Working with StarBioTrek package
2021-10-26
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 323 pathways"
## [1] "Querying............. Citrate cycle (TCA cycle) 2 of 323 pathways"
## [1] "Querying............. Pentose phosphate pathway 3 of 323 pathways"
## [1] "Querying............. Pentose and glucuronate interconversions 4 of 323 pathways"
## [1] "Querying............. Fructose and mannose metabolism 5 of 323 pathways"
## [1] "Querying............. Galactose metabolism 6 of 323 pathways"
## [1] "Querying............. Ascorbate and aldarate metabolism 7 of 323 pathways"
## [1] "Querying............. Fatty acid biosynthesis 8 of 323 pathways"
## [1] "Querying............. Fatty acid elongation 9 of 323 pathways"
## [1] "Querying............. Fatty acid degradation 10 of 323 pathways"
## [1] "Querying............. Steroid biosynthesis 11 of 323 pathways"
## [1] "Querying............. Primary bile acid biosynthesis 12 of 323 pathways"
## [1] "Querying............. Ubiquinone and other terpenoid-quinone biosynthesis 13 of 323 pathways"
## [1] "Querying............. Steroid hormone biosynthesis 14 of 323 pathways"
## [1] "Querying............. Oxidative phosphorylation 15 of 323 pathways"
## [1] "Querying............. Arginine biosynthesis 16 of 323 pathways"
## [1] "Querying............. Purine metabolism 17 of 323 pathways"
## [1] "Querying............. Caffeine metabolism 18 of 323 pathways"
## [1] "Querying............. Pyrimidine metabolism 19 of 323 pathways"
## [1] "Querying............. Alanine, aspartate and glutamate metabolism 20 of 323 pathways"
## [1] "Querying............. Glycine, serine and threonine metabolism 21 of 323 pathways"
## [1] "Querying............. Cysteine and methionine metabolism 22 of 323 pathways"
## [1] "Querying............. Valine, leucine and isoleucine degradation 23 of 323 pathways"
## [1] "Querying............. Lysine degradation 24 of 323 pathways"
## [1] "Querying............. Arginine and proline metabolism 25 of 323 pathways"
## [1] "Querying............. Histidine metabolism 26 of 323 pathways"
## [1] "Querying............. Tyrosine metabolism 27 of 323 pathways"
## [1] "Querying............. Phenylalanine metabolism 28 of 323 pathways"
## [1] "Querying............. Tryptophan metabolism 29 of 323 pathways"
## [1] "Querying............. Phenylalanine, tyrosine and tryptophan biosynthesis 30 of 323 pathways"
## [1] "Querying............. beta-Alanine metabolism 31 of 323 pathways"
## [1] "Querying............. Taurine and hypotaurine metabolism 32 of 323 pathways"
## [1] "Querying............. Phosphonate and phosphinate metabolism 33 of 323 pathways"
## [1] "Querying............. Selenocompound metabolism 34 of 323 pathways"
## [1] "Querying............. D-Amino acid metabolism 35 of 323 pathways"
## [1] "Querying............. Glutathione metabolism 36 of 323 pathways"
## [1] "Querying............. Starch and sucrose metabolism 37 of 323 pathways"
## [1] "Querying............. N-Glycan biosynthesis 38 of 323 pathways"
## [1] "Querying............. Mucin type O-glycan biosynthesis 39 of 323 pathways"
## [1] "Querying............. Various types of N-glycan biosynthesis 40 of 323 pathways"
## [1] "Querying............. Mannose type O-glycan biosynthesis 41 of 323 pathways"
## [1] "Querying............. Amino sugar and nucleotide sugar metabolism 42 of 323 pathways"
## [1] "Querying............. Glycosaminoglycan degradation 43 of 323 pathways"
## [1] "Querying............. Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate 44 of 323 pathways"
## [1] "Querying............. Glycosaminoglycan biosynthesis - heparan sulfate / heparin 45 of 323 pathways"
## [1] "Querying............. Glycerolipid metabolism 46 of 323 pathways"
## [1] "Querying............. Inositol phosphate metabolism 47 of 323 pathways"
## [1] "Querying............. Glycosylphosphatidylinositol (GPI)-anchor biosynthesis 48 of 323 pathways"
## [1] "Querying............. Glycerophospholipid metabolism 49 of 323 pathways"
## [1] "Querying............. Ether lipid metabolism 50 of 323 pathways"
## [1] "Querying............. Arachidonic acid metabolism 51 of 323 pathways"
## [1] "Querying............. Linoleic acid metabolism 52 of 323 pathways"
## [1] "Querying............. alpha-Linolenic acid metabolism 53 of 323 pathways"
## [1] "Querying............. Sphingolipid metabolism 54 of 323 pathways"
## [1] "Querying............. Glycosphingolipid biosynthesis - lacto and neolacto series 55 of 323 pathways"
## [1] "Querying............. Glycosphingolipid biosynthesis - globo and isoglobo series 56 of 323 pathways"
## [1] "Querying............. Glycosphingolipid biosynthesis - ganglio series 57 of 323 pathways"
## [1] "Querying............. Pyruvate metabolism 58 of 323 pathways"
## [1] "Querying............. Glyoxylate and dicarboxylate metabolism 59 of 323 pathways"
## [1] "Querying............. Propanoate metabolism 60 of 323 pathways"
## [1] "Querying............. Butanoate metabolism 61 of 323 pathways"
## [1] "Querying............. One carbon pool by folate 62 of 323 pathways"
## [1] "Querying............. Thiamine metabolism 63 of 323 pathways"
## [1] "Querying............. Riboflavin metabolism 64 of 323 pathways"
## [1] "Querying............. Vitamin B6 metabolism 65 of 323 pathways"
## [1] "Querying............. Nicotinate and nicotinamide metabolism 66 of 323 pathways"
## [1] "Querying............. Pantothenate and CoA biosynthesis 67 of 323 pathways"
## [1] "Querying............. Biotin metabolism 68 of 323 pathways"
## [1] "Querying............. Lipoic acid metabolism 69 of 323 pathways"
## [1] "Querying............. Folate biosynthesis 70 of 323 pathways"
## [1] "Querying............. Retinol metabolism 71 of 323 pathways"
## [1] "Querying............. Porphyrin and chlorophyll metabolism 72 of 323 pathways"
## [1] "Querying............. Terpenoid backbone biosynthesis 73 of 323 pathways"
## [1] "Querying............. Nitrogen metabolism 74 of 323 pathways"
## [1] "Querying............. Sulfur metabolism 75 of 323 pathways"
## [1] "Querying............. Aminoacyl-tRNA biosynthesis 76 of 323 pathways"
## [1] "Querying............. Metabolism of xenobiotics by cytochrome P450 77 of 323 pathways"
## [1] "Querying............. Drug metabolism - cytochrome P450 78 of 323 pathways"
## [1] "Querying............. Drug metabolism - other enzymes 79 of 323 pathways"
## [1] "Querying............. Biosynthesis of unsaturated fatty acids 80 of 323 pathways"
## [1] "Querying............. Metabolic pathways 81 of 323 pathways"
## [1] "Querying............. Carbon metabolism 82 of 323 pathways"
## [1] "Querying............. 2-Oxocarboxylic acid metabolism 83 of 323 pathways"
## [1] "Querying............. Fatty acid metabolism 84 of 323 pathways"
## [1] "Querying............. Biosynthesis of amino acids 85 of 323 pathways"
## [1] "Querying............. Biosynthesis of cofactors 86 of 323 pathways"
## [1] "Querying............. Biosynthesis of nucleotide sugars 87 of 323 pathways"
## [1] "Querying............. EGFR tyrosine kinase inhibitor resistance 88 of 323 pathways"
## [1] "Querying............. Endocrine resistance 89 of 323 pathways"
## [1] "Querying............. Antifolate resistance 90 of 323 pathways"
## [1] "Querying............. Platinum drug resistance 91 of 323 pathways"
## [1] "Querying............. mRNA surveillance pathway 92 of 323 pathways"
## [1] "Querying............. RNA degradation 93 of 323 pathways"
## [1] "Querying............. PPAR signaling pathway 94 of 323 pathways"
## [1] "Querying............. Homologous recombination 95 of 323 pathways"
## [1] "Querying............. Fanconi anemia pathway 96 of 323 pathways"
## [1] "Querying............. MAPK signaling pathway 97 of 323 pathways"
## [1] "Querying............. ErbB signaling pathway 98 of 323 pathways"
## [1] "Querying............. Ras signaling pathway 99 of 323 pathways"
## [1] "Querying............. Rap1 signaling pathway 100 of 323 pathways"
## [1] "Querying............. Calcium signaling pathway 101 of 323 pathways"
## [1] "Querying............. cGMP-PKG signaling pathway 102 of 323 pathways"
## [1] "Querying............. cAMP signaling pathway 103 of 323 pathways"
## [1] "Querying............. Cytokine-cytokine receptor interaction 104 of 323 pathways"
## [1] "Querying............. Viral protein interaction with cytokine and cytokine receptor 105 of 323 pathways"
## [1] "Querying............. Chemokine signaling pathway 106 of 323 pathways"
## [1] "Querying............. NF-kappa B signaling pathway 107 of 323 pathways"
## [1] "Querying............. HIF-1 signaling pathway 108 of 323 pathways"
## [1] "Querying............. FoxO signaling pathway 109 of 323 pathways"
## [1] "Querying............. Phosphatidylinositol signaling system 110 of 323 pathways"
## [1] "Querying............. Sphingolipid signaling pathway 111 of 323 pathways"
## [1] "Querying............. Phospholipase D signaling pathway 112 of 323 pathways"
## [1] "Querying............. Neuroactive ligand-receptor interaction 113 of 323 pathways"
## [1] "Querying............. Cell cycle 114 of 323 pathways"
## [1] "Querying............. Oocyte meiosis 115 of 323 pathways"
## [1] "Querying............. p53 signaling pathway 116 of 323 pathways"
## [1] "Querying............. Sulfur relay system 117 of 323 pathways"
## [1] "Querying............. SNARE interactions in vesicular transport 118 of 323 pathways"
## [1] "Querying............. Autophagy - other 119 of 323 pathways"
## [1] "Querying............. Mitophagy - animal 120 of 323 pathways"
## [1] "Querying............. Autophagy - animal 121 of 323 pathways"
## [1] "Querying............. Protein processing in endoplasmic reticulum 122 of 323 pathways"
## [1] "Querying............. Endocytosis 123 of 323 pathways"
## [1] "Querying............. Phagosome 124 of 323 pathways"
## [1] "Querying............. Peroxisome 125 of 323 pathways"
## [1] "Querying............. mTOR signaling pathway 126 of 323 pathways"
## [1] "Querying............. PI3K-Akt signaling pathway 127 of 323 pathways"
## [1] "Querying............. AMPK signaling pathway 128 of 323 pathways"
## [1] "Querying............. Apoptosis 129 of 323 pathways"
## [1] "Querying............. Longevity regulating pathway 130 of 323 pathways"
## [1] "Querying............. Longevity regulating pathway - multiple species 131 of 323 pathways"
## [1] "Querying............. Apoptosis - multiple species 132 of 323 pathways"
## [1] "Querying............. Ferroptosis 133 of 323 pathways"
## [1] "Querying............. Necroptosis 134 of 323 pathways"
## [1] "Querying............. Cellular senescence 135 of 323 pathways"
## [1] "Querying............. Cardiac muscle contraction 136 of 323 pathways"
## [1] "Querying............. Adrenergic signaling in cardiomyocytes 137 of 323 pathways"
## [1] "Querying............. Vascular smooth muscle contraction 138 of 323 pathways"
## [1] "Querying............. Wnt signaling pathway 139 of 323 pathways"
## [1] "Querying............. Notch signaling pathway 140 of 323 pathways"
## [1] "Querying............. Hedgehog signaling pathway 141 of 323 pathways"
## [1] "Querying............. TGF-beta signaling pathway 142 of 323 pathways"
## [1] "Querying............. Axon guidance 143 of 323 pathways"
## [1] "Querying............. VEGF signaling pathway 144 of 323 pathways"
## [1] "Querying............. Apelin signaling pathway 145 of 323 pathways"
## [1] "Querying............. Osteoclast differentiation 146 of 323 pathways"
## [1] "Querying............. Hippo signaling pathway 147 of 323 pathways"
## [1] "Querying............. Hippo signaling pathway - multiple species 148 of 323 pathways"
## [1] "Querying............. Focal adhesion 149 of 323 pathways"
## [1] "Querying............. ECM-receptor interaction 150 of 323 pathways"
## [1] "Querying............. Cell adhesion molecules 151 of 323 pathways"
## [1] "Querying............. Adherens junction 152 of 323 pathways"
## [1] "Querying............. Tight junction 153 of 323 pathways"
## [1] "Querying............. Gap junction 154 of 323 pathways"
## [1] "Querying............. Signaling pathways regulating pluripotency of stem cells 155 of 323 pathways"
## [1] "Querying............. Complement and coagulation cascades 156 of 323 pathways"
## [1] "Querying............. Platelet activation 157 of 323 pathways"
## [1] "Querying............. Antigen processing and presentation 158 of 323 pathways"
## [1] "Querying............. Neutrophil extracellular trap formation 159 of 323 pathways"
## [1] "Querying............. Renin-angiotensin system 160 of 323 pathways"
## [1] "Querying............. Toll-like receptor signaling pathway 161 of 323 pathways"
## [1] "Querying............. NOD-like receptor signaling pathway 162 of 323 pathways"
## [1] "Querying............. RIG-I-like receptor signaling pathway 163 of 323 pathways"
## [1] "Querying............. Cytosolic DNA-sensing pathway 164 of 323 pathways"
## [1] "Querying............. C-type lectin receptor signaling pathway 165 of 323 pathways"
## [1] "Querying............. JAK-STAT signaling pathway 166 of 323 pathways"
## [1] "Querying............. Natural killer cell mediated cytotoxicity 167 of 323 pathways"
## [1] "Querying............. IL-17 signaling pathway 168 of 323 pathways"
## [1] "Querying............. Th1 and Th2 cell differentiation 169 of 323 pathways"
## [1] "Querying............. Th17 cell differentiation 170 of 323 pathways"
## [1] "Querying............. T cell receptor signaling pathway 171 of 323 pathways"
## [1] "Querying............. B cell receptor signaling pathway 172 of 323 pathways"
## [1] "Querying............. Fc epsilon RI signaling pathway 173 of 323 pathways"
## [1] "Querying............. Fc gamma R-mediated phagocytosis 174 of 323 pathways"
## [1] "Querying............. TNF signaling pathway 175 of 323 pathways"
## [1] "Querying............. Leukocyte transendothelial migration 176 of 323 pathways"
## [1] "Querying............. Intestinal immune network for IgA production 177 of 323 pathways"
## [1] "Querying............. Circadian rhythm 178 of 323 pathways"
## [1] "Querying............. Circadian entrainment 179 of 323 pathways"
## [1] "Querying............. Thermogenesis 180 of 323 pathways"
## [1] "Querying............. Long-term potentiation 181 of 323 pathways"
## [1] "Querying............. Synaptic vesicle cycle 182 of 323 pathways"
## [1] "Querying............. Neurotrophin signaling pathway 183 of 323 pathways"
## [1] "Querying............. Retrograde endocannabinoid signaling 184 of 323 pathways"
## [1] "Querying............. Glutamatergic synapse 185 of 323 pathways"
## [1] "Querying............. Cholinergic synapse 186 of 323 pathways"
## [1] "Querying............. Serotonergic synapse 187 of 323 pathways"
## [1] "Querying............. GABAergic synapse 188 of 323 pathways"
## [1] "Querying............. Dopaminergic synapse 189 of 323 pathways"
## [1] "Querying............. Long-term depression 190 of 323 pathways"
## [1] "Querying............. Olfactory transduction 191 of 323 pathways"
## [1] "Querying............. Taste transduction 192 of 323 pathways"
## [1] "Querying............. Phototransduction 193 of 323 pathways"
## [1] "Querying............. Inflammatory mediator regulation of TRP channels 194 of 323 pathways"
## [1] "Querying............. Regulation of actin cytoskeleton 195 of 323 pathways"
## [1] "Querying............. Insulin signaling pathway 196 of 323 pathways"
## [1] "Querying............. Insulin secretion 197 of 323 pathways"
## [1] "Querying............. GnRH signaling pathway 198 of 323 pathways"
## [1] "Querying............. Ovarian steroidogenesis 199 of 323 pathways"
## [1] "Querying............. Progesterone-mediated oocyte maturation 200 of 323 pathways"
## [1] "Querying............. Estrogen signaling pathway 201 of 323 pathways"
## [1] "Querying............. Melanogenesis 202 of 323 pathways"
## [1] "Querying............. Prolactin signaling pathway 203 of 323 pathways"
## [1] "Querying............. Thyroid hormone synthesis 204 of 323 pathways"
## [1] "Querying............. Thyroid hormone signaling pathway 205 of 323 pathways"
## [1] "Querying............. Adipocytokine signaling pathway 206 of 323 pathways"
## [1] "Querying............. Oxytocin signaling pathway 207 of 323 pathways"
## [1] "Querying............. Glucagon signaling pathway 208 of 323 pathways"
## [1] "Querying............. Regulation of lipolysis in adipocytes 209 of 323 pathways"
## [1] "Querying............. Renin secretion 210 of 323 pathways"
## [1] "Querying............. Aldosterone synthesis and secretion 211 of 323 pathways"
## [1] "Querying............. Relaxin signaling pathway 212 of 323 pathways"
## [1] "Querying............. Cortisol synthesis and secretion 213 of 323 pathways"
## [1] "Querying............. Parathyroid hormone synthesis, secretion and action 214 of 323 pathways"
## [1] "Querying............. GnRH secretion 215 of 323 pathways"
## [1] "Querying............. Type II diabetes mellitus 216 of 323 pathways"
## [1] "Querying............. Insulin resistance 217 of 323 pathways"
## [1] "Querying............. Non-alcoholic fatty liver disease 218 of 323 pathways"
## [1] "Querying............. AGE-RAGE signaling pathway in diabetic complications 219 of 323 pathways"
## [1] "Querying............. Cushing syndrome 220 of 323 pathways"
## [1] "Querying............. Growth hormone synthesis, secretion and action 221 of 323 pathways"
## [1] "Querying............. Alcoholic liver disease 222 of 323 pathways"
## [1] "Querying............. Type I diabetes mellitus 223 of 323 pathways"
## [1] "Querying............. Maturity onset diabetes of the young 224 of 323 pathways"
## [1] "Querying............. Aldosterone-regulated sodium reabsorption 225 of 323 pathways"
## [1] "Querying............. Endocrine and other factor-regulated calcium reabsorption 226 of 323 pathways"
## [1] "Querying............. Vasopressin-regulated water reabsorption 227 of 323 pathways"
## [1] "Querying............. Proximal tubule bicarbonate reclamation 228 of 323 pathways"
## [1] "Querying............. Salivary secretion 229 of 323 pathways"
## [1] "Querying............. Gastric acid secretion 230 of 323 pathways"
## [1] "Querying............. Pancreatic secretion 231 of 323 pathways"
## [1] "Querying............. Carbohydrate digestion and absorption 232 of 323 pathways"
## [1] "Querying............. Fat digestion and absorption 233 of 323 pathways"
## [1] "Querying............. Bile secretion 234 of 323 pathways"
## [1] "Querying............. Vitamin digestion and absorption 235 of 323 pathways"
## [1] "Querying............. Mineral absorption 236 of 323 pathways"
## [1] "Querying............. Cholesterol metabolism 237 of 323 pathways"
## [1] "Querying............. Alzheimer disease 238 of 323 pathways"
## [1] "Querying............. Parkinson disease 239 of 323 pathways"
## [1] "Querying............. Amyotrophic lateral sclerosis 240 of 323 pathways"
## [1] "Querying............. Huntington disease 241 of 323 pathways"
## [1] "Querying............. Spinocerebellar ataxia 242 of 323 pathways"
## [1] "Querying............. Prion disease 243 of 323 pathways"
## [1] "Querying............. Pathways of neurodegeneration - multiple diseases 244 of 323 pathways"
## [1] "Querying............. Cocaine addiction 245 of 323 pathways"
## [1] "Querying............. Amphetamine addiction 246 of 323 pathways"
## [1] "Querying............. Morphine addiction 247 of 323 pathways"
## [1] "Querying............. Alcoholism 248 of 323 pathways"
## [1] "Querying............. Bacterial invasion of epithelial cells 249 of 323 pathways"
## [1] "Querying............. Vibrio cholerae infection 250 of 323 pathways"
## [1] "Querying............. Epithelial cell signaling in Helicobacter pylori infection 251 of 323 pathways"
## [1] "Querying............. Pathogenic Escherichia coli infection 252 of 323 pathways"
## [1] "Querying............. Shigellosis 253 of 323 pathways"
## [1] "Querying............. Salmonella infection 254 of 323 pathways"
## [1] "Querying............. Pertussis 255 of 323 pathways"
## [1] "Querying............. Legionellosis 256 of 323 pathways"
## [1] "Querying............. Yersinia infection 257 of 323 pathways"
## [1] "Querying............. Leishmaniasis 258 of 323 pathways"
## [1] "Querying............. Chagas disease 259 of 323 pathways"
## [1] "Querying............. African trypanosomiasis 260 of 323 pathways"
## [1] "Querying............. Malaria 261 of 323 pathways"
## [1] "Querying............. Toxoplasmosis 262 of 323 pathways"
## [1] "Querying............. Amoebiasis 263 of 323 pathways"
## [1] "Querying............. Staphylococcus aureus infection 264 of 323 pathways"
## [1] "Querying............. Tuberculosis 265 of 323 pathways"
## [1] "Querying............. Hepatitis C 266 of 323 pathways"
## [1] "Querying............. Hepatitis B 267 of 323 pathways"
## [1] "Querying............. Measles 268 of 323 pathways"
## [1] "Querying............. Human cytomegalovirus infection 269 of 323 pathways"
## [1] "Querying............. Influenza A 270 of 323 pathways"
## [1] "Querying............. Human papillomavirus infection 271 of 323 pathways"
## [1] "Querying............. Human T-cell leukemia virus 1 infection 272 of 323 pathways"
## [1] "Querying............. Kaposi sarcoma-associated herpesvirus infection 273 of 323 pathways"
## [1] "Querying............. Herpes simplex virus 1 infection 274 of 323 pathways"
## [1] "Querying............. Epstein-Barr virus infection 275 of 323 pathways"
## [1] "Querying............. Human immunodeficiency virus 1 infection 276 of 323 pathways"
## [1] "Querying............. Coronavirus disease - COVID-19 277 of 323 pathways"
## [1] "Querying............. Pathways in cancer 278 of 323 pathways"
## [1] "Querying............. Transcriptional misregulation in cancer 279 of 323 pathways"
## [1] "Querying............. Viral carcinogenesis 280 of 323 pathways"
## [1] "Querying............. Chemical carcinogenesis - DNA adducts 281 of 323 pathways"
## [1] "Querying............. Proteoglycans in cancer 282 of 323 pathways"
## [1] "Querying............. MicroRNAs in cancer 283 of 323 pathways"
## [1] "Querying............. Chemical carcinogenesis - receptor activation 284 of 323 pathways"
## [1] "Querying............. Chemical carcinogenesis - reactive oxygen species 285 of 323 pathways"
## [1] "Querying............. Colorectal cancer 286 of 323 pathways"
## [1] "Querying............. Renal cell carcinoma 287 of 323 pathways"
## [1] "Querying............. Pancreatic cancer 288 of 323 pathways"
## [1] "Querying............. Endometrial cancer 289 of 323 pathways"
## [1] "Querying............. Glioma 290 of 323 pathways"
## [1] "Querying............. Prostate cancer 291 of 323 pathways"
## [1] "Querying............. Thyroid cancer 292 of 323 pathways"
## [1] "Querying............. Basal cell carcinoma 293 of 323 pathways"
## [1] "Querying............. Melanoma 294 of 323 pathways"
## [1] "Querying............. Bladder cancer 295 of 323 pathways"
## [1] "Querying............. Chronic myeloid leukemia 296 of 323 pathways"
## [1] "Querying............. Acute myeloid leukemia 297 of 323 pathways"
## [1] "Querying............. Small cell lung cancer 298 of 323 pathways"
## [1] "Querying............. Non-small cell lung cancer 299 of 323 pathways"
## [1] "Querying............. Breast cancer 300 of 323 pathways"
## [1] "Querying............. Hepatocellular carcinoma 301 of 323 pathways"
## [1] "Querying............. Gastric cancer 302 of 323 pathways"
## [1] "Querying............. Central carbon metabolism in cancer 303 of 323 pathways"
## [1] "Querying............. Choline metabolism in cancer 304 of 323 pathways"
## [1] "Querying............. PD-L1 expression and PD-1 checkpoint pathway in cancer 305 of 323 pathways"
## [1] "Querying............. Asthma 306 of 323 pathways"
## [1] "Querying............. Autoimmune thyroid disease 307 of 323 pathways"
## [1] "Querying............. Inflammatory bowel disease 308 of 323 pathways"
## [1] "Querying............. Systemic lupus erythematosus 309 of 323 pathways"
## [1] "Querying............. Rheumatoid arthritis 310 of 323 pathways"
## [1] "Querying............. Allograft rejection 311 of 323 pathways"
## [1] "Querying............. Graft-versus-host disease 312 of 323 pathways"
## [1] "Querying............. Hypertrophic cardiomyopathy 313 of 323 pathways"
## [1] "Querying............. Arrhythmogenic right ventricular cardiomyopathy 314 of 323 pathways"
## [1] "Querying............. Dilated cardiomyopathy 315 of 323 pathways"
## [1] "Querying............. Diabetic cardiomyopathy 316 of 323 pathways"
## [1] "Querying............. Viral myocarditis 317 of 323 pathways"
## [1] "Querying............. Lipid and atherosclerosis 318 of 323 pathways"
## [1] "Querying............. Fluid shear stress and atherosclerosis 319 of 323 pathways"
## [1] "Querying............. Valine, leucine and isoleucine biosynthesis 320 of 323 pathways"
## [1] "Querying............. Neomycin, kanamycin and gentamicin biosynthesis 321 of 323 pathways"
## [1] "Querying............. Protein digestion and absorption 322 of 323 pathways"
## [1] "Querying............. Nicotine addiction 323 of 323 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 4.1.1 (2021-08-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.3 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.14-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.14-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 org.Hs.eg.db_3.14.0
## [4] graphite_1.40.0 StarBioTrek_1.20.0 miRNAtap_1.28.0
## [7] AnnotationDbi_1.56.0 IRanges_2.28.0 S4Vectors_0.32.0
## [10] Biobase_2.54.0 BiocGenerics_0.40.0 BiocStyle_2.22.0
##
## loaded via a namespace (and not attached):
## [1] backports_1.2.1 Hmisc_4.6-0 plyr_1.8.6
## [4] igraph_1.2.7 splines_4.1.1 usethis_2.1.2
## [7] GenomeInfoDb_1.30.0 ggplot2_3.3.5 digest_0.6.28
## [10] htmltools_0.5.2 magick_2.7.3 gdata_2.18.0
## [13] fansi_0.5.0 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_2.4.1 Biostrings_2.62.0
## [22] prettyunits_1.1.1 jpeg_0.1-9 colorspace_2.0-2
## [25] blob_1.2.2 rappdirs_0.3.3 xfun_0.27
## [28] dplyr_1.0.7 callr_3.7.0 crayon_1.4.1
## [31] RCurl_1.98-1.5 jsonlite_1.7.2 graph_1.72.0
## [34] survival_3.2-13 miRNAtap.db_0.99.10 glue_1.4.2
## [37] gtable_0.3.0 zlibbioc_1.40.0 XVector_0.34.0
## [40] pkgbuild_1.2.0 abind_1.4-5 scales_1.1.1
## [43] DBI_1.1.1 Rcpp_1.0.7 htmlTable_2.3.0
## [46] tmvnsim_1.0-2 foreign_0.8-81 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_1.1-2
## [55] lavaan_0.6-9 ellipsis_0.3.2 pkgconfig_2.0.3
## [58] nnet_7.3-16 sass_0.4.0 utf8_1.2.2
## [61] tidyselect_1.1.1 rlang_0.4.12 reshape2_1.4.4
## [64] munsell_0.5.0 tools_4.1.1 cachem_1.0.6
## [67] cli_3.0.1 gsubfn_0.7 generics_0.1.1
## [70] RSQLite_2.2.8 devtools_2.4.2 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_1.36
## [79] bit64_4.0.5 fs_1.5.0 purrr_0.3.4
## [82] KEGGREST_1.34.0 glasso_1.11 pbapply_1.5-0
## [85] nlme_3.1-153 compiler_4.1.1 rstudioapi_0.13
## [88] curl_4.3.2 e1071_1.7-9 testthat_3.1.0
## [91] tibble_3.1.5 bslib_0.3.1 pbivnorm_0.6.0
## [94] stringi_1.7.5 highr_0.9 ps_1.6.0
## [97] desc_1.4.0 lattice_0.20-45 Matrix_1.3-4
## [100] psych_2.1.9 vctrs_0.3.8 pillar_1.6.4
## [103] lifecycle_1.0.1 BiocManager_1.30.16 jquerylib_0.1.4
## [106] data.table_1.14.2 bitops_1.0-7 corpcor_1.6.10
## [109] R6_2.5.1 latticeExtra_0.6-29 bookdown_0.24
## [112] gridExtra_2.3 sessioninfo_1.1.1 gtools_3.9.2
## [115] assertthat_0.2.1 pkgload_1.2.3 chron_2.3-56
## [118] proto_1.0.0 rprojroot_2.0.2 withr_2.4.2
## [121] SpidermiR_1.24.0 mnormt_2.0.2 GenomeInfoDbData_1.2.7
## [124] parallel_4.1.1 rpart_4.1-15 class_7.3-19
## [127] rmarkdown_2.11 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.”