1] "Querying............. Ras signaling pathway 101 of 325 pathways"
## [1] "Querying............. Rap1 signaling pathway 102 of 325 pathways"
## [1] "Querying............. Calcium signaling pathway 103 of 325 pathways"
## [1] "Querying............. cGMP-PKG signaling pathway 104 of 325 pathways"
## [1] "Querying............. cAMP signaling pathway 105 of 325 pathways"
## [1] "Querying............. Cytokine-cytokine receptor interaction 106 of 325 pathways"
## [1] "Querying............. Viral protein interaction with cytokine and cytokine receptor 107 of 325 pathways"
## [1] "Querying............. Chemokine signaling pathway 108 of 325 pathways"
## [1] "Querying............. NF-kappa B signaling pathway 109 of 325 pathways"
## [1] "Querying............. HIF-1 signaling pathway 110 of 325 pathways"
## [1] "Querying............. FoxO signaling pathway 111 of 325 pathways"
## [1] "Querying............. Phosphatidylinositol signaling system 112 of 325 pathways"
## [1] "Querying............. Sphingolipid signaling pathway 113 of 325 pathways"
## [1] "Querying............. Phospholipase D signaling pathway 114 of 325 pathways"
## [1] "Querying............. Neuroactive ligand-receptor interaction 115 of 325 pathways"
## [1] "Querying............. Cell cycle 116 of 325 pathways"
## [1] "Querying............. Oocyte meiosis 117 of 325 pathways"
## [1] "Querying............. p53 signaling pathway 118 of 325 pathways"
## [1] "Querying............. Sulfur relay system 119 of 325 pathways"
## [1] "Querying............. SNARE interactions in vesicular transport 120 of 325 pathways"
## [1] "Querying............. Autophagy - other 121 of 325 pathways"
## [1] "Querying............. Mitophagy - animal 122 of 325 pathways"
## [1] "Querying............. Autophagy - animal 123 of 325 pathways"
## [1] "Querying............. Protein processing in endoplasmic reticulum 124 of 325 pathways"
## [1] "Querying............. Endocytosis 125 of 325 pathways"
## [1] "Querying............. Phagosome 126 of 325 pathways"
## [1] "Querying............. Peroxisome 127 of 325 pathways"
## [1] "Querying............. mTOR signaling pathway 128 of 325 pathways"
## [1] "Querying............. PI3K-Akt signaling pathway 129 of 325 pathways"
## [1] "Querying............. AMPK signaling pathway 130 of 325 pathways"
## [1] "Querying............. Apoptosis 131 of 325 pathways"
## [1] "Querying............. Longevity regulating pathway 132 of 325 pathways"
## [1] "Querying............. Longevity regulating pathway - multiple species 133 of 325 pathways"
## [1] "Querying............. Apoptosis - multiple species 134 of 325 pathways"
## [1] "Querying............. Ferroptosis 135 of 325 pathways"
## [1] "Querying............. Necroptosis 136 of 325 pathways"
## [1] "Querying............. Cellular senescence 137 of 325 pathways"
## [1] "Querying............. Cardiac muscle contraction 138 of 325 pathways"
## [1] "Querying............. Adrenergic signaling in cardiomyocytes 139 of 325 pathways"
## [1] "Querying............. Vascular smooth muscle contraction 140 of 325 pathways"
## [1] "Querying............. Wnt signaling pathway 141 of 325 pathways"
## [1] "Querying............. Notch signaling pathway 142 of 325 pathways"
## [1] "Querying............. Hedgehog signaling pathway 143 of 325 pathways"
## [1] "Querying............. TGF-beta signaling pathway 144 of 325 pathways"
## [1] "Querying............. Axon guidance 145 of 325 pathways"
## [1] "Querying............. VEGF signaling pathway 146 of 325 pathways"
## [1] "Querying............. Apelin signaling pathway 147 of 325 pathways"
## [1] "Querying............. Osteoclast differentiation 148 of 325 pathways"
## [1] "Querying............. Hippo signaling pathway 149 of 325 pathways"
## [1] "Querying............. Hippo signaling pathway - multiple species 150 of 325 pathways"
## [1] "Querying............. Focal adhesion 151 of 325 pathways"
## [1] "Querying............. ECM-receptor interaction 152 of 325 pathways"
## [1] "Querying............. Cell adhesion molecules 153 of 325 pathways"
## [1] "Querying............. Adherens junction 154 of 325 pathways"
## [1] "Querying............. Tight junction 155 of 325 pathways"
## [1] "Querying............. Gap junction 156 of 325 pathways"
## [1] "Querying............. Signaling pathways regulating pluripotency of stem cells 157 of 325 pathways"
## [1] "Querying............. Complement and coagulation cascades 158 of 325 pathways"
## [1] "Querying............. Platelet activation 159 of 325 pathways"
## [1] "Querying............. Antigen processing and presentation 160 of 325 pathways"
## [1] "Querying............. Neutrophil extracellular trap formation 161 of 325 pathways"
## [1] "Querying............. Renin-angiotensin system 162 of 325 pathways"
## [1] "Querying............. Toll-like receptor signaling pathway 163 of 325 pathways"
## [1] "Querying............. NOD-like receptor signaling pathway 164 of 325 pathways"
## [1] "Querying............. RIG-I-like receptor signaling pathway 165 of 325 pathways"
## [1] "Querying............. Cytosolic DNA-sensing pathway 166 of 325 pathways"
## [1] "Querying............. C-type lectin receptor signaling pathway 167 of 325 pathways"
## [1] "Querying............. JAK-STAT signaling pathway 168 of 325 pathways"
## [1] "Querying............. Natural killer cell mediated cytotoxicity 169 of 325 pathways"
## [1] "Querying............. IL-17 signaling pathway 170 of 325 pathways"
## [1] "Querying............. Th1 and Th2 cell differentiation 171 of 325 pathways"
## [1] "Querying............. Th17 cell differentiation 172 of 325 pathways"
## [1] "Querying............. T cell receptor signaling pathway 173 of 325 pathways"
## [1] "Querying............. B cell receptor signaling pathway 174 of 325 pathways"
## [1] "Querying............. Fc epsilon RI signaling pathway 175 of 325 pathways"
## [1] "Querying............. Fc gamma R-mediated phagocytosis 176 of 325 pathways"
## [1] "Querying............. TNF signaling pathway 177 of 325 pathways"
## [1] "Querying............. Leukocyte transendothelial migration 178 of 325 pathways"
## [1] "Querying............. Intestinal immune network for IgA production 179 of 325 pathways"
## [1] "Querying............. Circadian rhythm 180 of 325 pathways"
## [1] "Querying............. Circadian entrainment 181 of 325 pathways"
## [1] "Querying............. Thermogenesis 182 of 325 pathways"
## [1] "Querying............. Long-term potentiation 183 of 325 pathways"
## [1] "Querying............. Synaptic vesicle cycle 184 of 325 pathways"
## [1] "Querying............. Neurotrophin signaling pathway 185 of 325 pathways"
## [1] "Querying............. Retrograde endocannabinoid signaling 186 of 325 pathways"
## [1] "Querying............. Glutamatergic synapse 187 of 325 pathways"
## [1] "Querying............. Cholinergic synapse 188 of 325 pathways"
## [1] "Querying............. Serotonergic synapse 189 of 325 pathways"
## [1] "Querying............. GABAergic synapse 190 of 325 pathways"
## [1] "Querying............. Dopaminergic synapse 191 of 325 pathways"
## [1] "Querying............. Long-term depression 192 of 325 pathways"
## [1] "Querying............. Olfactory transduction 193 of 325 pathways"
## [1] "Querying............. Taste transduction 194 of 325 pathways"
## [1] "Querying............. Phototransduction 195 of 325 pathways"
## [1] "Querying............. Inflammatory mediator regulation of TRP channels 196 of 325 pathways"
## [1] "Querying............. Regulation of actin cytoskeleton 197 of 325 pathways"
## [1] "Querying............. Insulin signaling pathway 198 of 325 pathways"
## [1] "Querying............. Insulin secretion 199 of 325 pathways"
## [1] "Querying............. GnRH signaling pathway 200 of 325 pathways"
## [1] "Querying............. Ovarian steroidogenesis 201 of 325 pathways"
## [1] "Querying............. Progesterone-mediated oocyte maturation 202 of 325 pathways"
## [1] "Querying............. Estrogen signaling pathway 203 of 325 pathways"
## [1] "Querying............. Melanogenesis 204 of 325 pathways"
## [1] "Querying............. Prolactin signaling pathway 205 of 325 pathways"
## [1] "Querying............. Thyroid hormone synthesis 206 of 325 pathways"
## [1] "Querying............. Thyroid hormone signaling pathway 207 of 325 pathways"
## [1] "Querying............. Adipocytokine signaling pathway 208 of 325 pathways"
## [1] "Querying............. Oxytocin signaling pathway 209 of 325 pathways"
## [1] "Querying............. Glucagon signaling pathway 210 of 325 pathways"
## [1] "Querying............. Regulation of lipolysis in adipocytes 211 of 325 pathways"
## [1] "Querying............. Renin secretion 212 of 325 pathways"
## [1] "Querying............. Aldosterone synthesis and secretion 213 of 325 pathways"
## [1] "Querying............. Relaxin signaling pathway 214 of 325 pathways"
## [1] "Querying............. Cortisol synthesis and secretion 215 of 325 pathways"
## [1] "Querying............. Parathyroid hormone synthesis, secretion and action 216 of 325 pathways"
## [1] "Querying............. GnRH secretion 217 of 325 pathways"
## [1] "Querying............. Type II diabetes mellitus 218 of 325 pathways"
## [1] "Querying............. Insulin resistance 219 of 325 pathways"
## [1] "Querying............. Non-alcoholic fatty liver disease 220 of 325 pathways"
## [1] "Querying............. AGE-RAGE signaling pathway in diabetic complications 221 of 325 pathways"
## [1] "Querying............. Cushing syndrome 222 of 325 pathways"
## [1] "Querying............. Growth hormone synthesis, secretion and action 223 of 325 pathways"
## [1] "Querying............. Alcoholic liver disease 224 of 325 pathways"
## [1] "Querying............. Type I diabetes mellitus 225 of 325 pathways"
## [1] "Querying............. Maturity onset diabetes of the young 226 of 325 pathways"
## [1] "Querying............. Aldosterone-regulated sodium reabsorption 227 of 325 pathways"
## [1] "Querying............. Endocrine and other factor-regulated calcium reabsorption 228 of 325 pathways"
## [1] "Querying............. Vasopressin-regulated water reabsorption 229 of 325 pathways"
## [1] "Querying............. Proximal tubule bicarbonate reclamation 230 of 325 pathways"
## [1] "Querying............. Salivary secretion 231 of 325 pathways"
## [1] "Querying............. Gastric acid secretion 232 of 325 pathways"
## [1] "Querying............. Pancreatic secretion 233 of 325 pathways"
## [1] "Querying............. Carbohydrate digestion and absorption 234 of 325 pathways"
## [1] "Querying............. Fat digestion and absorption 235 of 325 pathways"
## [1] "Querying............. Bile secretion 236 of 325 pathways"
## [1] "Querying............. Vitamin digestion and absorption 237 of 325 pathways"
## [1] "Querying............. Mineral absorption 238 of 325 pathways"
## [1] "Querying............. Cholesterol metabolism 239 of 325 pathways"
## [1] "Querying............. Alzheimer disease 240 of 325 pathways"
## [1] "Querying............. Parkinson disease 241 of 325 pathways"
## [1] "Querying............. Amyotrophic lateral sclerosis 242 of 325 pathways"
## [1] "Querying............. Huntington disease 243 of 325 pathways"
## [1] "Querying............. Spinocerebellar ataxia 244 of 325 pathways"
## [1] "Querying............. Prion disease 245 of 325 pathways"
## [1] "Querying............. Pathways of neurodegeneration - multiple diseases 246 of 325 pathways"
## [1] "Querying............. Cocaine addiction 247 of 325 pathways"
## [1] "Querying............. Amphetamine addiction 248 of 325 pathways"
## [1] "Querying............. Morphine addiction 249 of 325 pathways"
## [1] "Querying............. Alcoholism 250 of 325 pathways"
## [1] "Querying............. Bacterial invasion of epithelial cells 251 of 325 pathways"
## [1] "Querying............. Vibrio cholerae infection 252 of 325 pathways"
## [1] "Querying............. Epithelial cell signaling in Helicobacter pylori infection 253 of 325 pathways"
## [1] "Querying............. Pathogenic Escherichia coli infection 254 of 325 pathways"
## [1] "Querying............. Shigellosis 255 of 325 pathways"
## [1] "Querying............. Salmonella infection 256 of 325 pathways"
## [1] "Querying............. Pertussis 257 of 325 pathways"
## [1] "Querying............. Legionellosis 258 of 325 pathways"
## [1] "Querying............. Yersinia infection 259 of 325 pathways"
## [1] "Querying............. Leishmaniasis 260 of 325 pathways"
## [1] "Querying............. Chagas disease 261 of 325 pathways"
## [1] "Querying............. African trypanosomiasis 262 of 325 pathways"
## [1] "Querying............. Malaria 263 of 325 pathways"
## [1] "Querying............. Toxoplasmosis 264 of 325 pathways"
## [1] "Querying............. Amoebiasis 265 of 325 pathways"
## [1] "Querying............. Staphylococcus aureus infection 266 of 325 pathways"
## [1] "Querying............. Tuberculosis 267 of 325 pathways"
## [1] "Querying............. Hepatitis C 268 of 325 pathways"
## [1] "Querying............. Hepatitis B 269 of 325 pathways"
## [1] "Querying............. Measles 270 of 325 pathways"
## [1] "Querying............. Human cytomegalovirus infection 271 of 325 pathways"
## [1] "Querying............. Influenza A 272 of 325 pathways"
## [1] "Querying............. Human papillomavirus infection 273 of 325 pathways"
## [1] "Querying............. Human T-cell leukemia virus 1 infection 274 of 325 pathways"
## [1] "Querying............. Kaposi sarcoma-associated herpesvirus infection 275 of 325 pathways"
## [1] "Querying............. Herpes simplex virus 1 infection 276 of 325 pathways"
## [1] "Querying............. Epstein-Barr virus infection 277 of 325 pathways"
## [1] "Querying............. Human immunodeficiency virus 1 infection 278 of 325 pathways"
## [1] "Querying............. Coronavirus disease - COVID-19 279 of 325 pathways"
## [1] "Querying............. Pathways in cancer 280 of 325 pathways"
## [1] "Querying............. Transcriptional misregulation in cancer 281 of 325 pathways"
## [1] "Querying............. Viral carcinogenesis 282 of 325 pathways"
## [1] "Querying............. Chemical carcinogenesis - DNA adducts 283 of 325 pathways"
## [1] "Querying............. Proteoglycans in cancer 284 of 325 pathways"
## [1] "Querying............. MicroRNAs in cancer 285 of 325 pathways"
## [1] "Querying............. Chemical carcinogenesis - receptor activation 286 of 325 pathways"
## [1] "Querying............. Chemical carcinogenesis - reactive oxygen species 287 of 325 pathways"
## [1] "Querying............. Colorectal cancer 288 of 325 pathways"
## [1] "Querying............. Renal cell carcinoma 289 of 325 pathways"
## [1] "Querying............. Pancreatic cancer 290 of 325 pathways"
## [1] "Querying............. Endometrial cancer 291 of 325 pathways"
## [1] "Querying............. Glioma 292 of 325 pathways"
## [1] "Querying............. Prostate cancer 293 of 325 pathways"
## [1] "Querying............. Thyroid cancer 294 of 325 pathways"
## [1] "Querying............. Basal cell carcinoma 295 of 325 pathways"
## [1] "Querying............. Melanoma 296 of 325 pathways"
## [1] "Querying............. Bladder cancer 297 of 325 pathways"
## [1] "Querying............. Chronic myeloid leukemia 298 of 325 pathways"
## [1] "Querying............. Acute myeloid leukemia 299 of 325 pathways"
## [1] "Querying............. Small cell lung cancer 300 of 325 pathways"
## [1] "Querying............. Non-small cell lung cancer 301 of 325 pathways"
## [1] "Querying............. Breast cancer 302 of 325 pathways"
## [1] "Querying............. Hepatocellular carcinoma 303 of 325 pathways"
## [1] "Querying............. Gastric cancer 304 of 325 pathways"
## [1] "Querying............. Central carbon metabolism in cancer 305 of 325 pathways"
## [1] "Querying............. Choline metabolism in cancer 306 of 325 pathways"
## [1] "Querying............. PD-L1 expression and PD-1 checkpoint pathway in cancer 307 of 325 pathways"
## [1] "Querying............. Asthma 308 of 325 pathways"
## [1] "Querying............. Autoimmune thyroid disease 309 of 325 pathways"
## [1] "Querying............. Inflammatory bowel disease 310 of 325 pathways"
## [1] "Querying............. Systemic lupus erythematosus 311 of 325 pathways"
## [1] "Querying............. Rheumatoid arthritis 312 of 325 pathways"
## [1] "Querying............. Allograft rejection 313 of 325 pathways"
## [1] "Querying............. Graft-versus-host disease 314 of 325 pathways"
## [1] "Querying............. Hypertrophic cardiomyopathy 315 of 325 pathways"
## [1] "Querying............. Arrhythmogenic right ventricular cardiomyopathy 316 of 325 pathways"
## [1] "Querying............. Dilated cardiomyopathy 317 of 325 pathways"
## [1] "Querying............. Diabetic cardiomyopathy 318 of 325 pathways"
## [1] "Querying............. Viral myocarditis 319 of 325 pathways"
## [1] "Querying............. Lipid and atherosclerosis 320 of 325 pathways"
## [1] "Querying............. Fluid shear stress and atherosclerosis 321 of 325 pathways"
## [1] "Querying............. Valine, leucine and isoleucine biosynthesis 322 of 325 pathways"
## [1] "Querying............. Neomycin, kanamycin and gentamicin biosynthesis 323 of 325 pathways"
## [1] "Querying............. Protein digestion and absorption 324 of 325 pathways"
## [1] "Querying............. Nicotine addiction 325 of 325 pathways"GetPathData: Get genes inside pathways
The user can identify the genes inside the pathways of interest
GetPathNet: Get interacting genes inside pathways
GetPathNet generates a list of interacting genes for each pathway
ConvertedIDgenes: Get genes inside pathways
The user can convert the gene ID into GeneSymbol
## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:1 mapping between keys and columns## [1] "Mapping Uniprot ID to Gene Symbol, using convertIdentifiers of graphite package.......... Glycolysis / Gluconeogenesis 1 of 10 pathways"## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:1 mapping between keys and columns## [1] "Mapping Uniprot ID to Gene Symbol, using convertIdentifiers of graphite package.......... Citrate cycle (TCA cycle) 2 of 10 pathways"## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:1 mapping between keys and columns## [1] "Mapping Uniprot ID to Gene Symbol, using convertIdentifiers of graphite package.......... Pentose phosphate pathway 3 of 10 pathways"## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:1 mapping between keys and columns## [1] "Mapping Uniprot ID to Gene Symbol, using convertIdentifiers of graphite package.......... Pentose and glucuronate interconversions 4 of 10 pathways"## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:1 mapping between keys and columns## [1] "Mapping Uniprot ID to Gene Symbol, using convertIdentifiers of graphite package.......... Fructose and mannose metabolism 5 of 10 pathways"## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:1 mapping between keys and columns## [1] "Mapping Uniprot ID to Gene Symbol, using convertIdentifiers of graphite package.......... Galactose metabolism 6 of 10 pathways"## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:1 mapping between keys and columns## [1] "Mapping Uniprot ID to Gene Symbol, using convertIdentifiers of graphite package.......... Ascorbate and aldarate metabolism 7 of 10 pathways"## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:1 mapping between keys and columns## [1] "Mapping Uniprot ID to Gene Symbol, using convertIdentifiers of graphite package.......... Fatty acid biosynthesis 8 of 10 pathways"## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:1 mapping between keys and columns## [1] "Mapping Uniprot ID to Gene Symbol, using convertIdentifiers of graphite package.......... Fatty acid elongation 9 of 10 pathways"## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:1 mapping between keys and columns
## 'select()' returned 1:1 mapping between keys and columns## [1] "Mapping Uniprot ID to Gene Symbol, using convertIdentifiers of graphite package.......... Fatty acid degradation 10 of 10 pathways"getNETdata: Searching network data for download
You can easily search human network data from GeneMania using the getNETdata function (Warde-Farley D, et al. 2010).
The network category can be filtered using the following parameters:
- PHint Physical_interactions
- COloc Co-localization
- GENint Genetic_interactions
- PATH Pathway
- SHpd Shared_protein_domains
The species can be filtered using the following parameters: * Arabidopsis_thaliana * Caenorhabditis_elegans * Danio_rerio * Drosophila_melanogaster * Escherichia_coli * Homo_sapiens * Mus_musculus * Rattus_norvegicus * Saccharomyces_cerevisiae
For default the organism is homo sapiens.
The example show the shared protein domain network for Saccharomyces_cerevisiae. For more information see SpidermiR package.
## [1] "Downloading: http://genemania.org/data/current/Saccharomyces_cerevisiae/Shared_protein_domains.INTERPRO.txt ... reference n. 1 of 2"
## [1] "Downloading: http://genemania.org/data/current/Saccharomyces_cerevisiae/Shared_protein_domains.PFAM.txt ... reference n. 2 of 2"
## [1] "Preprocessing of the network n. 1 of 2"
## [1] "Preprocessing of the network n. 2 of 2"Integration data: Integration between pathway and network data
path_net: Network of interacting genes for each pathway according a network type (PHint,COloc,GENint,PATH,SHpd)
The function path_net creates a network of interacting genes (downloaded from GeneMania) for each pathway. Interacting genes are genes belonging to the same pathway and the interaction is given from network chosen by the user, according the paramenters of the function getNETdata.
The output will be a network of genes belonging to the same pathway.
## [1] "Glycolysis / Gluconeogenesis"
## [1] "Citrate cycle (TCA cycle)"
## [1] "Pentose phosphate pathway"
## [1] "Pentose and glucuronate interconversions"
## [1] "Fructose and mannose metabolism"list_path_net: List of interacting genes for each pathway (list of genes) according a network type (PHint,COloc,GENint,PATH,SHpd)
The function list_path_net creates a list of interacting genes for each pathway. Interacting genes are genes belonging to the same pathway and the interaction is given from network chosen by the user, according the paramenters of the function getNETdata.
The output will be a list of genes belonging to the same pathway and those having an interaction in the network.
## [1] "List of genes interacting in the same pathway: Glycolysis / Gluconeogenesis"
## [1] "List of genes interacting in the same pathway: Citrate cycle (TCA cycle)"
## [1] "List of genes interacting in the same pathway: Pentose phosphate pathway"
## [1] "List of genes interacting in the same pathway: Pentose and glucuronate interconversions"
## [1] "List of genes interacting in the same pathway: Fructose and mannose metabolism"Pathway summary indexes: Score for each pathway
GE_matrix: grouping gene expression profiles in pathways
Get human KEGG pathway data and a gene expression matrix in order to obtain a matrix with the gene expression levels grouped by pathways.
Starting from a matrix of gene expression (rows are genes and columns are samples, TCGA data) the function GE_matrix creates a profile of gene expression levels for each pathway given by the user:
## [1] "Glycolysis / Gluconeogenesis"
## [1] "Citrate cycle (TCA cycle)"
## [1] "Pentose phosphate pathway"
## [1] "Pentose and glucuronate interconversions"
## [1] "Fructose and mannose metabolism"
## [1] "Galactose metabolism"
## [1] "Ascorbate and aldarate metabolism"
## [1] "Fatty acid biosynthesis"
## [1] "Fatty acid elongation"
## [1] "Fatty acid degradation"GE_matrix_mean:
Get human KEGG pathway data and a gene expression matrix in order to obtain a matrix PXG (in the columns there are the pathways and in the rows there are genes) with the mean gene expression for only genes given containing in the pathways given in input by the user.
## [1] "Glycolysis_/ Gluconeogenesis"
## [1] "Citrate_cycle (TCA cycle)"
## [1] "Pentose_phosphate pathway"
## [1] "Pentose_and glucuronate interconversions"
## [1] "Fructose_and mannose metabolism"
## [1] "Galactose_metabolism"
## [1] "Ascorbate_and aldarate metabolism"
## [1] "Fatty_acid biosynthesis"
## [1] "Fatty_acid elongation"
## [1] "Fatty_acid degradation"average: Average of genes for each pathway starting from a matrix of gene expression
Starting from a matrix of gene expression (rows are genes and columns are samples, TCGA data) the function average creates an average matrix (SXG: S are the samples and P the pathways) of gene expression for each pathway:
stdv: Standard deviations of genes for each pathway starting from a matrix of gene expression
Starting from a matrix of gene expression (rows are genes and columns are samples, TCGA data) the function stdv creates a standard deviation matrix of gene expression for each pathway:
Pathway cross-talk indexes: Score for pairwise pathways
eucdistcrtlk: Euclidean distance for cross-talk measure
Starting from a matrix of gene expression (rows are genes and columns are samples, TCGA data) the function eucdistcrtlk creates an euclidean distance matrix of gene expression for pairwise pathway.
dsscorecrtlk: Discriminating score for cross-talk measure
Starting from a matrix of gene expression (rows are genes and columns are samples, TCGA data) the function dsscorecrtlk creates an discriminating score matrix for pairwise pathway as measure of cross-talk. Discriminating score is given by |M1-M2|/S1+S2 where M1 and M2 are mean and S1 and S2 standard deviation of expression levels of genes in a pathway 1 and and in a pathway 2 .
Selection of pathway cross-talk: Selection of pathway cross-talk
svm_classification: SVM classification
Given the substantial difference in the activities of many pathways between two classes (e.g. normal and cancer), we examined the effectiveness to classify the classes based on their pairwise pathway profiles. This function is used to find the interacting pathways that are altered in a particular pathology in terms of Area Under Curve (AUC).AUC was estimated by cross-validation method (k-fold cross-validation, k=10).It randomly selected some fraction of TCGA data (e.g. nf= 60; 60% of original dataset) to form the training set and then assigned the rest of the points to the testing set (40% of original dataset). For each pairwise pathway the user can obtain using the methods mentioned above a score matrix ( e.g.dev_std_crtlk ) and can focus on the pairs of pathways able to differentiate a particular subtype with respect to the normal type.
IPPI: Driver genes for each pathway
The function IPPI, using pathways and networks data, calculates the driver genes for each pathway. Please see Cava et al. BMC Genomics 2017.
Visualization: Gene interactions and pathways
StarBioTrek presents several functions for the preparation to the visualization of gene-gene interactions and pathway cross-talk using the qgraph package (S. Epskamp, et al. 2012). The function plotcrosstalk prepares the data:
##
## Attaching package: 'qgraph'## The following object is masked from 'package:graphite':
##
## pathways## The following object is masked from 'package:StarBioTrek':
##
## pathways
qgraph(formatplot[[1]],groups=formatplot[[2]], layout="spring", diag = FALSE,
cut = 0.6,legend.cex = 0.5,vsize = 6,layoutScale=c(0.8,0.8))
A circle can be generated using the function circleplot (Walter W, et al. 2015). A score for each gene can be assigned.
formatplot<-plotcrosstalk(pathway_plot=pathway[1:6],gs_expre=tumo)
score<-runif(length(formatplot[[2]]), min=-10, max=+10)
circleplot(preplot=formatplot,scoregene=score)
Session Information
## R version 4.2.0 RC (2022-04-19 r82224)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.4 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.15-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.15-bioc/R/lib/libRlapack.so
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_GB LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] grid stats4 stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] png_0.1-7 qgraph_1.9.2 graphite_1.42.0
## [4] StarBioTrek_1.22.0 miRNAtap_1.30.0 AnnotationDbi_1.58.0
## [7] IRanges_2.30.0 S4Vectors_0.34.0 Biobase_2.56.0
## [10] BiocGenerics_0.42.0 BiocStyle_2.24.0
##
## loaded via a namespace (and not attached):
## [1] backports_1.4.1 Hmisc_4.7-0 plyr_1.8.7
## [4] igraph_1.3.1 splines_4.2.0 usethis_2.1.5
## [7] GenomeInfoDb_1.32.0 ggplot2_3.3.5 digest_0.6.29
## [10] htmltools_0.5.2 magick_2.7.3 gdata_2.18.0
## [13] fansi_1.0.3 magrittr_2.0.3 checkmate_2.1.0
## [16] memoise_2.0.1 MLmetrics_1.1.1 cluster_2.1.3
## [19] ROCR_1.0-11 remotes_2.4.2 Biostrings_2.64.0
## [22] prettyunits_1.1.1 jpeg_0.1-9 colorspace_2.0-3
## [25] blob_1.2.3 rappdirs_0.3.3 xfun_0.30
## [28] dplyr_1.0.8 callr_3.7.0 crayon_1.5.1
## [31] RCurl_1.98-1.6 jsonlite_1.8.0 graph_1.74.0
## [34] survival_3.3-1 miRNAtap.db_0.99.10 glue_1.6.2
## [37] gtable_0.3.0 zlibbioc_1.42.0 XVector_0.36.0
## [40] pkgbuild_1.3.1 abind_1.4-5 scales_1.2.0
## [43] DBI_1.1.2 Rcpp_1.0.8.3 htmlTable_2.4.0
## [46] tmvnsim_1.0-2 foreign_0.8-82 bit_4.0.4
## [49] proxy_0.4-26 Formula_1.2-4 sqldf_0.4-11
## [52] htmlwidgets_1.5.4 httr_1.4.2 RColorBrewer_1.1-3
## [55] lavaan_0.6-11 ellipsis_0.3.2 pkgconfig_2.0.3
## [58] nnet_7.3-17 sass_0.4.1 utf8_1.2.2
## [61] tidyselect_1.1.2 rlang_1.0.2 reshape2_1.4.4
## [64] munsell_0.5.0 tools_4.2.0 cachem_1.0.6
## [67] cli_3.3.0 gsubfn_0.7 generics_0.1.2
## [70] RSQLite_2.2.12 devtools_2.4.3 fdrtool_1.2.17
## [73] evaluate_0.15 stringr_1.4.0 fastmap_1.1.0
## [76] yaml_2.3.5 processx_3.5.3 org.Hs.eg.db_3.15.0
## [79] knitr_1.38 bit64_4.0.5 fs_1.5.2
## [82] purrr_0.3.4 KEGGREST_1.36.0 glasso_1.11
## [85] pbapply_1.5-0 nlme_3.1-157 brio_1.1.3
## [88] compiler_4.2.0 rstudioapi_0.13 curl_4.3.2
## [91] e1071_1.7-9 testthat_3.1.4 tibble_3.1.6
## [94] bslib_0.3.1 pbivnorm_0.6.0 stringi_1.7.6
## [97] highr_0.9 ps_1.7.0 desc_1.4.1
## [100] lattice_0.20-45 Matrix_1.4-1 psych_2.2.3
## [103] vctrs_0.4.1 pillar_1.7.0 lifecycle_1.0.1
## [106] BiocManager_1.30.17 jquerylib_0.1.4 data.table_1.14.2
## [109] bitops_1.0-7 corpcor_1.6.10 R6_2.5.1
## [112] latticeExtra_0.6-29 bookdown_0.26 gridExtra_2.3
## [115] sessioninfo_1.2.2 gtools_3.9.2 assertthat_0.2.1
## [118] pkgload_1.2.4 chron_2.3-56 proto_1.0.0
## [121] rprojroot_2.0.3 withr_2.5.0 SpidermiR_1.26.0
## [124] mnormt_2.0.2 GenomeInfoDbData_1.2.8 parallel_4.2.0
## [127] rpart_4.1.16 class_7.3-20 rmarkdown_2.14
## [130] base64enc_0.1-3References
Cancer Genome Atlas Research Network and others. 2012. “Comprehensive Molecular Characterization of Human Colon and Rectal Cancer.” https://doi.org/10.1038/nature11252.
Sales G, et al. 2012. “Graphite - a Bioconductor Package to Convert Pathway Topology to Gene Network.” https://doi.org/10.1186/1471-2105-13-20.
S. Epskamp, et al. 2012. “Qgraph Network Visualizations of Relationships in Psychometric Data.”
Walter W, et al. 2015. “GOplot an R Package for Visually Combining Expression Data with Functional Analysis.”
Warde-Farley D, et al. 2010. “The GeneMANIA Prediction Server Biological Network Integration for Gene Prioritization and Predicting Gene Function.”