And Cell Molecularbiological databases Swissprot Entrez Pharm Gkb

Система And. Cell: автоматическая реконструкция ассоциативных сетей знаний и фактов по живым системам Molecular-biological databases Swissprot, Entrez, Pharm. Gkb, etc Dictionaries of objects names Proteins, Genes, Metabolites, Pathways, Cell components, Micro. RNAs, Cells, Organisms, Diseases Molecular interaction databases (protein -protein, protein-DNA, proteinsubstance) Int. Act, MINT, NCBI GENE, TRRD, KEGG, PIMRider, Inter. Pro Data-mining module C binds D ANDCell knowledge database Text-mining module Abstract 1: A regulates B Abstract 2: B regulates C. . Pub. Med database Integration of knowledge obtained by text-mining and data-mining modules A regulates B regulates C binds D Associative network visualizer ANDVisio A B C D 8

Реконструкция фрагмента ассоциативной семантической сети жизненного цикла вируса гепатита С Hepatitis C virus (HCV) NS 5 B protein is a membrane-associated phosphoprotein that possesses an RNA-dependent RNA polymerase activity. We recently reported that NS 5 A protein interacts with TRAF 2 and modulates tumor necrosis factor alpha (TNF-alpha)induced NF-kappa. B and Jun N-terminal protein kinase (JNK). Since NS 5 A and NS 5 B are the essential components of the HCV replication complex, we examined whether NS 5 B could modulate TNF-alpha-induced NF-kappa. B and JNK activation. In this study, we have demonstrated that TNF-alpha-induced NF-kappa. B activation is inhibited by NS 5 B protein in HEK 293 and hepatic cells. Furthermore, NS 5 B protein inhibited both TRAF 2 and IKK-induced NF-kappa. B activation. Using coimmunoprecipitation assays, we show that NS 5 B interacts with IKKalpha. Most importantly, NS 5 B protein in HCV subgenomic replicon cells interacted with endogenous IKKalpha, and then TNF-alpha-mediated IKKalpha kinase activation was significantly decreased by NS 5 B. Using in vitro kinase assay, we have further found that NS 5 B protein synergistically activated TNF-alphamediated JNK activity in HEK 293 and hepatic cells. These data suggest that NS 5 B protein modulates TNF-alpha signaling pathways and may contribute to HCV pathogenesis. белки усиление активности подавление активности образование комплекса NS 5 A JNK NS 5 B NK-k. B TRAF 2 TNF-alpha IKKalpha 10

Dictionaries of molecular-genetic object names the Gene Ontology Protein names 370097 Gene names 2474201 Disease names 46109 Metabolite names 79914 Organism names 428439 Micro. RNA names 4515 Pathway names Cell component names Cell names 90 000 (42864 – GO; 47136 – Pub. Med) 5249 396841 -Pub. Med 12

Онтология типов взаимодействий Direct interaction Cleavage Catalytic reaction Co-expression Upregulation Regulation Function/activity Expression Pathways Transport/release Conversion Treatment Downregulation Degradation/stability Diseases Association 13

Статистика типов взаимодействий association 3423732 conversion involvement 728947 coexpression 6617 Interaction 242580 cleavage 2170 treatment 51162 catalyze 49164 catalyze modification 23519 430 Регуляторные связи: expression regulation 155835 activity downregulation 44314 expression downregulation 33680 activity upregulation 40564 expression upregulation 46578 activity regulation 16982 pathway regulation 104983 degradation downregulation 8455 pathway upregulation 64701 degradation upregulation 8265 pathway downregulation 64289 degradation regulation 1026 transport regulation 64801 mi. RNA regulation 23576 Всего 5 206 370 14

Организмы, представленные в базе знаний ANDCell Homo sapiens 1261815 Rattus norvegicus 646694 Escherichia coli 223873 Gallus gallus 216535 Caenorhabditis elegans 181336 Saccharomyces cerevisiae 174413 Arabidopsis thaliana 164908 . ………………………… …. . . . ………. . . Total 5206370 15

The associative network of human genes and proteins involved in HCV life cycle 223 proteins 172 genes 16

Associative network of proteins regulating genes involved in the HCV life cycle 17

Only genes and proteins associated with expression downregulation are shown 18

The biological processes in which HCV Core protein and NS 5 A are involved Core protein NS 5 A 19

The network of diseases associated with hepatitis C 125 diseases 20

Некоторые из разделов словаря наноструктур: уровень II 1. NANOPARTICLES (наночастицы) 1. 1. Organic nanoparticles. 1. 2. Lipid nanoparticles 1. 3. Hydrogel nanoparticles 1. 4. DNA nanoparticles 1. 5. Peptide nanoparticles 1. 6. Quantum dots 1. 7. Functionalized nanoparticles 1. 8. Dendrimers nanoparticles 1. 9. Magnetic nanoparticles 1. 10. Ferrosoferric Oxide nanoparticles 1. 11. Ceramic nanoparticles 1. 12. Alumina nanoparticle 1. 13. Gold nanoparticles 1. 14. Silver-silica composite nanoparticles ……………… 23

Некоторые из разделов словаря наноструктур: уровень III 1. NANOPARTICLES (наночастицы) 1. 1. Organic nanoparticles. 1. 1. 1. Polymer nanoparticles 1. 1. 2. Perfluorocarbon nanoparticles …. . 1. 2. Lipid nanoparticles 1. 3. Hydrogel nanoparticles 1. 4. DNA nanoparticles 1. 5. Peptide nanoparticles 1. 6. Quantum dots 1. 7. Functionalized nanoparticles 1. 8. Dendrimers nanoparticles 1. 9. Magnetic nanoparticles 1. 10. Ferrosoferric Oxide nanoparticles 1. 11. Ceramic nanoparticles 1. 12. Alumina nanoparticle 1. 13. Gold nanoparticles 1. 14. Silver-silica composite nanoparticles ……………… 24

НЕКОТОРЫЕ ИЗ РАЗДЕЛОВ СЛОВАРЯ НАНОПРОДУКТОВ: УРОВЕНЬ I 1. NANOSENSORS/BIOSENSORS 2. NANODEVICES 3. NANOBIOCHIPS 4. DRUG NANOCARRIERS 5. BLOOD SUBSTITUTES 6. BIOMARKERS 7. ANTIMICROBIAL AGENT 8. ROOM SPRAY 9. ANTICOAGULANT 10. WATER DISINFECTANT ………………. …. …………………. 25

НЕКОТОРЫЕ ИЗ РАЗДЕЛОВ СЛОВАРЯ НАНОПРОДУКТОВ: УРОВЕНЬ II 1. NANOSENSORS/BIOSENSORS 1. 1. mechanical nanosensors for biological detection (virus, antigen, DNA, protein, ets) 1. 2. Electronic nanobiosensors 1. 3. Ion channel switch biosensor 1. 4. Nanowire biosensors 1. 4. Nanocantilevers as biosensors 1. 5. FRET-based DNA nanosensor 1. 6. Optical biosensors using laser, nanoshell, SPR, SERS, m. RNA PEBBLE 1. 7. Quartz nanobalance DNA sensor 1. 8. Carbon nanotube biosensors 1. 9 Viral nanosensor 1. 10. Genosensors 2. 3. 4. 5. . . NANODEVICES NANOBIOCHIPS DRUG NANOCARRIERS. . ……………………………. . 26

Пример выдачи результата по запросу “Doxorubicin Cds nanoparticles” к базе знаний Nano. Bio. Warehouse Nanomaterial: Doxorubicin-Cd. S nanoparticles Constituents: doxorubicin, cadmium sulfide (Cd. S) Biomedical properties: facilitate drug uptake Biotargets: Diseases: cancer Bio. Processes: biorecognition, signal transfer pathway Organism: human Tissue: blood Cells: leukemia K 562 cells Извлечено из базовой статьи Извлечено из других источников Source: PMID: 17450775 Applied technologies: Liquid-liquid interfacial nanoparticle assemblies. Patent: US 20040202682 Related entries: 1. doxorubicin loaded poly(butyl cyanoacrylate) nanoparticles 2. micelle-encapsulated doxorubicin 3. mechanochemically activated doxorubicin (ma doxo) nanoparticles 4. il-13 -conjugated liposomes carrying doxorubicin 5. doxorubicin (dox)-loaded chitosan (cs)-poly(acrylic acid) (paa) hollow nanospheres 6. doxorubicin (dox)-loaded poly(l-glutamic acid) nanocapsules 7. ………………………………………. 8. ………………………………………. 9. …………………. (всего болеее 50) 28

ПРИМЕРЫ СЛОЖНО-СОСТАВНЫХ ТЕРМИНОВ, ИСПОЛЬЗУЕМЫХ ДЛЯ ОПИСАНИЯ НАНОБИООБЪЕКТОВ НАНОМАТЕРИАЛЫ: • interpenetrating polymer networks (IPNs) of polyacrylic acid (PAAc) and poly(N-isopropylacrylamide) (PNIPAM) • single- and double-stranded deoxy ribonucleic acid (DNA) molecules attached to self-assembled monolayers (SAMs) on gold surfaces НАНОТЕХНОЛОГИИ: • single-molecule nanopore sequencing technology • low invasive single cell DNA delivery technology КОНЕЧНЫЕ ПРОДУКТЫ: • surface plasmon resonance-based optical biosensor • CU/LDPE nanocomposite intrauterine device • polydimethylsiloxane (pdms) microfluidic device 29

Ассоциативная сеть связей инсулина с наноматериалами, построенная на основе обращения к базе знаний Nano. Bio. Ware. House (более 100 объектов) 1. Nanogels 2. Nanocapsules 3. Nanogold particles 4. Nannoparticle-chitosan 5. Solid lipid nanoparticles 6. Carbon nanotubes ………………………. 110. Nanopore membranes 111. Cobalt nanoparticles 30

АНАЛИЗ СЛОЖНОСОСТАВНЫХ ТЕРМИНОВ И РЕКОНСТРУКЦИЯ ЭТАПОВ ФОРМИРОВАНИЯ НАНОЧАСТИЦ С УЧАСТИЕМ ИНСУЛИНА We developed nanospheres of crosslinked networks of methacrylic acid grafted with poly(ethylene glycol) nanospheres, and acrylic acid grafted with poly(ethylene glycol) nanospheres for use as oral insulin delivery devices. Составной термин (уровень II) methacrylic acid grafted with poly(ethylene glycol) nanospheres Составной термин (уровень II) acrylic acid grafted with poly(ethylene glycol) nanospheres methacrylic acid grafted with poly(ethylene glycol) nanospheres, and acrylic acid grafted with poly(ethylene glycol) nanospheres Сложносоставной термин (уровень III) термин 31

Сеть семантических связей между терминами различных уровней: Sentence: We developed nanospheres of crosslinked networks of methacrylic acid grafted with poly(ethylene glycol) nanospheres, and acrylic acid grafted with poly(ethylene glycol) nanospheres for use as oral insulin delivery devices. Name 1: methacrylic acid Type: constituent; Role: part_of Name 3 Name 2: poly(ethylene glycol) nanospheres Type: nanomaterial|constituent; Role: part_of Name 3; part_of Name 5; Name 3: methacrylic acid grafted with poly(ethylene glycol) nanospheres Type: nanomaterial|constituent; Role: part_of Name 6; Name 4: acrylic acid Type: constituent; Role: part_of Name 5: acrylic acid grafted with poly(ethylene glycol) nanospheres Type: nanomaterial|constituent; Role: part_of Name 6; Name 6: methacrylic acid grafted with poly(ethylene glycol) nanospheres, and acrylic acid grafted with poly(ethylene glycol) nanospheres Type: nanomaterial; Role: is_a Name 7; Name 7: insulin delivery devices Type: device; Role: subjected Уровень II Уровень I methacrylic acid (1) methacrylic acid grafted with poly(ethylene glycol) nanospheres (3) Уровень III methacrylic acid grafted with poly(ethylene glycol) nanospheres, and acrylic acid grafted with poly(ethylene glycol) nanospheres (6) Уровень IV insulin delivery devices (7) poly(ethylene glycol) nanospheres (2) acrylic acid (4) acrylic acid grafted with poly(ethylene glycol) nanospheres (5) 32

Ассоциативная сеть взаимосвязей хитозана с наноматериалами, нанотехнологиями, нанопродуктами и областями применений Наноматериалы • fibrous chitosan scaffold • chitosan-coated AU nanoparticles • composite chitosan-hydroxyapatite films • bsa-loaded chitosan-tpp nanoparticles • cationic chitosan/plga nanoparticles • chitosan spontaneously formed DNA nanoparticles • biosensing nanocomposite films ………………………………. . Области применений 1. gene therapy 2. drug delivery 3. tissue regeneration 4. biosensor fabrication… Нанотехнологии • • layer-by-layer self assembly techniques laser-activated chitosan techniques tissue engineering techniques nanoimprinting lithographies ………………………. Нанопродукты Chondrocyte cells attached to a fibrous chitosan scaffold 1. nanoparticles composed of chitosan/poly-γ-glutamic acid Patent US 5285430 2. CHITOSANTE Patent US 6823570 3. Gene expression vaccine Patent US 7118888 ………………………………. . 34

Аналитические и исполняющие нанобиоустройства на основе квантовых точек Quantum dots as donors in fluorescence resonance energy transfer for the bioanalysis of nucleic acids, proteins, and other biological molecules W. Russ Algar & Ulrich J. Krull; Anal Bioanal Chem (2008) 391: 1609– 1618 44