Working with StarBioTrek package
2021-05-19
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 321 pathways"
## [1] "Querying............. Citrate cycle (TCA cycle) 2 of 321 pathways"
## [1] "Querying............. Pentose phosphate pathway 3 of 321 pathways"
## [1] "Querying............. Pentose and glucuronate interconversions 4 of 321 pathways"
## [1] "Querying............. Fructose and mannose metabolism 5 of 321 pathways"
## [1] "Querying............. Galactose metabolism 6 of 321 pathways"
## [1] "Querying............. Ascorbate and aldarate metabolism 7 of 321 pathways"
## [1] "Querying............. Fatty acid biosynthesis 8 of 321 pathways"
## [1] "Querying............. Fatty acid elongation 9 of 321 pathways"
## [1] "Querying............. Fatty acid degradation 10 of 321 pathways"
## [1] "Querying............. Synthesis and degradation of ketone bodies 11 of 321 pathways"
## [1] "Querying............. Steroid biosynthesis 12 of 321 pathways"
## [1] "Querying............. Primary bile acid biosynthesis 13 of 321 pathways"
## [1] "Querying............. Ubiquinone and other terpenoid-quinone biosynthesis 14 of 321 pathways"
## [1] "Querying............. Steroid hormone biosynthesis 15 of 321 pathways"
## [1] "Querying............. Oxidative phosphorylation 16 of 321 pathways"
## [1] "Querying............. Arginine biosynthesis 17 of 321 pathways"
## [1] "Querying............. Purine metabolism 18 of 321 pathways"
## [1] "Querying............. Caffeine metabolism 19 of 321 pathways"
## [1] "Querying............. Pyrimidine metabolism 20 of 321 pathways"
## [1] "Querying............. Alanine, aspartate and glutamate metabolism 21 of 321 pathways"
## [1] "Querying............. Glycine, serine and threonine metabolism 22 of 321 pathways"
## [1] "Querying............. Cysteine and methionine metabolism 23 of 321 pathways"
## [1] "Querying............. Valine, leucine and isoleucine degradation 24 of 321 pathways"
## [1] "Querying............. Lysine degradation 25 of 321 pathways"
## [1] "Querying............. Arginine and proline metabolism 26 of 321 pathways"
## [1] "Querying............. Histidine metabolism 27 of 321 pathways"
## [1] "Querying............. Tyrosine metabolism 28 of 321 pathways"
## [1] "Querying............. Phenylalanine metabolism 29 of 321 pathways"
## [1] "Querying............. Tryptophan metabolism 30 of 321 pathways"
## [1] "Querying............. Phenylalanine, tyrosine and tryptophan biosynthesis 31 of 321 pathways"
## [1] "Querying............. beta-Alanine metabolism 32 of 321 pathways"
## [1] "Querying............. Taurine and hypotaurine metabolism 33 of 321 pathways"
## [1] "Querying............. Phosphonate and phosphinate metabolism 34 of 321 pathways"
## [1] "Querying............. Selenocompound metabolism 35 of 321 pathways"
## [1] "Querying............. D-Glutamine and D-glutamate metabolism 36 of 321 pathways"
## [1] "Querying............. Glutathione metabolism 37 of 321 pathways"
## [1] "Querying............. Starch and sucrose metabolism 38 of 321 pathways"
## [1] "Querying............. N-Glycan biosynthesis 39 of 321 pathways"
## [1] "Querying............. Mucin type O-glycan biosynthesis 40 of 321 pathways"
## [1] "Querying............. Various types of N-glycan biosynthesis 41 of 321 pathways"
## [1] "Querying............. Mannose type O-glycan biosynthesis 42 of 321 pathways"
## [1] "Querying............. Amino sugar and nucleotide sugar metabolism 43 of 321 pathways"
## [1] "Querying............. Glycosaminoglycan degradation 44 of 321 pathways"
## [1] "Querying............. Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate 45 of 321 pathways"
## [1] "Querying............. Glycosaminoglycan biosynthesis - heparan sulfate / heparin 46 of 321 pathways"
## [1] "Querying............. Glycerolipid metabolism 47 of 321 pathways"
## [1] "Querying............. Inositol phosphate metabolism 48 of 321 pathways"
## [1] "Querying............. Glycosylphosphatidylinositol (GPI)-anchor biosynthesis 49 of 321 pathways"
## [1] "Querying............. Glycerophospholipid metabolism 50 of 321 pathways"
## [1] "Querying............. Ether lipid metabolism 51 of 321 pathways"
## [1] "Querying............. Arachidonic acid metabolism 52 of 321 pathways"
## [1] "Querying............. Linoleic acid metabolism 53 of 321 pathways"
## [1] "Querying............. alpha-Linolenic acid metabolism 54 of 321 pathways"
## [1] "Querying............. Sphingolipid metabolism 55 of 321 pathways"
## [1] "Querying............. Glycosphingolipid biosynthesis - lacto and neolacto series 56 of 321 pathways"
## [1] "Querying............. Glycosphingolipid biosynthesis - globo and isoglobo series 57 of 321 pathways"
## [1] "Querying............. Glycosphingolipid biosynthesis - ganglio series 58 of 321 pathways"
## [1] "Querying............. Pyruvate metabolism 59 of 321 pathways"
## [1] "Querying............. Glyoxylate and dicarboxylate metabolism 60 of 321 pathways"
## [1] "Querying............. Propanoate metabolism 61 of 321 pathways"
## [1] "Querying............. Butanoate metabolism 62 of 321 pathways"
## [1] "Querying............. One carbon pool by folate 63 of 321 pathways"
## [1] "Querying............. Thiamine metabolism 64 of 321 pathways"
## [1] "Querying............. Riboflavin metabolism 65 of 321 pathways"
## [1] "Querying............. Vitamin B6 metabolism 66 of 321 pathways"
## [1] "Querying............. Nicotinate and nicotinamide metabolism 67 of 321 pathways"
## [1] "Querying............. Pantothenate and CoA biosynthesis 68 of 321 pathways"
## [1] "Querying............. Biotin metabolism 69 of 321 pathways"
## [1] "Querying............. Lipoic acid metabolism 70 of 321 pathways"
## [1] "Querying............. Folate biosynthesis 71 of 321 pathways"
## [1] "Querying............. Retinol metabolism 72 of 321 pathways"
## [1] "Querying............. Porphyrin and chlorophyll metabolism 73 of 321 pathways"
## [1] "Querying............. Terpenoid backbone biosynthesis 74 of 321 pathways"
## [1] "Querying............. Nitrogen metabolism 75 of 321 pathways"
## [1] "Querying............. Sulfur metabolism 76 of 321 pathways"
## [1] "Querying............. Aminoacyl-tRNA biosynthesis 77 of 321 pathways"
## [1] "Querying............. Metabolism of xenobiotics by cytochrome P450 78 of 321 pathways"
## [1] "Querying............. Drug metabolism - cytochrome P450 79 of 321 pathways"
## [1] "Querying............. Drug metabolism - other enzymes 80 of 321 pathways"
## [1] "Querying............. Biosynthesis of unsaturated fatty acids 81 of 321 pathways"
## [1] "Querying............. Metabolic pathways 82 of 321 pathways"
## [1] "Querying............. Carbon metabolism 83 of 321 pathways"
## [1] "Querying............. 2-Oxocarboxylic acid metabolism 84 of 321 pathways"
## [1] "Querying............. Fatty acid metabolism 85 of 321 pathways"
## [1] "Querying............. Biosynthesis of amino acids 86 of 321 pathways"
## [1] "Querying............. Biosynthesis of cofactors 87 of 321 pathways"
## [1] "Querying............. EGFR tyrosine kinase inhibitor resistance 88 of 321 pathways"
## [1] "Querying............. Endocrine resistance 89 of 321 pathways"
## [1] "Querying............. Antifolate resistance 90 of 321 pathways"
## [1] "Querying............. Platinum drug resistance 91 of 321 pathways"
## [1] "Querying............. mRNA surveillance pathway 92 of 321 pathways"
## [1] "Querying............. RNA degradation 93 of 321 pathways"
## [1] "Querying............. PPAR signaling pathway 94 of 321 pathways"
## [1] "Querying............. Homologous recombination 95 of 321 pathways"
## [1] "Querying............. Fanconi anemia pathway 96 of 321 pathways"
## [1] "Querying............. MAPK signaling pathway 97 of 321 pathways"
## [1] "Querying............. ErbB signaling pathway 98 of 321 pathways"
## [1] "Querying............. Ras signaling pathway 99 of 321 pathways"
## [1] "Querying............. Rap1 signaling pathway 100 of 321 pathways"
## [1] "Querying............. Calcium signaling pathway 101 of 321 pathways"
## [1] "Querying............. cGMP-PKG signaling pathway 102 of 321 pathways"
## [1] "Querying............. cAMP signaling pathway 103 of 321 pathways"
## [1] "Querying............. Cytokine-cytokine receptor interaction 104 of 321 pathways"
## [1] "Querying............. Viral protein interaction with cytokine and cytokine receptor 105 of 321 pathways"
## [1] "Querying............. Chemokine signaling pathway 106 of 321 pathways"
## [1] "Querying............. NF-kappa B signaling pathway 107 of 321 pathways"
## [1] "Querying............. HIF-1 signaling pathway 108 of 321 pathways"
## [1] "Querying............. FoxO signaling pathway 109 of 321 pathways"
## [1] "Querying............. Phosphatidylinositol signaling system 110 of 321 pathways"
## [1] "Querying............. Sphingolipid signaling pathway 111 of 321 pathways"
## [1] "Querying............. Phospholipase D signaling pathway 112 of 321 pathways"
## [1] "Querying............. Neuroactive ligand-receptor interaction 113 of 321 pathways"
## [1] "Querying............. Cell cycle 114 of 321 pathways"
## [1] "Querying............. Oocyte meiosis 115 of 321 pathways"
## [1] "Querying............. p53 signaling pathway 116 of 321 pathways"
## [1] "Querying............. Sulfur relay system 117 of 321 pathways"
## [1] "Querying............. SNARE interactions in vesicular transport 118 of 321 pathways"
## [1] "Querying............. Autophagy - other 119 of 321 pathways"
## [1] "Querying............. Mitophagy - animal 120 of 321 pathways"
## [1] "Querying............. Autophagy - animal 121 of 321 pathways"
## [1] "Querying............. Protein processing in endoplasmic reticulum 122 of 321 pathways"
## [1] "Querying............. Endocytosis 123 of 321 pathways"
## [1] "Querying............. Phagosome 124 of 321 pathways"
## [1] "Querying............. Peroxisome 125 of 321 pathways"
## [1] "Querying............. mTOR signaling pathway 126 of 321 pathways"
## [1] "Querying............. PI3K-Akt signaling pathway 127 of 321 pathways"
## [1] "Querying............. AMPK signaling pathway 128 of 321 pathways"
## [1] "Querying............. Apoptosis 129 of 321 pathways"
## [1] "Querying............. Longevity regulating pathway 130 of 321 pathways"
## [1] "Querying............. Longevity regulating pathway - multiple species 131 of 321 pathways"
## [1] "Querying............. Apoptosis - multiple species 132 of 321 pathways"
## [1] "Querying............. Ferroptosis 133 of 321 pathways"
## [1] "Querying............. Necroptosis 134 of 321 pathways"
## [1] "Querying............. Cellular senescence 135 of 321 pathways"
## [1] "Querying............. Cardiac muscle contraction 136 of 321 pathways"
## [1] "Querying............. Adrenergic signaling in cardiomyocytes 137 of 321 pathways"
## [1] "Querying............. Vascular smooth muscle contraction 138 of 321 pathways"
## [1] "Querying............. Wnt signaling pathway 139 of 321 pathways"
## [1] "Querying............. Notch signaling pathway 140 of 321 pathways"
## [1] "Querying............. Hedgehog signaling pathway 141 of 321 pathways"
## [1] "Querying............. TGF-beta signaling pathway 142 of 321 pathways"
## [1] "Querying............. Axon guidance 143 of 321 pathways"
## [1] "Querying............. VEGF signaling pathway 144 of 321 pathways"
## [1] "Querying............. Apelin signaling pathway 145 of 321 pathways"
## [1] "Querying............. Osteoclast differentiation 146 of 321 pathways"
## [1] "Querying............. Hippo signaling pathway 147 of 321 pathways"
## [1] "Querying............. Hippo signaling pathway - multiple species 148 of 321 pathways"
## [1] "Querying............. Focal adhesion 149 of 321 pathways"
## [1] "Querying............. ECM-receptor interaction 150 of 321 pathways"
## [1] "Querying............. Cell adhesion molecules 151 of 321 pathways"
## [1] "Querying............. Adherens junction 152 of 321 pathways"
## [1] "Querying............. Tight junction 153 of 321 pathways"
## [1] "Querying............. Gap junction 154 of 321 pathways"
## [1] "Querying............. Signaling pathways regulating pluripotency of stem cells 155 of 321 pathways"
## [1] "Querying............. Complement and coagulation cascades 156 of 321 pathways"
## [1] "Querying............. Platelet activation 157 of 321 pathways"
## [1] "Querying............. Antigen processing and presentation 158 of 321 pathways"
## [1] "Querying............. Neutrophil extracellular trap formation 159 of 321 pathways"
## [1] "Querying............. Renin-angiotensin system 160 of 321 pathways"
## [1] "Querying............. Toll-like receptor signaling pathway 161 of 321 pathways"
## [1] "Querying............. NOD-like receptor signaling pathway 162 of 321 pathways"
## [1] "Querying............. RIG-I-like receptor signaling pathway 163 of 321 pathways"
## [1] "Querying............. Cytosolic DNA-sensing pathway 164 of 321 pathways"
## [1] "Querying............. C-type lectin receptor signaling pathway 165 of 321 pathways"
## [1] "Querying............. JAK-STAT signaling pathway 166 of 321 pathways"
## [1] "Querying............. Natural killer cell mediated cytotoxicity 167 of 321 pathways"
## [1] "Querying............. IL-17 signaling pathway 168 of 321 pathways"
## [1] "Querying............. Th1 and Th2 cell differentiation 169 of 321 pathways"
## [1] "Querying............. Th17 cell differentiation 170 of 321 pathways"
## [1] "Querying............. T cell receptor signaling pathway 171 of 321 pathways"
## [1] "Querying............. B cell receptor signaling pathway 172 of 321 pathways"
## [1] "Querying............. Fc epsilon RI signaling pathway 173 of 321 pathways"
## [1] "Querying............. Fc gamma R-mediated phagocytosis 174 of 321 pathways"
## [1] "Querying............. TNF signaling pathway 175 of 321 pathways"
## [1] "Querying............. Leukocyte transendothelial migration 176 of 321 pathways"
## [1] "Querying............. Intestinal immune network for IgA production 177 of 321 pathways"
## [1] "Querying............. Circadian rhythm 178 of 321 pathways"
## [1] "Querying............. Circadian entrainment 179 of 321 pathways"
## [1] "Querying............. Thermogenesis 180 of 321 pathways"
## [1] "Querying............. Long-term potentiation 181 of 321 pathways"
## [1] "Querying............. Synaptic vesicle cycle 182 of 321 pathways"
## [1] "Querying............. Neurotrophin signaling pathway 183 of 321 pathways"
## [1] "Querying............. Retrograde endocannabinoid signaling 184 of 321 pathways"
## [1] "Querying............. Glutamatergic synapse 185 of 321 pathways"
## [1] "Querying............. Cholinergic synapse 186 of 321 pathways"
## [1] "Querying............. Serotonergic synapse 187 of 321 pathways"
## [1] "Querying............. GABAergic synapse 188 of 321 pathways"
## [1] "Querying............. Dopaminergic synapse 189 of 321 pathways"
## [1] "Querying............. Long-term depression 190 of 321 pathways"
## [1] "Querying............. Olfactory transduction 191 of 321 pathways"
## [1] "Querying............. Taste transduction 192 of 321 pathways"
## [1] "Querying............. Phototransduction 193 of 321 pathways"
## [1] "Querying............. Inflammatory mediator regulation of TRP channels 194 of 321 pathways"
## [1] "Querying............. Regulation of actin cytoskeleton 195 of 321 pathways"
## [1] "Querying............. Insulin signaling pathway 196 of 321 pathways"
## [1] "Querying............. Insulin secretion 197 of 321 pathways"
## [1] "Querying............. GnRH signaling pathway 198 of 321 pathways"
## [1] "Querying............. Ovarian steroidogenesis 199 of 321 pathways"
## [1] "Querying............. Progesterone-mediated oocyte maturation 200 of 321 pathways"
## [1] "Querying............. Estrogen signaling pathway 201 of 321 pathways"
## [1] "Querying............. Melanogenesis 202 of 321 pathways"
## [1] "Querying............. Prolactin signaling pathway 203 of 321 pathways"
## [1] "Querying............. Thyroid hormone synthesis 204 of 321 pathways"
## [1] "Querying............. Thyroid hormone signaling pathway 205 of 321 pathways"
## [1] "Querying............. Adipocytokine signaling pathway 206 of 321 pathways"
## [1] "Querying............. Oxytocin signaling pathway 207 of 321 pathways"
## [1] "Querying............. Glucagon signaling pathway 208 of 321 pathways"
## [1] "Querying............. Regulation of lipolysis in adipocytes 209 of 321 pathways"
## [1] "Querying............. Renin secretion 210 of 321 pathways"
## [1] "Querying............. Aldosterone synthesis and secretion 211 of 321 pathways"
## [1] "Querying............. Relaxin signaling pathway 212 of 321 pathways"
## [1] "Querying............. Cortisol synthesis and secretion 213 of 321 pathways"
## [1] "Querying............. Parathyroid hormone synthesis, secretion and action 214 of 321 pathways"
## [1] "Querying............. GnRH secretion 215 of 321 pathways"
## [1] "Querying............. Type II diabetes mellitus 216 of 321 pathways"
## [1] "Querying............. Insulin resistance 217 of 321 pathways"
## [1] "Querying............. Non-alcoholic fatty liver disease 218 of 321 pathways"
## [1] "Querying............. AGE-RAGE signaling pathway in diabetic complications 219 of 321 pathways"
## [1] "Querying............. Cushing syndrome 220 of 321 pathways"
## [1] "Querying............. Growth hormone synthesis, secretion and action 221 of 321 pathways"
## [1] "Querying............. Type I diabetes mellitus 222 of 321 pathways"
## [1] "Querying............. Maturity onset diabetes of the young 223 of 321 pathways"
## [1] "Querying............. Aldosterone-regulated sodium reabsorption 224 of 321 pathways"
## [1] "Querying............. Endocrine and other factor-regulated calcium reabsorption 225 of 321 pathways"
## [1] "Querying............. Vasopressin-regulated water reabsorption 226 of 321 pathways"
## [1] "Querying............. Proximal tubule bicarbonate reclamation 227 of 321 pathways"
## [1] "Querying............. Salivary secretion 228 of 321 pathways"
## [1] "Querying............. Gastric acid secretion 229 of 321 pathways"
## [1] "Querying............. Pancreatic secretion 230 of 321 pathways"
## [1] "Querying............. Carbohydrate digestion and absorption 231 of 321 pathways"
## [1] "Querying............. Fat digestion and absorption 232 of 321 pathways"
## [1] "Querying............. Bile secretion 233 of 321 pathways"
## [1] "Querying............. Vitamin digestion and absorption 234 of 321 pathways"
## [1] "Querying............. Mineral absorption 235 of 321 pathways"
## [1] "Querying............. Cholesterol metabolism 236 of 321 pathways"
## [1] "Querying............. Alzheimer disease 237 of 321 pathways"
## [1] "Querying............. Parkinson disease 238 of 321 pathways"
## [1] "Querying............. Amyotrophic lateral sclerosis 239 of 321 pathways"
## [1] "Querying............. Huntington disease 240 of 321 pathways"
## [1] "Querying............. Spinocerebellar ataxia 241 of 321 pathways"
## [1] "Querying............. Prion disease 242 of 321 pathways"
## [1] "Querying............. Pathways of neurodegeneration - multiple diseases 243 of 321 pathways"
## [1] "Querying............. Cocaine addiction 244 of 321 pathways"
## [1] "Querying............. Amphetamine addiction 245 of 321 pathways"
## [1] "Querying............. Morphine addiction 246 of 321 pathways"
## [1] "Querying............. Alcoholism 247 of 321 pathways"
## [1] "Querying............. Bacterial invasion of epithelial cells 248 of 321 pathways"
## [1] "Querying............. Vibrio cholerae infection 249 of 321 pathways"
## [1] "Querying............. Epithelial cell signaling in Helicobacter pylori infection 250 of 321 pathways"
## [1] "Querying............. Pathogenic Escherichia coli infection 251 of 321 pathways"
## [1] "Querying............. Shigellosis 252 of 321 pathways"
## [1] "Querying............. Salmonella infection 253 of 321 pathways"
## [1] "Querying............. Pertussis 254 of 321 pathways"
## [1] "Querying............. Legionellosis 255 of 321 pathways"
## [1] "Querying............. Yersinia infection 256 of 321 pathways"
## [1] "Querying............. Leishmaniasis 257 of 321 pathways"
## [1] "Querying............. Chagas disease 258 of 321 pathways"
## [1] "Querying............. African trypanosomiasis 259 of 321 pathways"
## [1] "Querying............. Malaria 260 of 321 pathways"
## [1] "Querying............. Toxoplasmosis 261 of 321 pathways"
## [1] "Querying............. Amoebiasis 262 of 321 pathways"
## [1] "Querying............. Staphylococcus aureus infection 263 of 321 pathways"
## [1] "Querying............. Tuberculosis 264 of 321 pathways"
## [1] "Querying............. Hepatitis C 265 of 321 pathways"
## [1] "Querying............. Hepatitis B 266 of 321 pathways"
## [1] "Querying............. Measles 267 of 321 pathways"
## [1] "Querying............. Human cytomegalovirus infection 268 of 321 pathways"
## [1] "Querying............. Influenza A 269 of 321 pathways"
## [1] "Querying............. Human papillomavirus infection 270 of 321 pathways"
## [1] "Querying............. Human T-cell leukemia virus 1 infection 271 of 321 pathways"
## [1] "Querying............. Kaposi sarcoma-associated herpesvirus infection 272 of 321 pathways"
## [1] "Querying............. Herpes simplex virus 1 infection 273 of 321 pathways"
## [1] "Querying............. Epstein-Barr virus infection 274 of 321 pathways"
## [1] "Querying............. Human immunodeficiency virus 1 infection 275 of 321 pathways"
## [1] "Querying............. Coronavirus disease - COVID-19 276 of 321 pathways"
## [1] "Querying............. Pathways in cancer 277 of 321 pathways"
## [1] "Querying............. Transcriptional misregulation in cancer 278 of 321 pathways"
## [1] "Querying............. Viral carcinogenesis 279 of 321 pathways"
## [1] "Querying............. Chemical carcinogenesis 280 of 321 pathways"
## [1] "Querying............. Proteoglycans in cancer 281 of 321 pathways"
## [1] "Querying............. MicroRNAs in cancer 282 of 321 pathways"
## [1] "Querying............. Colorectal cancer 283 of 321 pathways"
## [1] "Querying............. Renal cell carcinoma 284 of 321 pathways"
## [1] "Querying............. Pancreatic cancer 285 of 321 pathways"
## [1] "Querying............. Endometrial cancer 286 of 321 pathways"
## [1] "Querying............. Glioma 287 of 321 pathways"
## [1] "Querying............. Prostate cancer 288 of 321 pathways"
## [1] "Querying............. Thyroid cancer 289 of 321 pathways"
## [1] "Querying............. Basal cell carcinoma 290 of 321 pathways"
## [1] "Querying............. Melanoma 291 of 321 pathways"
## [1] "Querying............. Bladder cancer 292 of 321 pathways"
## [1] "Querying............. Chronic myeloid leukemia 293 of 321 pathways"
## [1] "Querying............. Acute myeloid leukemia 294 of 321 pathways"
## [1] "Querying............. Small cell lung cancer 295 of 321 pathways"
## [1] "Querying............. Non-small cell lung cancer 296 of 321 pathways"
## [1] "Querying............. Breast cancer 297 of 321 pathways"
## [1] "Querying............. Hepatocellular carcinoma 298 of 321 pathways"
## [1] "Querying............. Gastric cancer 299 of 321 pathways"
## [1] "Querying............. Central carbon metabolism in cancer 300 of 321 pathways"
## [1] "Querying............. Choline metabolism in cancer 301 of 321 pathways"
## [1] "Querying............. PD-L1 expression and PD-1 checkpoint pathway in cancer 302 of 321 pathways"
## [1] "Querying............. Asthma 303 of 321 pathways"
## [1] "Querying............. Autoimmune thyroid disease 304 of 321 pathways"
## [1] "Querying............. Inflammatory bowel disease 305 of 321 pathways"
## [1] "Querying............. Systemic lupus erythematosus 306 of 321 pathways"
## [1] "Querying............. Rheumatoid arthritis 307 of 321 pathways"
## [1] "Querying............. Allograft rejection 308 of 321 pathways"
## [1] "Querying............. Graft-versus-host disease 309 of 321 pathways"
## [1] "Querying............. Hypertrophic cardiomyopathy 310 of 321 pathways"
## [1] "Querying............. Arrhythmogenic right ventricular cardiomyopathy 311 of 321 pathways"
## [1] "Querying............. Dilated cardiomyopathy 312 of 321 pathways"
## [1] "Querying............. Diabetic cardiomyopathy 313 of 321 pathways"
## [1] "Querying............. Viral myocarditis 314 of 321 pathways"
## [1] "Querying............. Lipid and atherosclerosis 315 of 321 pathways"
## [1] "Querying............. Fluid shear stress and atherosclerosis 316 of 321 pathways"
## [1] "Querying............. Valine, leucine and isoleucine biosynthesis 317 of 321 pathways"
## [1] "Querying............. D-Arginine and D-ornithine metabolism 318 of 321 pathways"
## [1] "Querying............. Neomycin, kanamycin and gentamicin biosynthesis 319 of 321 pathways"
## [1] "Querying............. Protein digestion and absorption 320 of 321 pathways"
## [1] "Querying............. Nicotine addiction 321 of 321 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 4.1.0 (2021-05-18)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.2 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.13-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.13-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 parallel stats4 stats graphics grDevices utils
## [8] datasets methods base
##
## other attached packages:
## [1] png_0.1-7 qgraph_1.6.9 org.Hs.eg.db_3.13.0
## [4] graphite_1.38.0 StarBioTrek_1.18.0 miRNAtap_1.26.0
## [7] AnnotationDbi_1.54.0 IRanges_2.26.0 S4Vectors_0.30.0
## [10] Biobase_2.52.0 BiocGenerics_0.38.0 BiocStyle_2.20.0
##
## loaded via a namespace (and not attached):
## [1] backports_1.2.1 Hmisc_4.5-0 plyr_1.8.6
## [4] igraph_1.2.6 splines_4.1.0 usethis_2.0.1
## [7] GenomeInfoDb_1.28.0 ggplot2_3.3.3 digest_0.6.27
## [10] htmltools_0.5.1.1 magick_2.7.2 gdata_2.18.0
## [13] fansi_0.4.2 magrittr_2.0.1 checkmate_2.0.0
## [16] memoise_2.0.0 MLmetrics_1.1.1 cluster_2.1.2
## [19] ROCR_1.0-11 remotes_2.3.0 Biostrings_2.60.0
## [22] prettyunits_1.1.1 jpeg_0.1-8.1 colorspace_2.0-1
## [25] blob_1.2.1 rappdirs_0.3.3 xfun_0.23
## [28] dplyr_1.0.6 callr_3.7.0 crayon_1.4.1
## [31] RCurl_1.98-1.3 jsonlite_1.7.2 graph_1.70.0
## [34] survival_3.2-11 miRNAtap.db_0.99.10 glue_1.4.2
## [37] gtable_0.3.0 zlibbioc_1.38.0 XVector_0.32.0
## [40] pkgbuild_1.2.0 abind_1.4-5 scales_1.1.1
## [43] DBI_1.1.1 Rcpp_1.0.6 htmlTable_2.2.1
## [46] tmvnsim_1.0-2 foreign_0.8-81 bit_4.0.4
## [49] proxy_0.4-25 Formula_1.2-4 sqldf_0.4-11
## [52] htmlwidgets_1.5.3 httr_1.4.2 lavaan_0.6-8
## [55] RColorBrewer_1.1-2 ellipsis_0.3.2 pkgconfig_2.0.3
## [58] nnet_7.3-16 sass_0.4.0 utf8_1.2.1
## [61] tidyselect_1.1.1 rlang_0.4.11 reshape2_1.4.4
## [64] munsell_0.5.0 tools_4.1.0 cachem_1.0.5
## [67] cli_2.5.0 gsubfn_0.7 generics_0.1.0
## [70] RSQLite_2.2.7 devtools_2.4.1 fdrtool_1.2.16
## [73] evaluate_0.14 stringr_1.4.0 fastmap_1.1.0
## [76] yaml_2.2.1 processx_3.5.2 knitr_1.33
## [79] bit64_4.0.5 fs_1.5.0 purrr_0.3.4
## [82] KEGGREST_1.32.0 glasso_1.11 pbapply_1.4-3
## [85] nlme_3.1-152 compiler_4.1.0 rstudioapi_0.13
## [88] curl_4.3.1 e1071_1.7-6 testthat_3.0.2
## [91] tibble_3.1.2 pbivnorm_0.6.0 bslib_0.2.5.1
## [94] stringi_1.6.2 highr_0.9 ps_1.6.0
## [97] desc_1.3.0 lattice_0.20-44 Matrix_1.3-3
## [100] psych_2.1.3 vctrs_0.3.8 pillar_1.6.1
## [103] lifecycle_1.0.0 networkD3_0.4 BiocManager_1.30.15
## [106] jquerylib_0.1.4 data.table_1.14.0 bitops_1.0-7
## [109] corpcor_1.6.9 R6_2.5.0 latticeExtra_0.6-29
## [112] bookdown_0.22 gridExtra_2.3 sessioninfo_1.1.1
## [115] gtools_3.8.2 assertthat_0.2.1 pkgload_1.2.1
## [118] chron_2.3-56 proto_1.0.0 rprojroot_2.0.2
## [121] withr_2.4.2 SpidermiR_1.22.0 mnormt_2.0.2
## [124] GenomeInfoDbData_1.2.6 rpart_4.1-15 class_7.3-19
## [127] rmarkdown_2.8 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.”