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 pathwaysMotivation:
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.
To install use the code below.
Get data
: Get pathway and network dataSELECT_path_species
: Select the pathway database and species of interestThe 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 downloadThe 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 326 pathways"
## [1] "Querying............. Citrate cycle (TCA cycle) 2 of 326 pathways"
## [1] "Querying............. Pentose phosphate pathway 3 of 326 pathways"
## [1] "Querying............. Pentose and glucuronate interconversions 4 of 326 pathways"
## [1] "Querying............. Fructose and mannose metabolism 5 of 326 pathways"
## [1] "Querying............. Galactose metabolism 6 of 326 pathways"
## [1] "Querying............. Ascorbate and aldarate metabolism 7 of 326 pathways"
## [1] "Querying............. Fatty acid biosynthesis 8 of 326 pathways"
## [1] "Querying............. Fatty acid elongation 9 of 326 pathways"
## [1] "Querying............. Fatty acid degradation 10 of 326 pathways"
## [1] "Querying............. Steroid biosynthesis 11 of 326 pathways"
## [1] "Querying............. Primary bile acid biosynthesis 12 of 326 pathways"
## [1] "Querying............. Ubiquinone and other terpenoid-quinone biosynthesis 13 of 326 pathways"
## [1] "Querying............. Steroid hormone biosynthesis 14 of 326 pathways"
## [1] "Querying............. Oxidative phosphorylation 15 of 326 pathways"
## [1] "Querying............. Arginine biosynthesis 16 of 326 pathways"
## [1] "Querying............. Purine metabolism 17 of 326 pathways"
## [1] "Querying............. Caffeine metabolism 18 of 326 pathways"
## [1] "Querying............. Pyrimidine metabolism 19 of 326 pathways"
## [1] "Querying............. Alanine, aspartate and glutamate metabolism 20 of 326 pathways"
## [1] "Querying............. Glycine, serine and threonine metabolism 21 of 326 pathways"
## [1] "Querying............. Cysteine and methionine metabolism 22 of 326 pathways"
## [1] "Querying............. Valine, leucine and isoleucine degradation 23 of 326 pathways"
## [1] "Querying............. Lysine degradation 24 of 326 pathways"
## [1] "Querying............. Arginine and proline metabolism 25 of 326 pathways"
## [1] "Querying............. Histidine metabolism 26 of 326 pathways"
## [1] "Querying............. Tyrosine metabolism 27 of 326 pathways"
## [1] "Querying............. Phenylalanine metabolism 28 of 326 pathways"
## [1] "Querying............. Tryptophan metabolism 29 of 326 pathways"
## [1] "Querying............. Phenylalanine, tyrosine and tryptophan biosynthesis 30 of 326 pathways"
## [1] "Querying............. beta-Alanine metabolism 31 of 326 pathways"
## [1] "Querying............. Taurine and hypotaurine metabolism 32 of 326 pathways"
## [1] "Querying............. Phosphonate and phosphinate metabolism 33 of 326 pathways"
## [1] "Querying............. Selenocompound metabolism 34 of 326 pathways"
## [1] "Querying............. D-Amino acid metabolism 35 of 326 pathways"
## [1] "Querying............. Glutathione metabolism 36 of 326 pathways"
## [1] "Querying............. Starch and sucrose metabolism 37 of 326 pathways"
## [1] "Querying............. N-Glycan biosynthesis 38 of 326 pathways"
## [1] "Querying............. Mucin type O-glycan biosynthesis 39 of 326 pathways"
## [1] "Querying............. Various types of N-glycan biosynthesis 40 of 326 pathways"
## [1] "Querying............. Mannose type O-glycan biosynthesis 41 of 326 pathways"
## [1] "Querying............. Amino sugar and nucleotide sugar metabolism 42 of 326 pathways"
## [1] "Querying............. Glycosaminoglycan degradation 43 of 326 pathways"
## [1] "Querying............. Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate 44 of 326 pathways"
## [1] "Querying............. Glycosaminoglycan biosynthesis - heparan sulfate / heparin 45 of 326 pathways"
## [1] "Querying............. Glycerolipid metabolism 46 of 326 pathways"
## [1] "Querying............. Inositol phosphate metabolism 47 of 326 pathways"
## [1] "Querying............. Glycosylphosphatidylinositol (GPI)-anchor biosynthesis 48 of 326 pathways"
## [1] "Querying............. Glycerophospholipid metabolism 49 of 326 pathways"
## [1] "Querying............. Ether lipid metabolism 50 of 326 pathways"
## [1] "Querying............. Arachidonic acid metabolism 51 of 326 pathways"
## [1] "Querying............. Linoleic acid metabolism 52 of 326 pathways"
## [1] "Querying............. alpha-Linolenic acid metabolism 53 of 326 pathways"
## [1] "Querying............. Sphingolipid metabolism 54 of 326 pathways"
## [1] "Querying............. Glycosphingolipid biosynthesis - lacto and neolacto series 55 of 326 pathways"
## [1] "Querying............. Glycosphingolipid biosynthesis - globo and isoglobo series 56 of 326 pathways"
## [1] "Querying............. Glycosphingolipid biosynthesis - ganglio series 57 of 326 pathways"
## [1] "Querying............. Pyruvate metabolism 58 of 326 pathways"
## [1] "Querying............. Glyoxylate and dicarboxylate metabolism 59 of 326 pathways"
## [1] "Querying............. Propanoate metabolism 60 of 326 pathways"
## [1] "Querying............. Butanoate metabolism 61 of 326 pathways"
## [1] "Querying............. One carbon pool by folate 62 of 326 pathways"
## [1] "Querying............. Thiamine metabolism 63 of 326 pathways"
## [1] "Querying............. Riboflavin metabolism 64 of 326 pathways"
## [1] "Querying............. Vitamin B6 metabolism 65 of 326 pathways"
## [1] "Querying............. Nicotinate and nicotinamide metabolism 66 of 326 pathways"
## [1] "Querying............. Pantothenate and CoA biosynthesis 67 of 326 pathways"
## [1] "Querying............. Biotin metabolism 68 of 326 pathways"
## [1] "Querying............. Lipoic acid metabolism 69 of 326 pathways"
## [1] "Querying............. Folate biosynthesis 70 of 326 pathways"
## [1] "Querying............. Retinol metabolism 71 of 326 pathways"
## [1] "Querying............. Porphyrin metabolism 72 of 326 pathways"
## [1] "Querying............. Terpenoid backbone biosynthesis 73 of 326 pathways"
## [1] "Querying............. Nitrogen metabolism 74 of 326 pathways"
## [1] "Querying............. Sulfur metabolism 75 of 326 pathways"
## [1] "Querying............. Aminoacyl-tRNA biosynthesis 76 of 326 pathways"
## [1] "Querying............. Metabolism of xenobiotics by cytochrome P450 77 of 326 pathways"
## [1] "Querying............. Drug metabolism - cytochrome P450 78 of 326 pathways"
## [1] "Querying............. Drug metabolism - other enzymes 79 of 326 pathways"
## [1] "Querying............. Biosynthesis of unsaturated fatty acids 80 of 326 pathways"
## [1] "Querying............. Metabolic pathways 81 of 326 pathways"
## [1] "Querying............. Carbon metabolism 82 of 326 pathways"
## [1] "Querying............. 2-Oxocarboxylic acid metabolism 83 of 326 pathways"
## [1] "Querying............. Fatty acid metabolism 84 of 326 pathways"
## [1] "Querying............. Biosynthesis of amino acids 85 of 326 pathways"
## [1] "Querying............. Nucleotide metabolism 86 of 326 pathways"
## [1] "Querying............. Biosynthesis of cofactors 87 of 326 pathways"
## [1] "Querying............. Biosynthesis of nucleotide sugars 88 of 326 pathways"
## [1] "Querying............. EGFR tyrosine kinase inhibitor resistance 89 of 326 pathways"
## [1] "Querying............. Endocrine resistance 90 of 326 pathways"
## [1] "Querying............. Antifolate resistance 91 of 326 pathways"
## [1] "Querying............. Platinum drug resistance 92 of 326 pathways"
## [1] "Querying............. mRNA surveillance pathway 93 of 326 pathways"
## [1] "Querying............. RNA degradation 94 of 326 pathways"
## [1] "Querying............. Viral life cycle - HIV-1 95 of 326 pathways"
## [1] "Querying............. PPAR signaling pathway 96 of 326 pathways"
## [1] "Querying............. Homologous recombination 97 of 326 pathways"
## [1] "Querying............. Fanconi anemia pathway 98 of 326 pathways"
## [1] "Querying............. MAPK signaling pathway 99 of 326 pathways"
## [1] "Querying............. ErbB signaling pathway 100 of 326 pathways"
## [1] "Querying............. Ras signaling pathway 101 of 326 pathways"
## [1] "Querying............. Rap1 signaling pathway 102 of 326 pathways"
## [1] "Querying............. Calcium signaling pathway 103 of 326 pathways"
## [1] "Querying............. cGMP-PKG signaling pathway 104 of 326 pathways"
## [1] "Querying............. cAMP signaling pathway 105 of 326 pathways"
## [1] "Querying............. Cytokine-cytokine receptor interaction 106 of 326 pathways"
## [1] "Querying............. Viral protein interaction with cytokine and cytokine receptor 107 of 326 pathways"
## [1] "Querying............. Chemokine signaling pathway 108 of 326 pathways"
## [1] "Querying............. NF-kappa B signaling pathway 109 of 326 pathways"
## [1] "Querying............. HIF-1 signaling pathway 110 of 326 pathways"
## [1] "Querying............. FoxO signaling pathway 111 of 326 pathways"
## [1] "Querying............. Phosphatidylinositol signaling system 112 of 326 pathways"
## [1] "Querying............. Sphingolipid signaling pathway 113 of 326 pathways"
## [1] "Querying............. Phospholipase D signaling pathway 114 of 326 pathways"
## [1] "Querying............. Neuroactive ligand-receptor interaction 115 of 326 pathways"
## [1] "Querying............. Cell cycle 116 of 326 pathways"
## [1] "Querying............. Oocyte meiosis 117 of 326 pathways"
## [1] "Querying............. p53 signaling pathway 118 of 326 pathways"
## [1] "Querying............. Sulfur relay system 119 of 326 pathways"
## [1] "Querying............. SNARE interactions in vesicular transport 120 of 326 pathways"
## [1] "Querying............. Autophagy - other 121 of 326 pathways"
## [1] "Querying............. Mitophagy - animal 122 of 326 pathways"
## [1] "Querying............. Autophagy - animal 123 of 326 pathways"
## [1] "Querying............. Protein processing in endoplasmic reticulum 124 of 326 pathways"
## [1] "Querying............. Endocytosis 125 of 326 pathways"
## [1] "Querying............. Phagosome 126 of 326 pathways"
## [1] "Querying............. Peroxisome 127 of 326 pathways"
## [1] "Querying............. Efferocytosis 128 of 326 pathways"
## [1] "Querying............. mTOR signaling pathway 129 of 326 pathways"
## [1] "Querying............. PI3K-Akt signaling pathway 130 of 326 pathways"
## [1] "Querying............. AMPK signaling pathway 131 of 326 pathways"
## [1] "Querying............. Apoptosis 132 of 326 pathways"
## [1] "Querying............. Longevity regulating pathway 133 of 326 pathways"
## [1] "Querying............. Longevity regulating pathway - multiple species 134 of 326 pathways"
## [1] "Querying............. Apoptosis - multiple species 135 of 326 pathways"
## [1] "Querying............. Ferroptosis 136 of 326 pathways"
## [1] "Querying............. Necroptosis 137 of 326 pathways"
## [1] "Querying............. Cellular senescence 138 of 326 pathways"
## [1] "Querying............. Cardiac muscle contraction 139 of 326 pathways"
## [1] "Querying............. Adrenergic signaling in cardiomyocytes 140 of 326 pathways"
## [1] "Querying............. Vascular smooth muscle contraction 141 of 326 pathways"
## [1] "Querying............. Wnt signaling pathway 142 of 326 pathways"
## [1] "Querying............. Notch signaling pathway 143 of 326 pathways"
## [1] "Querying............. Hedgehog signaling pathway 144 of 326 pathways"
## [1] "Querying............. TGF-beta signaling pathway 145 of 326 pathways"
## [1] "Querying............. Axon guidance 146 of 326 pathways"
## [1] "Querying............. VEGF signaling pathway 147 of 326 pathways"
## [1] "Querying............. Apelin signaling pathway 148 of 326 pathways"
## [1] "Querying............. Osteoclast differentiation 149 of 326 pathways"
## [1] "Querying............. Hippo signaling pathway 150 of 326 pathways"
## [1] "Querying............. Hippo signaling pathway - multiple species 151 of 326 pathways"
## [1] "Querying............. Focal adhesion 152 of 326 pathways"
## [1] "Querying............. ECM-receptor interaction 153 of 326 pathways"
## [1] "Querying............. Cell adhesion molecules 154 of 326 pathways"
## [1] "Querying............. Adherens junction 155 of 326 pathways"
## [1] "Querying............. Tight junction 156 of 326 pathways"
## [1] "Querying............. Gap junction 157 of 326 pathways"
## [1] "Querying............. Signaling pathways regulating pluripotency of stem cells 158 of 326 pathways"
## [1] "Querying............. Complement and coagulation cascades 159 of 326 pathways"
## [1] "Querying............. Platelet activation 160 of 326 pathways"
## [1] "Querying............. Antigen processing and presentation 161 of 326 pathways"
## [1] "Querying............. Neutrophil extracellular trap formation 162 of 326 pathways"
## [1] "Querying............. Renin-angiotensin system 163 of 326 pathways"
## [1] "Querying............. Toll-like receptor signaling pathway 164 of 326 pathways"
## [1] "Querying............. NOD-like receptor signaling pathway 165 of 326 pathways"
## [1] "Querying............. RIG-I-like receptor signaling pathway 166 of 326 pathways"
## [1] "Querying............. Cytosolic DNA-sensing pathway 167 of 326 pathways"
## [1] "Querying............. C-type lectin receptor signaling pathway 168 of 326 pathways"
## [1] "Querying............. JAK-STAT signaling pathway 169 of 326 pathways"
## [1] "Querying............. Natural killer cell mediated cytotoxicity 170 of 326 pathways"
## [1] "Querying............. IL-17 signaling pathway 171 of 326 pathways"
## [1] "Querying............. Th1 and Th2 cell differentiation 172 of 326 pathways"
## [1] "Querying............. Th17 cell differentiation 173 of 326 pathways"
## [1] "Querying............. T cell receptor signaling pathway 174 of 326 pathways"
## [1] "Querying............. B cell receptor signaling pathway 175 of 326 pathways"
## [1] "Querying............. Fc epsilon RI signaling pathway 176 of 326 pathways"
## [1] "Querying............. Fc gamma R-mediated phagocytosis 177 of 326 pathways"
## [1] "Querying............. TNF signaling pathway 178 of 326 pathways"
## [1] "Querying............. Leukocyte transendothelial migration 179 of 326 pathways"
## [1] "Querying............. Intestinal immune network for IgA production 180 of 326 pathways"
## [1] "Querying............. Circadian rhythm 181 of 326 pathways"
## [1] "Querying............. Circadian entrainment 182 of 326 pathways"
## [1] "Querying............. Thermogenesis 183 of 326 pathways"
## [1] "Querying............. Long-term potentiation 184 of 326 pathways"
## [1] "Querying............. Synaptic vesicle cycle 185 of 326 pathways"
## [1] "Querying............. Neurotrophin signaling pathway 186 of 326 pathways"
## [1] "Querying............. Retrograde endocannabinoid signaling 187 of 326 pathways"
## [1] "Querying............. Glutamatergic synapse 188 of 326 pathways"
## [1] "Querying............. Cholinergic synapse 189 of 326 pathways"
## [1] "Querying............. Serotonergic synapse 190 of 326 pathways"
## [1] "Querying............. GABAergic synapse 191 of 326 pathways"
## [1] "Querying............. Dopaminergic synapse 192 of 326 pathways"
## [1] "Querying............. Long-term depression 193 of 326 pathways"
## [1] "Querying............. Olfactory transduction 194 of 326 pathways"
## [1] "Querying............. Taste transduction 195 of 326 pathways"
## [1] "Querying............. Phototransduction 196 of 326 pathways"
## [1] "Querying............. Inflammatory mediator regulation of TRP channels 197 of 326 pathways"
## [1] "Querying............. Regulation of actin cytoskeleton 198 of 326 pathways"
## [1] "Querying............. Insulin signaling pathway 199 of 326 pathways"
## [1] "Querying............. Insulin secretion 200 of 326 pathways"
## [1] "Querying............. GnRH signaling pathway 201 of 326 pathways"
## [1] "Querying............. Ovarian steroidogenesis 202 of 326 pathways"
## [1] "Querying............. Progesterone-mediated oocyte maturation 203 of 326 pathways"
## [1] "Querying............. Estrogen signaling pathway 204 of 326 pathways"
## [1] "Querying............. Melanogenesis 205 of 326 pathways"
## [1] "Querying............. Prolactin signaling pathway 206 of 326 pathways"
## [1] "Querying............. Thyroid hormone synthesis 207 of 326 pathways"
## [1] "Querying............. Thyroid hormone signaling pathway 208 of 326 pathways"
## [1] "Querying............. Adipocytokine signaling pathway 209 of 326 pathways"
## [1] "Querying............. Oxytocin signaling pathway 210 of 326 pathways"
## [1] "Querying............. Glucagon signaling pathway 211 of 326 pathways"
## [1] "Querying............. Regulation of lipolysis in adipocytes 212 of 326 pathways"
## [1] "Querying............. Renin secretion 213 of 326 pathways"
## [1] "Querying............. Aldosterone synthesis and secretion 214 of 326 pathways"
## [1] "Querying............. Relaxin signaling pathway 215 of 326 pathways"
## [1] "Querying............. Cortisol synthesis and secretion 216 of 326 pathways"
## [1] "Querying............. Parathyroid hormone synthesis, secretion and action 217 of 326 pathways"
## [1] "Querying............. GnRH secretion 218 of 326 pathways"
## [1] "Querying............. Type II diabetes mellitus 219 of 326 pathways"
## [1] "Querying............. Insulin resistance 220 of 326 pathways"
## [1] "Querying............. Non-alcoholic fatty liver disease 221 of 326 pathways"
## [1] "Querying............. AGE-RAGE signaling pathway in diabetic complications 222 of 326 pathways"
## [1] "Querying............. Cushing syndrome 223 of 326 pathways"
## [1] "Querying............. Growth hormone synthesis, secretion and action 224 of 326 pathways"
## [1] "Querying............. Alcoholic liver disease 225 of 326 pathways"
## [1] "Querying............. Type I diabetes mellitus 226 of 326 pathways"
## [1] "Querying............. Maturity onset diabetes of the young 227 of 326 pathways"
## [1] "Querying............. Aldosterone-regulated sodium reabsorption 228 of 326 pathways"
## [1] "Querying............. Endocrine and other factor-regulated calcium reabsorption 229 of 326 pathways"
## [1] "Querying............. Vasopressin-regulated water reabsorption 230 of 326 pathways"
## [1] "Querying............. Proximal tubule bicarbonate reclamation 231 of 326 pathways"
## [1] "Querying............. Salivary secretion 232 of 326 pathways"
## [1] "Querying............. Gastric acid secretion 233 of 326 pathways"
## [1] "Querying............. Pancreatic secretion 234 of 326 pathways"
## [1] "Querying............. Carbohydrate digestion and absorption 235 of 326 pathways"
## [1] "Querying............. Fat digestion and absorption 236 of 326 pathways"
## [1] "Querying............. Bile secretion 237 of 326 pathways"
## [1] "Querying............. Vitamin digestion and absorption 238 of 326 pathways"
## [1] "Querying............. Mineral absorption 239 of 326 pathways"
## [1] "Querying............. Cholesterol metabolism 240 of 326 pathways"
## [1] "Querying............. Alzheimer disease 241 of 326 pathways"
## [1] "Querying............. Parkinson disease 242 of 326 pathways"
## [1] "Querying............. Amyotrophic lateral sclerosis 243 of 326 pathways"
## [1] "Querying............. Huntington disease 244 of 326 pathways"
## [1] "Querying............. Spinocerebellar ataxia 245 of 326 pathways"
## [1] "Querying............. Prion disease 246 of 326 pathways"
## [1] "Querying............. Pathways of neurodegeneration - multiple diseases 247 of 326 pathways"
## [1] "Querying............. Cocaine addiction 248 of 326 pathways"
## [1] "Querying............. Amphetamine addiction 249 of 326 pathways"
## [1] "Querying............. Morphine addiction 250 of 326 pathways"
## [1] "Querying............. Alcoholism 251 of 326 pathways"
## [1] "Querying............. Bacterial invasion of epithelial cells 252 of 326 pathways"
## [1] "Querying............. Vibrio cholerae infection 253 of 326 pathways"
## [1] "Querying............. Epithelial cell signaling in Helicobacter pylori infection 254 of 326 pathways"
## [1] "Querying............. Pathogenic Escherichia coli infection 255 of 326 pathways"
## [1] "Querying............. Shigellosis 256 of 326 pathways"
## [1] "Querying............. Salmonella infection 257 of 326 pathways"
## [1] "Querying............. Pertussis 258 of 326 pathways"
## [1] "Querying............. Legionellosis 259 of 326 pathways"
## [1] "Querying............. Yersinia infection 260 of 326 pathways"
## [1] "Querying............. Leishmaniasis 261 of 326 pathways"
## [1] "Querying............. Chagas disease 262 of 326 pathways"
## [1] "Querying............. African trypanosomiasis 263 of 326 pathways"
## [1] "Querying............. Malaria 264 of 326 pathways"
## [1] "Querying............. Toxoplasmosis 265 of 326 pathways"
## [1] "Querying............. Amoebiasis 266 of 326 pathways"
## [1] "Querying............. Staphylococcus aureus infection 267 of 326 pathways"
## [1] "Querying............. Tuberculosis 268 of 326 pathways"
## [1] "Querying............. Hepatitis C 269 of 326 pathways"
## [1] "Querying............. Hepatitis B 270 of 326 pathways"
## [1] "Querying............. Measles 271 of 326 pathways"
## [1] "Querying............. Human cytomegalovirus infection 272 of 326 pathways"
## [1] "Querying............. Influenza A 273 of 326 pathways"
## [1] "Querying............. Human papillomavirus infection 274 of 326 pathways"
## [1] "Querying............. Human T-cell leukemia virus 1 infection 275 of 326 pathways"
## [1] "Querying............. Kaposi sarcoma-associated herpesvirus infection 276 of 326 pathways"
## [1] "Querying............. Herpes simplex virus 1 infection 277 of 326 pathways"
## [1] "Querying............. Epstein-Barr virus infection 278 of 326 pathways"
## [1] "Querying............. Human immunodeficiency virus 1 infection 279 of 326 pathways"
## [1] "Querying............. Coronavirus disease - COVID-19 280 of 326 pathways"
## [1] "Querying............. Pathways in cancer 281 of 326 pathways"
## [1] "Querying............. Transcriptional misregulation in cancer 282 of 326 pathways"
## [1] "Querying............. Viral carcinogenesis 283 of 326 pathways"
## [1] "Querying............. Chemical carcinogenesis - DNA adducts 284 of 326 pathways"
## [1] "Querying............. Proteoglycans in cancer 285 of 326 pathways"
## [1] "Querying............. MicroRNAs in cancer 286 of 326 pathways"
## [1] "Querying............. Chemical carcinogenesis - receptor activation 287 of 326 pathways"
## [1] "Querying............. Chemical carcinogenesis - reactive oxygen species 288 of 326 pathways"
## [1] "Querying............. Colorectal cancer 289 of 326 pathways"
## [1] "Querying............. Renal cell carcinoma 290 of 326 pathways"
## [1] "Querying............. Pancreatic cancer 291 of 326 pathways"
## [1] "Querying............. Endometrial cancer 292 of 326 pathways"
## [1] "Querying............. Glioma 293 of 326 pathways"
## [1] "Querying............. Prostate cancer 294 of 326 pathways"
## [1] "Querying............. Thyroid cancer 295 of 326 pathways"
## [1] "Querying............. Basal cell carcinoma 296 of 326 pathways"
## [1] "Querying............. Melanoma 297 of 326 pathways"
## [1] "Querying............. Bladder cancer 298 of 326 pathways"
## [1] "Querying............. Chronic myeloid leukemia 299 of 326 pathways"
## [1] "Querying............. Acute myeloid leukemia 300 of 326 pathways"
## [1] "Querying............. Small cell lung cancer 301 of 326 pathways"
## [1] "Querying............. Non-small cell lung cancer 302 of 326 pathways"
## [1] "Querying............. Breast cancer 303 of 326 pathways"
## [1] "Querying............. Hepatocellular carcinoma 304 of 326 pathways"
## [1] "Querying............. Gastric cancer 305 of 326 pathways"
## [1] "Querying............. Central carbon metabolism in cancer 306 of 326 pathways"
## [1] "Querying............. Choline metabolism in cancer 307 of 326 pathways"
## [1] "Querying............. PD-L1 expression and PD-1 checkpoint pathway in cancer 308 of 326 pathways"
## [1] "Querying............. Asthma 309 of 326 pathways"
## [1] "Querying............. Autoimmune thyroid disease 310 of 326 pathways"
## [1] "Querying............. Inflammatory bowel disease 311 of 326 pathways"
## [1] "Querying............. Systemic lupus erythematosus 312 of 326 pathways"
## [1] "Querying............. Rheumatoid arthritis 313 of 326 pathways"
## [1] "Querying............. Allograft rejection 314 of 326 pathways"
## [1] "Querying............. Graft-versus-host disease 315 of 326 pathways"
## [1] "Querying............. Hypertrophic cardiomyopathy 316 of 326 pathways"
## [1] "Querying............. Arrhythmogenic right ventricular cardiomyopathy 317 of 326 pathways"
## [1] "Querying............. Dilated cardiomyopathy 318 of 326 pathways"
## [1] "Querying............. Diabetic cardiomyopathy 319 of 326 pathways"
## [1] "Querying............. Viral myocarditis 320 of 326 pathways"
## [1] "Querying............. Lipid and atherosclerosis 321 of 326 pathways"
## [1] "Querying............. Fluid shear stress and atherosclerosis 322 of 326 pathways"
## [1] "Querying............. Valine, leucine and isoleucine biosynthesis 323 of 326 pathways"
## [1] "Querying............. Neomycin, kanamycin and gentamicin biosynthesis 324 of 326 pathways"
## [1] "Querying............. Protein digestion and absorption 325 of 326 pathways"
## [1] "Querying............. Nicotine addiction 326 of 326 pathways"
GetPathData
: Get genes inside pathwaysThe user can identify the genes inside the pathways of interest
GetPathNet
: Get interacting genes inside pathwaysGetPathNet
generates a list of interacting genes for each pathway
ConvertedIDgenes
: Get genes inside pathwaysThe user can convert the gene ID into GeneSymbol
## [1] "Mapping Uniprot ID to Gene Symbol, using convertIdentifiers of graphite package.......... Glycolysis / Gluconeogenesis 1 of 10 pathways"
## [1] "Mapping Uniprot ID to Gene Symbol, using convertIdentifiers of graphite package.......... Citrate cycle (TCA cycle) 2 of 10 pathways"
## [1] "Mapping Uniprot ID to Gene Symbol, using convertIdentifiers of graphite package.......... Pentose phosphate pathway 3 of 10 pathways"
## [1] "Mapping Uniprot ID to Gene Symbol, using convertIdentifiers of graphite package.......... Pentose and glucuronate interconversions 4 of 10 pathways"
## [1] "Mapping Uniprot ID to Gene Symbol, using convertIdentifiers of graphite package.......... Fructose and mannose metabolism 5 of 10 pathways"
## [1] "Mapping Uniprot ID to Gene Symbol, using convertIdentifiers of graphite package.......... Galactose metabolism 6 of 10 pathways"
## [1] "Mapping Uniprot ID to Gene Symbol, using convertIdentifiers of graphite package.......... Ascorbate and aldarate metabolism 7 of 10 pathways"
## [1] "Mapping Uniprot ID to Gene Symbol, using convertIdentifiers of graphite package.......... Fatty acid biosynthesis 8 of 10 pathways"
## [1] "Mapping Uniprot ID to Gene Symbol, using convertIdentifiers of graphite package.......... Fatty acid elongation 9 of 10 pathways"
## [1] "Mapping Uniprot ID to Gene Symbol, using convertIdentifiers of graphite package.......... Fatty acid degradation 10 of 10 pathways"
getNETdata
: Searching network data for downloadYou 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:
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 datapath_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 pathwayGE_matrix
: grouping gene expression profiles in pathwaysGet 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 expressionStarting 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 expressionStarting 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 pathwayseucdistcrtlk
: Euclidean distance for cross-talk measureStarting 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 measureStarting 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-talksvm_classification
: SVM classificationGiven 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 pathwayThe 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 pathwaysStarBioTrek 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