Pathview

Pathway based data integration and visualization

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Example 1
Example 2
Example 3
Example 4
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Example Analysis 4: Integrated Pathway Analysis (takes longer time)

Input & Output
Graphics
Coloration

Gene Data:

gse16873.3.txt

Compound Data:

sim.cpd.gse16873.csv

Gene data

Control/Reference

Case/Sample

Compare:

Paired

Compound data

Control/Reference

Case/Sample

Compare:

Paired

Species:

Gene ID Type:

Compound ID Type:

Pathway Selection:

Pathway ID:

Note: Remove items by deleting

Output Suffix:

Kegg Native:

Same Layer:

Discrete Gene:

Discrete Compound:

Multi State:

Match Data:

Compound Label Offset:

Key Alignment:

Signature Position:

Key

Position:

Node Sum:

NA Color:

Attribute

Gene Compound

Limit:

Bins:

Low:

Mid:

High:

HN_1
DCIS_1
HN_2
DCIS_2
HN_3
DCIS_3

HN_1
DCIS_1
HN_2
DCIS_2
HN_3
DCIS_3

cont1
cont2
exp1
exp2

cont1
cont2
exp1
exp2

00010-Glycolysis / Gluconeogenesis
00020-Citrate cycle (TCA cycle)
00030-Pentose phosphate pathway
00040-Pentose and glucuronate interconversions
00051-Fructose and mannose metabolism
00052-Galactose metabolism
00053-Ascorbate and aldarate metabolism
00061-Fatty acid biosynthesis
00062-Fatty acid elongation
00071-Fatty acid degradation
00073-Cutin, suberine and wax biosynthesis
00074-Mycolic acid biosynthesis
00100-Steroid biosynthesis
00120-Primary bile acid biosynthesis
00121-Secondary bile acid biosynthesis
00130-Ubiquinone and other terpenoid-quinone biosynthesis
00140-Steroid hormone biosynthesis
00190-Oxidative phosphorylation
00195-Photosynthesis
00196-Photosynthesis - antenna proteins
00220-Arginine biosynthesis
00230-Purine metabolism
00232-Caffeine metabolism
00240-Pyrimidine metabolism
00250-Alanine, aspartate and glutamate metabolism
00253-Tetracycline biosynthesis
00254-Aflatoxin biosynthesis
00260-Glycine, serine and threonine metabolism
00261-Monobactam biosynthesis
00270-Cysteine and methionine metabolism
00280-Valine, leucine and isoleucine degradation
00290-Valine, leucine and isoleucine biosynthesis
00300-Lysine biosynthesis
00310-Lysine degradation
00311-Penicillin and cephalosporin biosynthesis
00330-Arginine and proline metabolism
00331-Clavulanic acid biosynthesis
00332-Carbapenem biosynthesis
00333-Prodigiosin biosynthesis
00340-Histidine metabolism
00350-Tyrosine metabolism
00360-Phenylalanine metabolism
00361-Chlorocyclohexane and chlorobenzene degradation
00362-Benzoate degradation
00363-Bisphenol degradation
00364-Fluorobenzoate degradation
00365-Furfural degradation
00380-Tryptophan metabolism
00400-Phenylalanine, tyrosine and tryptophan biosynthesis
00401-Novobiocin biosynthesis
00402-Benzoxazinoid biosynthesis
00403-Indole diterpene alkaloid biosynthesis
00404-Staurosporine biosynthesis
00405-Phenazine biosynthesis
00410-beta-Alanine metabolism
00430-Taurine and hypotaurine metabolism
00440-Phosphonate and phosphinate metabolism
00450-Selenocompound metabolism
00460-Cyanoamino acid metabolism
00470-D-Amino acid metabolism
00480-Glutathione metabolism
00500-Starch and sucrose metabolism
00510-N-Glycan biosynthesis
00511-Other glycan degradation
00512-Mucin type O-glycan biosynthesis
00513-Various types of N-glycan biosynthesis
00514-Other types of O-glycan biosynthesis
00515-Mannose type O-glycan biosynthesis
00520-Amino sugar and nucleotide sugar metabolism
00521-Streptomycin biosynthesis
00522-Biosynthesis of 12-, 14- and 16-membered macrolides
00523-Polyketide sugar unit biosynthesis
00524-Neomycin, kanamycin and gentamicin biosynthesis
00525-Acarbose and validamycin biosynthesis
00531-Glycosaminoglycan degradation
00532-Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate
00533-Glycosaminoglycan biosynthesis - keratan sulfate
00534-Glycosaminoglycan biosynthesis - heparan sulfate / heparin
00540-Lipopolysaccharide biosynthesis
00541-O-Antigen nucleotide sugar biosynthesis
00542-O-Antigen repeat unit biosynthesis
00543-Exopolysaccharide biosynthesis
00550-Peptidoglycan biosynthesis
00552-Teichoic acid biosynthesis
00561-Glycerolipid metabolism
00562-Inositol phosphate metabolism
00563-Glycosylphosphatidylinositol (GPI)-anchor biosynthesis
00564-Glycerophospholipid metabolism
00565-Ether lipid metabolism
00571-Lipoarabinomannan (LAM) biosynthesis
00572-Arabinogalactan biosynthesis - Mycobacterium
00590-Arachidonic acid metabolism
00591-Linoleic acid metabolism
00592-alpha-Linolenic acid metabolism
00600-Sphingolipid metabolism
00601-Glycosphingolipid biosynthesis - lacto and neolacto series
00603-Glycosphingolipid biosynthesis - globo and isoglobo series
00604-Glycosphingolipid biosynthesis - ganglio series
00620-Pyruvate metabolism
00621-Dioxin degradation
00622-Xylene degradation
00623-Toluene degradation
00624-Polycyclic aromatic hydrocarbon degradation
00625-Chloroalkane and chloroalkene degradation
00626-Naphthalene degradation
00627-Aminobenzoate degradation
00630-Glyoxylate and dicarboxylate metabolism
00633-Nitrotoluene degradation
00640-Propanoate metabolism
00642-Ethylbenzene degradation
00643-Styrene degradation
00650-Butanoate metabolism
00660-C5-Branched dibasic acid metabolism
00670-One carbon pool by folate
00680-Methane metabolism
00710-Carbon fixation by Calvin cycle
00720-Other carbon fixation pathways
00730-Thiamine metabolism
00740-Riboflavin metabolism
00750-Vitamin B6 metabolism
00760-Nicotinate and nicotinamide metabolism
00770-Pantothenate and CoA biosynthesis
00780-Biotin metabolism
00785-Lipoic acid metabolism
00790-Folate biosynthesis
00791-Atrazine degradation
00830-Retinol metabolism
00860-Porphyrin metabolism
00900-Terpenoid backbone biosynthesis
00901-Indole alkaloid biosynthesis
00902-Monoterpenoid biosynthesis
00903-Limonene degradation
00904-Diterpenoid biosynthesis
00905-Brassinosteroid biosynthesis
00906-Carotenoid biosynthesis
00907-Pinene, camphor and geraniol degradation
00908-Zeatin biosynthesis
00909-Sesquiterpenoid and triterpenoid biosynthesis
00910-Nitrogen metabolism
00920-Sulfur metabolism
00930-Caprolactam degradation
00940-Phenylpropanoid biosynthesis
00941-Flavonoid biosynthesis
00942-Anthocyanin biosynthesis
00943-Isoflavonoid biosynthesis
00944-Flavone and flavonol biosynthesis
00945-Stilbenoid, diarylheptanoid and gingerol biosynthesis
00946-Degradation of flavonoids
00950-Isoquinoline alkaloid biosynthesis
00960-Tropane, piperidine and pyridine alkaloid biosynthesis
00965-Betalain biosynthesis
00966-Glucosinolate biosynthesis
00970-Aminoacyl-tRNA biosynthesis
00980-Metabolism of xenobiotics by cytochrome P450
00981-Insect hormone biosynthesis
00982-Drug metabolism - cytochrome P450
00983-Drug metabolism - other enzymes
00984-Steroid degradation
00996-Biosynthesis of various alkaloids
00997-Biosynthesis of various other secondary metabolites
00998-Biosynthesis of various antibiotics
00999-Biosynthesis of various plant secondary metabolites
01040-Biosynthesis of unsaturated fatty acids
01051-Biosynthesis of ansamycins
01052-Type I polyketide structures
01053-Biosynthesis of siderophore group nonribosomal peptides
01054-Nonribosomal peptide structures
01055-Biosynthesis of vancomycin group antibiotics
01056-Biosynthesis of type II polyketide backbone
01057-Biosynthesis of type II polyketide products
01059-Biosynthesis of enediyne antibiotics
01100-Metabolic pathways
01110-Biosynthesis of secondary metabolites
01120-Microbial metabolism in diverse environments
01200-Carbon metabolism
01210-2-Oxocarboxylic acid metabolism
01212-Fatty acid metabolism
01220-Degradation of aromatic compounds
01230-Biosynthesis of amino acids
01232-Nucleotide metabolism
01240-Biosynthesis of cofactors
01250-Biosynthesis of nucleotide sugars
01501-beta-Lactam resistance
01502-Vancomycin resistance
01503-Cationic antimicrobial peptide (CAMP) resistance
01521-EGFR tyrosine kinase inhibitor resistance
01522-Endocrine resistance
01523-Antifolate resistance
01524-Platinum drug resistance
02010-ABC transporters
02020-Two-component system
02024-Quorum sensing
02025-Biofilm formation - Pseudomonas aeruginosa
02026-Biofilm formation - Escherichia coli
02030-Bacterial chemotaxis
02040-Flagellar assembly
02060-Phosphotransferase system (PTS)
03008-Ribosome biogenesis in eukaryotes
03010-Ribosome
03013-Nucleocytoplasmic transport
03015-mRNA surveillance pathway
03018-RNA degradation
03020-RNA polymerase
03022-Basal transcription factors
03030-DNA replication
03040-Spliceosome
03050-Proteasome
03060-Protein export
03070-Bacterial secretion system
03082-ATP-dependent chromatin remodeling
03083-Polycomb repressive complex
03230-Viral genome structure
03240-Viral replication
03250-Viral life cycle - HIV-1
03258-Virion - Bacteriophage lambda
03259-Virion - Bacteriophages T4 and T7
03260-Virion - Human immunodeficiency virus
03261-Virion - Influenza virus
03262-Virion - Coronavirus
03263-Virion - Enterovirus
03264-Virion - Flavivirus
03265-Virion - Ebolavirus, Lyssavirus and Morbillivirus
03266-Virion - Herpesvirus
03267-Virion - Adenovirus
03268-Virion - Orthopoxvirus
03271-Virion - Rotavirus
03320-PPAR signaling pathway
03410-Base excision repair
03420-Nucleotide excision repair
03430-Mismatch repair
03440-Homologous recombination
03450-Non-homologous end-joining
03460-Fanconi anemia pathway
04010-MAPK signaling pathway
04011-MAPK signaling pathway - yeast
04012-ErbB signaling pathway
04013-MAPK signaling pathway - fly
04014-Ras signaling pathway
04015-Rap1 signaling pathway
04016-MAPK signaling pathway - plant
04020-Calcium signaling pathway
04022-cGMP-PKG signaling pathway
04024-cAMP signaling pathway
04060-Cytokine-cytokine receptor interaction
04061-Viral protein interaction with cytokine and cytokine receptor
04062-Chemokine signaling pathway
04064-NF-kappa B signaling pathway
04066-HIF-1 signaling pathway
04068-FoxO signaling pathway
04070-Phosphatidylinositol signaling system
04071-Sphingolipid signaling pathway
04072-Phospholipase D signaling pathway
04075-Plant hormone signal transduction
04080-Neuroactive ligand-receptor interaction
04110-Cell cycle
04111-Cell cycle - yeast
04112-Cell cycle - Caulobacter
04113-Meiosis - yeast
04114-Oocyte meiosis
04115-p53 signaling pathway
04120-Ubiquitin mediated proteolysis
04122-Sulfur relay system
04130-SNARE interactions in vesicular transport
04136-Autophagy - other
04137-Mitophagy - animal
04138-Autophagy - yeast
04139-Mitophagy - yeast
04140-Autophagy - animal
04141-Protein processing in endoplasmic reticulum
04142-Lysosome
04144-Endocytosis
04145-Phagosome
04146-Peroxisome
04148-Efferocytosis
04150-mTOR signaling pathway
04151-PI3K-Akt signaling pathway
04152-AMPK signaling pathway
04210-Apoptosis
04211-Longevity regulating pathway
04212-Longevity regulating pathway - worm
04213-Longevity regulating pathway - multiple species
04214-Apoptosis - fly
04215-Apoptosis - multiple species
04216-Ferroptosis
04217-Necroptosis
04218-Cellular senescence
04260-Cardiac muscle contraction
04261-Adrenergic signaling in cardiomyocytes
04270-Vascular smooth muscle contraction
04310-Wnt signaling pathway
04320-Dorso-ventral axis formation
04330-Notch signaling pathway
04340-Hedgehog signaling pathway
04341-Hedgehog signaling pathway - fly
04350-TGF-beta signaling pathway
04360-Axon guidance
04361-Axon regeneration
04370-VEGF signaling pathway
04371-Apelin signaling pathway
04380-Osteoclast differentiation
04390-Hippo signaling pathway
04391-Hippo signaling pathway - fly
04392-Hippo signaling pathway - multiple species
04510-Focal adhesion
04512-ECM-receptor interaction
04514-Cell adhesion molecules
04520-Adherens junction
04530-Tight junction
04540-Gap junction
04550-Signaling pathways regulating pluripotency of stem cells
04610-Complement and coagulation cascades
04611-Platelet activation
04612-Antigen processing and presentation
04613-Neutrophil extracellular trap formation
04614-Renin-angiotensin system
04620-Toll-like receptor signaling pathway
04621-NOD-like receptor signaling pathway
04622-RIG-I-like receptor signaling pathway
04623-Cytosolic DNA-sensing pathway
04624-Toll and Imd signaling pathway
04625-C-type lectin receptor signaling pathway
04626-Plant-pathogen interaction
04630-JAK-STAT signaling pathway
04640-Hematopoietic cell lineage
04650-Natural killer cell mediated cytotoxicity
04657-IL-17 signaling pathway
04658-Th1 and Th2 cell differentiation
04659-Th17 cell differentiation
04660-T cell receptor signaling pathway
04662-B cell receptor signaling pathway
04664-Fc epsilon RI signaling pathway
04666-Fc gamma R-mediated phagocytosis
04668-TNF signaling pathway
04670-Leukocyte transendothelial migration
04672-Intestinal immune network for IgA production
04710-Circadian rhythm
04711-Circadian rhythm - fly
04712-Circadian rhythm - plant
04713-Circadian entrainment
04714-Thermogenesis
04720-Long-term potentiation
04721-Synaptic vesicle cycle
04722-Neurotrophin signaling pathway
04723-Retrograde endocannabinoid signaling
04724-Glutamatergic synapse
04725-Cholinergic synapse
04726-Serotonergic synapse
04727-GABAergic synapse
04728-Dopaminergic synapse
04730-Long-term depression
04740-Olfactory transduction
04742-Taste transduction
04744-Phototransduction
04745-Phototransduction - fly
04750-Inflammatory mediator regulation of TRP channels
04810-Regulation of actin cytoskeleton
04814-Motor proteins
04820-Cytoskeleton in muscle cells
04910-Insulin signaling pathway
04911-Insulin secretion
04912-GnRH signaling pathway
04913-Ovarian steroidogenesis
04914-Progesterone-mediated oocyte maturation
04915-Estrogen signaling pathway
04916-Melanogenesis
04917-Prolactin signaling pathway
04918-Thyroid hormone synthesis
04919-Thyroid hormone signaling pathway
04920-Adipocytokine signaling pathway
04921-Oxytocin signaling pathway
04922-Glucagon signaling pathway
04923-Regulation of lipolysis in adipocytes
04924-Renin secretion
04925-Aldosterone synthesis and secretion
04926-Relaxin signaling pathway
04927-Cortisol synthesis and secretion
04928-Parathyroid hormone synthesis, secretion and action
04929-GnRH secretion
04930-Type II diabetes mellitus
04931-Insulin resistance
04932-Non-alcoholic fatty liver disease
04933-AGE-RAGE signaling pathway in diabetic complications
04934-Cushing syndrome
04935-Growth hormone synthesis, secretion and action
04936-Alcoholic liver disease
04940-Type I diabetes mellitus
04950-Maturity onset diabetes of the young
04960-Aldosterone-regulated sodium reabsorption
04961-Endocrine and other factor-regulated calcium reabsorption
04962-Vasopressin-regulated water reabsorption
04964-Proximal tubule bicarbonate reclamation
04966-Collecting duct acid secretion
04970-Salivary secretion
04971-Gastric acid secretion
04972-Pancreatic secretion
04973-Carbohydrate digestion and absorption
04974-Protein digestion and absorption
04975-Fat digestion and absorption
04976-Bile secretion
04977-Vitamin digestion and absorption
04978-Mineral absorption
04979-Cholesterol metabolism
04980-Cobalamin transport and metabolism
05010-Alzheimer disease
05012-Parkinson disease
05014-Amyotrophic lateral sclerosis
05016-Huntington disease
05017-Spinocerebellar ataxia
05020-Prion disease
05022-Pathways of neurodegeneration - multiple diseases
05030-Cocaine addiction
05031-Amphetamine addiction
05032-Morphine addiction
05033-Nicotine addiction
05034-Alcoholism
05100-Bacterial invasion of epithelial cells
05110-Vibrio cholerae infection
05111-Biofilm formation - Vibrio cholerae
05120-Epithelial cell signaling in Helicobacter pylori infection
05130-Pathogenic Escherichia coli infection
05131-Shigellosis
05132-Salmonella infection
05133-Pertussis
05134-Legionellosis
05135-Yersinia infection
05140-Leishmaniasis
05142-Chagas disease
05143-African trypanosomiasis
05144-Malaria
05145-Toxoplasmosis
05146-Amoebiasis
05150-Staphylococcus aureus infection
05152-Tuberculosis
05160-Hepatitis C
05161-Hepatitis B
05162-Measles
05163-Human cytomegalovirus infection
05164-Influenza A
05165-Human papillomavirus infection
05166-Human T-cell leukemia virus 1 infection
05167-Kaposi sarcoma-associated herpesvirus infection
05168-Herpes simplex virus 1 infection
05169-Epstein-Barr virus infection
05170-Human immunodeficiency virus 1 infection
05171-Coronavirus disease - COVID-19
05200-Pathways in cancer
05202-Transcriptional misregulation in cancer
05203-Viral carcinogenesis
05204-Chemical carcinogenesis - DNA adducts
05205-Proteoglycans in cancer
05206-MicroRNAs in cancer
05207-Chemical carcinogenesis - receptor activation
05208-Chemical carcinogenesis - reactive oxygen species
05210-Colorectal cancer
05211-Renal cell carcinoma
05212-Pancreatic cancer
05213-Endometrial cancer
05214-Glioma
05215-Prostate cancer
05216-Thyroid cancer
05217-Basal cell carcinoma
05218-Melanoma
05219-Bladder cancer
05220-Chronic myeloid leukemia
05221-Acute myeloid leukemia
05222-Small cell lung cancer
05223-Non-small cell lung cancer
05224-Breast cancer
05225-Hepatocellular carcinoma
05226-Gastric cancer
05230-Central carbon metabolism in cancer
05231-Choline metabolism in cancer
05235-PD-L1 expression and PD-1 checkpoint pathway in cancer
05310-Asthma
05320-Autoimmune thyroid disease
05321-Inflammatory bowel disease
05322-Systemic lupus erythematosus
05323-Rheumatoid arthritis
05330-Allograft rejection
05332-Graft-versus-host disease
05340-Primary immunodeficiency
05410-Hypertrophic cardiomyopathy
05412-Arrhythmogenic right ventricular cardiomyopathy
05414-Dilated cardiomyopathy
05415-Diabetic cardiomyopathy
05416-Viral myocarditis
05417-Lipid and atherosclerosis
05418-Fluid shear stress and atherosclerosis

Note: Remove items by deleting

Key

Position:

Bioinformatics Services Division - Department of Bioinformatics and Genomics - UNC Charlotte