Working with StarBioTrek package
2020-10-27
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 |
| btaurus | kegg |
| btaurus | pathbank |
| btaurus | reactome |
| celegans | kegg |
| celegans | pathbank |
| celegans | reactome |
| cfamiliaris | kegg |
| cfamiliaris | reactome |
| dmelanogaster | kegg |
| dmelanogaster | pathbank |
| dmelanogaster | reactome |
| drerio | kegg |
| drerio | reactome |
| ecoli | kegg |
| ecoli | pathbank |
| ggallus | kegg |
| ggallus | reactome |
| hsapiens | biocarta |
| hsapiens | kegg |
| hsapiens | nci |
| hsapiens | panther |
| hsapiens | pathbank |
| hsapiens | pharmgkb |
| hsapiens | reactome |
| hsapiens | smpdb |
| mmusculus | kegg |
| mmusculus | pathbank |
| mmusculus | reactome |
| rnorvegicus | kegg |
| rnorvegicus | pathbank |
| rnorvegicus | reactome |
| scerevisiae | kegg |
| scerevisiae | pathbank |
| scerevisiae | reactome |
| sscrofa | kegg |
| sscrofa | reactome |
| 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 317 pathways"
## [1] "Querying............. Citrate cycle (TCA cycle) 2 of 317 pathways"
## [1] "Querying............. Pentose phosphate pathway 3 of 317 pathways"
## [1] "Querying............. Pentose and glucuronate interconversions 4 of 317 pathways"
## [1] "Querying............. Fructose and mannose metabolism 5 of 317 pathways"
## [1] "Querying............. Galactose metabolism 6 of 317 pathways"
## [1] "Querying............. Ascorbate and aldarate metabolism 7 of 317 pathways"
## [1] "Querying............. Fatty acid biosynthesis 8 of 317 pathways"
## [1] "Querying............. Fatty acid elongation 9 of 317 pathways"
## [1] "Querying............. Fatty acid degradation 10 of 317 pathways"
## [1] "Querying............. Synthesis and degradation of ketone bodies 11 of 317 pathways"
## [1] "Querying............. Steroid biosynthesis 12 of 317 pathways"
## [1] "Querying............. Primary bile acid biosynthesis 13 of 317 pathways"
## [1] "Querying............. Ubiquinone and other terpenoid-quinone biosynthesis 14 of 317 pathways"
## [1] "Querying............. Steroid hormone biosynthesis 15 of 317 pathways"
## [1] "Querying............. Oxidative phosphorylation 16 of 317 pathways"
## [1] "Querying............. Arginine biosynthesis 17 of 317 pathways"
## [1] "Querying............. Purine metabolism 18 of 317 pathways"
## [1] "Querying............. Caffeine metabolism 19 of 317 pathways"
## [1] "Querying............. Pyrimidine metabolism 20 of 317 pathways"
## [1] "Querying............. Alanine, aspartate and glutamate metabolism 21 of 317 pathways"
## [1] "Querying............. Glycine, serine and threonine metabolism 22 of 317 pathways"
## [1] "Querying............. Cysteine and methionine metabolism 23 of 317 pathways"
## [1] "Querying............. Valine, leucine and isoleucine degradation 24 of 317 pathways"
## [1] "Querying............. Lysine degradation 25 of 317 pathways"
## [1] "Querying............. Arginine and proline metabolism 26 of 317 pathways"
## [1] "Querying............. Histidine metabolism 27 of 317 pathways"
## [1] "Querying............. Tyrosine metabolism 28 of 317 pathways"
## [1] "Querying............. Phenylalanine metabolism 29 of 317 pathways"
## [1] "Querying............. Tryptophan metabolism 30 of 317 pathways"
## [1] "Querying............. Phenylalanine, tyrosine and tryptophan biosynthesis 31 of 317 pathways"
## [1] "Querying............. beta-Alanine metabolism 32 of 317 pathways"
## [1] "Querying............. Taurine and hypotaurine metabolism 33 of 317 pathways"
## [1] "Querying............. Phosphonate and phosphinate metabolism 34 of 317 pathways"
## [1] "Querying............. Selenocompound metabolism 35 of 317 pathways"
## [1] "Querying............. D-Glutamine and D-glutamate metabolism 36 of 317 pathways"
## [1] "Querying............. Glutathione metabolism 37 of 317 pathways"
## [1] "Querying............. Starch and sucrose metabolism 38 of 317 pathways"
## [1] "Querying............. N-Glycan biosynthesis 39 of 317 pathways"
## [1] "Querying............. Mucin type O-glycan biosynthesis 40 of 317 pathways"
## [1] "Querying............. Various types of N-glycan biosynthesis 41 of 317 pathways"
## [1] "Querying............. Mannose type O-glycan biosynthesis 42 of 317 pathways"
## [1] "Querying............. Amino sugar and nucleotide sugar metabolism 43 of 317 pathways"
## [1] "Querying............. Glycosaminoglycan degradation 44 of 317 pathways"
## [1] "Querying............. Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate 45 of 317 pathways"
## [1] "Querying............. Glycosaminoglycan biosynthesis - heparan sulfate / heparin 46 of 317 pathways"
## [1] "Querying............. Glycerolipid metabolism 47 of 317 pathways"
## [1] "Querying............. Inositol phosphate metabolism 48 of 317 pathways"
## [1] "Querying............. Glycosylphosphatidylinositol (GPI)-anchor biosynthesis 49 of 317 pathways"
## [1] "Querying............. Glycerophospholipid metabolism 50 of 317 pathways"
## [1] "Querying............. Ether lipid metabolism 51 of 317 pathways"
## [1] "Querying............. Arachidonic acid metabolism 52 of 317 pathways"
## [1] "Querying............. Linoleic acid metabolism 53 of 317 pathways"
## [1] "Querying............. alpha-Linolenic acid metabolism 54 of 317 pathways"
## [1] "Querying............. Sphingolipid metabolism 55 of 317 pathways"
## [1] "Querying............. Glycosphingolipid biosynthesis - lacto and neolacto series 56 of 317 pathways"
## [1] "Querying............. Glycosphingolipid biosynthesis - globo and isoglobo series 57 of 317 pathways"
## [1] "Querying............. Glycosphingolipid biosynthesis - ganglio series 58 of 317 pathways"
## [1] "Querying............. Pyruvate metabolism 59 of 317 pathways"
## [1] "Querying............. Glyoxylate and dicarboxylate metabolism 60 of 317 pathways"
## [1] "Querying............. Propanoate metabolism 61 of 317 pathways"
## [1] "Querying............. Butanoate metabolism 62 of 317 pathways"
## [1] "Querying............. One carbon pool by folate 63 of 317 pathways"
## [1] "Querying............. Thiamine metabolism 64 of 317 pathways"
## [1] "Querying............. Riboflavin metabolism 65 of 317 pathways"
## [1] "Querying............. Vitamin B6 metabolism 66 of 317 pathways"
## [1] "Querying............. Nicotinate and nicotinamide metabolism 67 of 317 pathways"
## [1] "Querying............. Pantothenate and CoA biosynthesis 68 of 317 pathways"
## [1] "Querying............. Biotin metabolism 69 of 317 pathways"
## [1] "Querying............. Lipoic acid metabolism 70 of 317 pathways"
## [1] "Querying............. Folate biosynthesis 71 of 317 pathways"
## [1] "Querying............. Retinol metabolism 72 of 317 pathways"
## [1] "Querying............. Porphyrin and chlorophyll metabolism 73 of 317 pathways"
## [1] "Querying............. Terpenoid backbone biosynthesis 74 of 317 pathways"
## [1] "Querying............. Nitrogen metabolism 75 of 317 pathways"
## [1] "Querying............. Sulfur metabolism 76 of 317 pathways"
## [1] "Querying............. Aminoacyl-tRNA biosynthesis 77 of 317 pathways"
## [1] "Querying............. Metabolism of xenobiotics by cytochrome P450 78 of 317 pathways"
## [1] "Querying............. Drug metabolism - cytochrome P450 79 of 317 pathways"
## [1] "Querying............. Drug metabolism - other enzymes 80 of 317 pathways"
## [1] "Querying............. Biosynthesis of unsaturated fatty acids 81 of 317 pathways"
## [1] "Querying............. Metabolic pathways 82 of 317 pathways"
## [1] "Querying............. Carbon metabolism 83 of 317 pathways"
## [1] "Querying............. 2-Oxocarboxylic acid metabolism 84 of 317 pathways"
## [1] "Querying............. Fatty acid metabolism 85 of 317 pathways"
## [1] "Querying............. Biosynthesis of amino acids 86 of 317 pathways"
## [1] "Querying............. EGFR tyrosine kinase inhibitor resistance 87 of 317 pathways"
## [1] "Querying............. Endocrine resistance 88 of 317 pathways"
## [1] "Querying............. Antifolate resistance 89 of 317 pathways"
## [1] "Querying............. Platinum drug resistance 90 of 317 pathways"
## [1] "Querying............. Ribosome biogenesis in eukaryotes 91 of 317 pathways"
## [1] "Querying............. RNA transport 92 of 317 pathways"
## [1] "Querying............. mRNA surveillance pathway 93 of 317 pathways"
## [1] "Querying............. RNA degradation 94 of 317 pathways"
## [1] "Querying............. PPAR signaling pathway 95 of 317 pathways"
## [1] "Querying............. Homologous recombination 96 of 317 pathways"
## [1] "Querying............. Fanconi anemia pathway 97 of 317 pathways"
## [1] "Querying............. MAPK signaling pathway 98 of 317 pathways"
## [1] "Querying............. ErbB signaling pathway 99 of 317 pathways"
## [1] "Querying............. Ras signaling pathway 100 of 317 pathways"
## [1] "Querying............. Rap1 signaling pathway 101 of 317 pathways"
## [1] "Querying............. Calcium signaling pathway 102 of 317 pathways"
## [1] "Querying............. cGMP-PKG signaling pathway 103 of 317 pathways"
## [1] "Querying............. cAMP signaling pathway 104 of 317 pathways"
## [1] "Querying............. Cytokine-cytokine receptor interaction 105 of 317 pathways"
## [1] "Querying............. Viral protein interaction with cytokine and cytokine receptor 106 of 317 pathways"
## [1] "Querying............. Chemokine signaling pathway 107 of 317 pathways"
## [1] "Querying............. NF-kappa B signaling pathway 108 of 317 pathways"
## [1] "Querying............. HIF-1 signaling pathway 109 of 317 pathways"
## [1] "Querying............. FoxO signaling pathway 110 of 317 pathways"
## [1] "Querying............. Phosphatidylinositol signaling system 111 of 317 pathways"
## [1] "Querying............. Sphingolipid signaling pathway 112 of 317 pathways"
## [1] "Querying............. Phospholipase D signaling pathway 113 of 317 pathways"
## [1] "Querying............. Neuroactive ligand-receptor interaction 114 of 317 pathways"
## [1] "Querying............. Cell cycle 115 of 317 pathways"
## [1] "Querying............. Oocyte meiosis 116 of 317 pathways"
## [1] "Querying............. p53 signaling pathway 117 of 317 pathways"
## [1] "Querying............. Sulfur relay system 118 of 317 pathways"
## [1] "Querying............. SNARE interactions in vesicular transport 119 of 317 pathways"
## [1] "Querying............. Autophagy - other 120 of 317 pathways"
## [1] "Querying............. Mitophagy - animal 121 of 317 pathways"
## [1] "Querying............. Autophagy - animal 122 of 317 pathways"
## [1] "Querying............. Protein processing in endoplasmic reticulum 123 of 317 pathways"
## [1] "Querying............. Endocytosis 124 of 317 pathways"
## [1] "Querying............. Phagosome 125 of 317 pathways"
## [1] "Querying............. Peroxisome 126 of 317 pathways"
## [1] "Querying............. mTOR signaling pathway 127 of 317 pathways"
## [1] "Querying............. PI3K-Akt signaling pathway 128 of 317 pathways"
## [1] "Querying............. AMPK signaling pathway 129 of 317 pathways"
## [1] "Querying............. Apoptosis 130 of 317 pathways"
## [1] "Querying............. Longevity regulating pathway 131 of 317 pathways"
## [1] "Querying............. Longevity regulating pathway - multiple species 132 of 317 pathways"
## [1] "Querying............. Apoptosis - multiple species 133 of 317 pathways"
## [1] "Querying............. Ferroptosis 134 of 317 pathways"
## [1] "Querying............. Necroptosis 135 of 317 pathways"
## [1] "Querying............. Cellular senescence 136 of 317 pathways"
## [1] "Querying............. Cardiac muscle contraction 137 of 317 pathways"
## [1] "Querying............. Adrenergic signaling in cardiomyocytes 138 of 317 pathways"
## [1] "Querying............. Vascular smooth muscle contraction 139 of 317 pathways"
## [1] "Querying............. Wnt signaling pathway 140 of 317 pathways"
## [1] "Querying............. Notch signaling pathway 141 of 317 pathways"
## [1] "Querying............. Hedgehog signaling pathway 142 of 317 pathways"
## [1] "Querying............. TGF-beta signaling pathway 143 of 317 pathways"
## [1] "Querying............. Axon guidance 144 of 317 pathways"
## [1] "Querying............. VEGF signaling pathway 145 of 317 pathways"
## [1] "Querying............. Apelin signaling pathway 146 of 317 pathways"
## [1] "Querying............. Osteoclast differentiation 147 of 317 pathways"
## [1] "Querying............. Hippo signaling pathway 148 of 317 pathways"
## [1] "Querying............. Hippo signaling pathway - multiple species 149 of 317 pathways"
## [1] "Querying............. Focal adhesion 150 of 317 pathways"
## [1] "Querying............. ECM-receptor interaction 151 of 317 pathways"
## [1] "Querying............. Cell adhesion molecules 152 of 317 pathways"
## [1] "Querying............. Adherens junction 153 of 317 pathways"
## [1] "Querying............. Tight junction 154 of 317 pathways"
## [1] "Querying............. Gap junction 155 of 317 pathways"
## [1] "Querying............. Signaling pathways regulating pluripotency of stem cells 156 of 317 pathways"
## [1] "Querying............. Complement and coagulation cascades 157 of 317 pathways"
## [1] "Querying............. Platelet activation 158 of 317 pathways"
## [1] "Querying............. Antigen processing and presentation 159 of 317 pathways"
## [1] "Querying............. Renin-angiotensin system 160 of 317 pathways"
## [1] "Querying............. Toll-like receptor signaling pathway 161 of 317 pathways"
## [1] "Querying............. NOD-like receptor signaling pathway 162 of 317 pathways"
## [1] "Querying............. RIG-I-like receptor signaling pathway 163 of 317 pathways"
## [1] "Querying............. Cytosolic DNA-sensing pathway 164 of 317 pathways"
## [1] "Querying............. C-type lectin receptor signaling pathway 165 of 317 pathways"
## [1] "Querying............. JAK-STAT signaling pathway 166 of 317 pathways"
## [1] "Querying............. Natural killer cell mediated cytotoxicity 167 of 317 pathways"
## [1] "Querying............. IL-17 signaling pathway 168 of 317 pathways"
## [1] "Querying............. Th1 and Th2 cell differentiation 169 of 317 pathways"
## [1] "Querying............. Th17 cell differentiation 170 of 317 pathways"
## [1] "Querying............. T cell receptor signaling pathway 171 of 317 pathways"
## [1] "Querying............. B cell receptor signaling pathway 172 of 317 pathways"
## [1] "Querying............. Fc epsilon RI signaling pathway 173 of 317 pathways"
## [1] "Querying............. Fc gamma R-mediated phagocytosis 174 of 317 pathways"
## [1] "Querying............. TNF signaling pathway 175 of 317 pathways"
## [1] "Querying............. Leukocyte transendothelial migration 176 of 317 pathways"
## [1] "Querying............. Intestinal immune network for IgA production 177 of 317 pathways"
## [1] "Querying............. Circadian rhythm 178 of 317 pathways"
## [1] "Querying............. Circadian entrainment 179 of 317 pathways"
## [1] "Querying............. Thermogenesis 180 of 317 pathways"
## [1] "Querying............. Long-term potentiation 181 of 317 pathways"
## [1] "Querying............. Synaptic vesicle cycle 182 of 317 pathways"
## [1] "Querying............. Neurotrophin signaling pathway 183 of 317 pathways"
## [1] "Querying............. Retrograde endocannabinoid signaling 184 of 317 pathways"
## [1] "Querying............. Glutamatergic synapse 185 of 317 pathways"
## [1] "Querying............. Cholinergic synapse 186 of 317 pathways"
## [1] "Querying............. Serotonergic synapse 187 of 317 pathways"
## [1] "Querying............. GABAergic synapse 188 of 317 pathways"
## [1] "Querying............. Dopaminergic synapse 189 of 317 pathways"
## [1] "Querying............. Long-term depression 190 of 317 pathways"
## [1] "Querying............. Olfactory transduction 191 of 317 pathways"
## [1] "Querying............. Taste transduction 192 of 317 pathways"
## [1] "Querying............. Phototransduction 193 of 317 pathways"
## [1] "Querying............. Inflammatory mediator regulation of TRP channels 194 of 317 pathways"
## [1] "Querying............. Regulation of actin cytoskeleton 195 of 317 pathways"
## [1] "Querying............. Insulin signaling pathway 196 of 317 pathways"
## [1] "Querying............. Insulin secretion 197 of 317 pathways"
## [1] "Querying............. GnRH signaling pathway 198 of 317 pathways"
## [1] "Querying............. Ovarian steroidogenesis 199 of 317 pathways"
## [1] "Querying............. Progesterone-mediated oocyte maturation 200 of 317 pathways"
## [1] "Querying............. Estrogen signaling pathway 201 of 317 pathways"
## [1] "Querying............. Melanogenesis 202 of 317 pathways"
## [1] "Querying............. Prolactin signaling pathway 203 of 317 pathways"
## [1] "Querying............. Thyroid hormone synthesis 204 of 317 pathways"
## [1] "Querying............. Thyroid hormone signaling pathway 205 of 317 pathways"
## [1] "Querying............. Adipocytokine signaling pathway 206 of 317 pathways"
## [1] "Querying............. Oxytocin signaling pathway 207 of 317 pathways"
## [1] "Querying............. Glucagon signaling pathway 208 of 317 pathways"
## [1] "Querying............. Regulation of lipolysis in adipocytes 209 of 317 pathways"
## [1] "Querying............. Renin secretion 210 of 317 pathways"
## [1] "Querying............. Aldosterone synthesis and secretion 211 of 317 pathways"
## [1] "Querying............. Relaxin signaling pathway 212 of 317 pathways"
## [1] "Querying............. Cortisol synthesis and secretion 213 of 317 pathways"
## [1] "Querying............. Parathyroid hormone synthesis, secretion and action 214 of 317 pathways"
## [1] "Querying............. GnRH secretion 215 of 317 pathways"
## [1] "Querying............. Type II diabetes mellitus 216 of 317 pathways"
## [1] "Querying............. Insulin resistance 217 of 317 pathways"
## [1] "Querying............. Non-alcoholic fatty liver disease 218 of 317 pathways"
## [1] "Querying............. AGE-RAGE signaling pathway in diabetic complications 219 of 317 pathways"
## [1] "Querying............. Cushing syndrome 220 of 317 pathways"
## [1] "Querying............. Growth hormone synthesis, secretion and action 221 of 317 pathways"
## [1] "Querying............. Type I diabetes mellitus 222 of 317 pathways"
## [1] "Querying............. Maturity onset diabetes of the young 223 of 317 pathways"
## [1] "Querying............. Aldosterone-regulated sodium reabsorption 224 of 317 pathways"
## [1] "Querying............. Endocrine and other factor-regulated calcium reabsorption 225 of 317 pathways"
## [1] "Querying............. Vasopressin-regulated water reabsorption 226 of 317 pathways"
## [1] "Querying............. Proximal tubule bicarbonate reclamation 227 of 317 pathways"
## [1] "Querying............. Salivary secretion 228 of 317 pathways"
## [1] "Querying............. Gastric acid secretion 229 of 317 pathways"
## [1] "Querying............. Pancreatic secretion 230 of 317 pathways"
## [1] "Querying............. Carbohydrate digestion and absorption 231 of 317 pathways"
## [1] "Querying............. Fat digestion and absorption 232 of 317 pathways"
## [1] "Querying............. Bile secretion 233 of 317 pathways"
## [1] "Querying............. Vitamin digestion and absorption 234 of 317 pathways"
## [1] "Querying............. Mineral absorption 235 of 317 pathways"
## [1] "Querying............. Cholesterol metabolism 236 of 317 pathways"
## [1] "Querying............. Alzheimer disease 237 of 317 pathways"
## [1] "Querying............. Parkinson disease 238 of 317 pathways"
## [1] "Querying............. Amyotrophic lateral sclerosis 239 of 317 pathways"
## [1] "Querying............. Huntington disease 240 of 317 pathways"
## [1] "Querying............. Spinocerebellar ataxia 241 of 317 pathways"
## [1] "Querying............. Prion disease 242 of 317 pathways"
## [1] "Querying............. Cocaine addiction 243 of 317 pathways"
## [1] "Querying............. Amphetamine addiction 244 of 317 pathways"
## [1] "Querying............. Morphine addiction 245 of 317 pathways"
## [1] "Querying............. Alcoholism 246 of 317 pathways"
## [1] "Querying............. Bacterial invasion of epithelial cells 247 of 317 pathways"
## [1] "Querying............. Vibrio cholerae infection 248 of 317 pathways"
## [1] "Querying............. Epithelial cell signaling in Helicobacter pylori infection 249 of 317 pathways"
## [1] "Querying............. Pathogenic Escherichia coli infection 250 of 317 pathways"
## [1] "Querying............. Shigellosis 251 of 317 pathways"
## [1] "Querying............. Salmonella infection 252 of 317 pathways"
## [1] "Querying............. Pertussis 253 of 317 pathways"
## [1] "Querying............. Legionellosis 254 of 317 pathways"
## [1] "Querying............. Yersinia infection 255 of 317 pathways"
## [1] "Querying............. Leishmaniasis 256 of 317 pathways"
## [1] "Querying............. Chagas disease 257 of 317 pathways"
## [1] "Querying............. African trypanosomiasis 258 of 317 pathways"
## [1] "Querying............. Malaria 259 of 317 pathways"
## [1] "Querying............. Toxoplasmosis 260 of 317 pathways"
## [1] "Querying............. Amoebiasis 261 of 317 pathways"
## [1] "Querying............. Staphylococcus aureus infection 262 of 317 pathways"
## [1] "Querying............. Tuberculosis 263 of 317 pathways"
## [1] "Querying............. Hepatitis C 264 of 317 pathways"
## [1] "Querying............. Hepatitis B 265 of 317 pathways"
## [1] "Querying............. Measles 266 of 317 pathways"
## [1] "Querying............. Human cytomegalovirus infection 267 of 317 pathways"
## [1] "Querying............. Influenza A 268 of 317 pathways"
## [1] "Querying............. Human papillomavirus infection 269 of 317 pathways"
## [1] "Querying............. Human T-cell leukemia virus 1 infection 270 of 317 pathways"
## [1] "Querying............. Kaposi sarcoma-associated herpesvirus infection 271 of 317 pathways"
## [1] "Querying............. Herpes simplex virus 1 infection 272 of 317 pathways"
## [1] "Querying............. Epstein-Barr virus infection 273 of 317 pathways"
## [1] "Querying............. Human immunodeficiency virus 1 infection 274 of 317 pathways"
## [1] "Querying............. Pathways in cancer 275 of 317 pathways"
## [1] "Querying............. Transcriptional misregulation in cancer 276 of 317 pathways"
## [1] "Querying............. Viral carcinogenesis 277 of 317 pathways"
## [1] "Querying............. Chemical carcinogenesis 278 of 317 pathways"
## [1] "Querying............. Proteoglycans in cancer 279 of 317 pathways"
## [1] "Querying............. MicroRNAs in cancer 280 of 317 pathways"
## [1] "Querying............. Colorectal cancer 281 of 317 pathways"
## [1] "Querying............. Renal cell carcinoma 282 of 317 pathways"
## [1] "Querying............. Pancreatic cancer 283 of 317 pathways"
## [1] "Querying............. Endometrial cancer 284 of 317 pathways"
## [1] "Querying............. Glioma 285 of 317 pathways"
## [1] "Querying............. Prostate cancer 286 of 317 pathways"
## [1] "Querying............. Thyroid cancer 287 of 317 pathways"
## [1] "Querying............. Basal cell carcinoma 288 of 317 pathways"
## [1] "Querying............. Melanoma 289 of 317 pathways"
## [1] "Querying............. Bladder cancer 290 of 317 pathways"
## [1] "Querying............. Chronic myeloid leukemia 291 of 317 pathways"
## [1] "Querying............. Acute myeloid leukemia 292 of 317 pathways"
## [1] "Querying............. Small cell lung cancer 293 of 317 pathways"
## [1] "Querying............. Non-small cell lung cancer 294 of 317 pathways"
## [1] "Querying............. Breast cancer 295 of 317 pathways"
## [1] "Querying............. Hepatocellular carcinoma 296 of 317 pathways"
## [1] "Querying............. Gastric cancer 297 of 317 pathways"
## [1] "Querying............. Central carbon metabolism in cancer 298 of 317 pathways"
## [1] "Querying............. Choline metabolism in cancer 299 of 317 pathways"
## [1] "Querying............. PD-L1 expression and PD-1 checkpoint pathway in cancer 300 of 317 pathways"
## [1] "Querying............. Asthma 301 of 317 pathways"
## [1] "Querying............. Autoimmune thyroid disease 302 of 317 pathways"
## [1] "Querying............. Inflammatory bowel disease 303 of 317 pathways"
## [1] "Querying............. Systemic lupus erythematosus 304 of 317 pathways"
## [1] "Querying............. Rheumatoid arthritis 305 of 317 pathways"
## [1] "Querying............. Allograft rejection 306 of 317 pathways"
## [1] "Querying............. Graft-versus-host disease 307 of 317 pathways"
## [1] "Querying............. Hypertrophic cardiomyopathy 308 of 317 pathways"
## [1] "Querying............. Arrhythmogenic right ventricular cardiomyopathy 309 of 317 pathways"
## [1] "Querying............. Dilated cardiomyopathy 310 of 317 pathways"
## [1] "Querying............. Viral myocarditis 311 of 317 pathways"
## [1] "Querying............. Fluid shear stress and atherosclerosis 312 of 317 pathways"
## [1] "Querying............. Valine, leucine and isoleucine biosynthesis 313 of 317 pathways"
## [1] "Querying............. D-Arginine and D-ornithine metabolism 314 of 317 pathways"
## [1] "Querying............. Neomycin, kanamycin and gentamicin biosynthesis 315 of 317 pathways"
## [1] "Querying............. Protein digestion and absorption 316 of 317 pathways"
## [1] "Querying............. Nicotine addiction 317 of 317 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:
## Registered S3 methods overwritten by 'huge':
## method from
## plot.sim BDgraph
## print.sim BDgraph##
## 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 4.0.3 (2020-10-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.5 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.12-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.12-bioc/R/lib/libRlapack.so
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 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_1.6.5 org.Hs.eg.db_3.12.0
## [4] graphite_1.36.0 StarBioTrek_1.16.0 miRNAtap_1.24.0
## [7] AnnotationDbi_1.52.0 IRanges_2.24.0 S4Vectors_0.28.0
## [10] Biobase_2.50.0 BiocGenerics_0.36.0 BiocStyle_2.18.0
##
## loaded via a namespace (and not attached):
## [1] shadowtext_0.0.7 backports_1.1.10 Hmisc_4.4-1
## [4] BDgraph_2.63 fastmatch_1.1-0 plyr_1.8.6
## [7] igraph_1.2.6 splines_4.0.3 BiocParallel_1.24.0
## [10] usethis_1.6.3 ggplot2_3.3.2 digest_0.6.27
## [13] htmltools_0.5.0 GOSemSim_2.16.0 magick_2.5.0
## [16] viridis_0.5.1 GO.db_3.12.0 gdata_2.18.0
## [19] fansi_0.4.1 MLmetrics_1.1.1 magrittr_1.5
## [22] checkmate_2.0.0 memoise_1.1.0 cluster_2.1.0
## [25] ROCR_1.0-11 remotes_2.2.0 graphlayouts_0.7.1
## [28] enrichplot_1.10.0 prettyunits_1.1.1 jpeg_0.1-8.1
## [31] colorspace_1.4-1 blob_1.2.1 rappdirs_0.3.1
## [34] ggrepel_0.8.2 xfun_0.18 dplyr_1.0.2
## [37] callr_3.5.1 crayon_1.3.4 jsonlite_1.7.1
## [40] graph_1.68.0 scatterpie_0.1.5 survival_3.2-7
## [43] miRNAtap.db_0.99.10 glue_1.4.2 polyclip_1.10-0
## [46] gtable_0.3.0 pkgbuild_1.1.0 abind_1.4-5
## [49] scales_1.1.1 DOSE_3.16.0 DBI_1.1.0
## [52] Rcpp_1.0.5 htmlTable_2.1.0 viridisLite_0.3.0
## [55] tmvnsim_1.0-2 foreign_0.8-80 bit_4.0.4
## [58] Formula_1.2-4 sqldf_0.4-11 htmlwidgets_1.5.2
## [61] httr_1.4.2 fgsea_1.16.0 lavaan_0.6-7
## [64] gplots_3.1.0 RColorBrewer_1.1-2 ellipsis_0.3.1
## [67] pkgconfig_2.0.3 farver_2.0.3 nnet_7.3-14
## [70] tidyselect_1.1.0 rlang_0.4.8 reshape2_1.4.4
## [73] munsell_0.5.0 tools_4.0.3 visNetwork_2.0.9
## [76] downloader_0.4 cli_2.1.0 gsubfn_0.7
## [79] generics_0.0.2 RSQLite_2.2.1 devtools_2.3.2
## [82] fdrtool_1.2.15 evaluate_0.14 stringr_1.4.0
## [85] yaml_2.2.1 processx_3.4.4 knitr_1.30
## [88] bit64_4.0.5 fs_1.5.0 tidygraph_1.2.0
## [91] caTools_1.18.0 purrr_0.3.4 ggraph_2.0.3
## [94] glasso_1.11 pbapply_1.4-3 nlme_3.1-150
## [97] whisker_0.4 DO.db_2.9 MAGeCKFlute_1.10.0
## [100] compiler_4.0.3 rstudioapi_0.11 curl_4.3
## [103] e1071_1.7-4 testthat_2.3.2 huge_1.3.4.1
## [106] tibble_3.0.4 tweenr_1.0.1 pbivnorm_0.6.0
## [109] stringi_1.5.3 highr_0.8 ps_1.4.0
## [112] desc_1.2.0 lattice_0.20-41 Matrix_1.2-18
## [115] psych_2.0.9 vctrs_0.3.4 pillar_1.4.6
## [118] lifecycle_0.2.0 networkD3_0.4 BiocManager_1.30.10
## [121] corpcor_1.6.9 data.table_1.13.2 cowplot_1.1.0
## [124] bitops_1.0-6 qvalue_2.22.0 R6_2.4.1
## [127] latticeExtra_0.6-29 bookdown_0.21 KernSmooth_2.23-17
## [130] gridExtra_2.3 sessioninfo_1.1.1 MASS_7.3-53
## [133] gtools_3.8.2 assertthat_0.2.1 pkgload_1.1.0
## [136] chron_2.3-56 proto_1.0.0 rjson_0.2.20
## [139] rprojroot_1.3-2 withr_2.3.0 mnormt_2.0.2
## [142] SpidermiR_1.20.0 clusterProfiler_3.18.0 rpart_4.1-15
## [145] tidyr_1.1.2 class_7.3-17 rmarkdown_2.5
## [148] rvcheck_0.1.8 d3Network_0.5.2.1 ggforce_0.3.2
## [151] 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.
S. Epskamp, et al. 2012. “Qgraph Network Visualizations of Relationships in Psychometric Data.”
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.
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.”