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PritiShaw/mesh-to-indra-issue19.ipynb

Last active August 12, 2020 20:06
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MeSH to INDRA issue19.ipynb
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mesh-to-indra-issue19.ipynb
{
"nbformat": 4,
"nbformat_minor": 0,
"metadata": {
"colab": {
"name": "MeSH to INDRA issue19.ipynb",
"provenance": [],
"collapsed_sections": [],
"authorship_tag": "ABX9TyMmyQ8eJoQGo6sAEJQv5ilv",
"include_colab_link": true
},
"kernelspec": {
"name": "python3",
"display_name": "Python 3"
}
},
"cells": [
{
"cell_type": "markdown",
"metadata": {
"id": "view-in-github",
"colab_type": "text"
},
"source": [
"<a href=\"https://colab.research.google.com/gist/PritiShaw/f52719e184e6bc29e8336dbea44b0819/mesh-to-indra-issue19.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
]
},
{
"cell_type": "code",
"metadata": {
"id": "0ulwkc57Iftt",
"colab_type": "code",
"colab": {}
},
"source": [
"%%capture\n",
"!pip install indra"
],
"execution_count": 2,
"outputs": []
},
{
"cell_type": "code",
"metadata": {
"id": "CdMHwq0MKpqI",
"colab_type": "code",
"colab": {}
},
"source": [
"import os\n",
"os.environ[\"INDRA_DB_REST_URL\"] = \"SET API\"\n",
"from indra.literature import pubmed_client\n",
"from indra.sources import indra_db_rest"
],
"execution_count": 3,
"outputs": []
},
{
"cell_type": "code",
"metadata": {
"id": "oLFR_2ydLOZk",
"colab_type": "code",
"colab": {}
},
"source": [
"def get_stmts_from_term(search_term, maximum_articles = 10):\n",
" pmid_list = pubmed_client.get_ids(search_term.strip(), retmax = maximum_articles)\n",
" search_pmid_list = [('pmid',pmid) for pmid in pmid_list]\n",
" stmts = []\n",
" if search_pmid_list:\n",
" stmts = indra_db_rest.get_statements_for_paper(search_pmid_list).statements\n",
" return stmts"
],
"execution_count": 4,
"outputs": []
},
{
"cell_type": "code",
"metadata": {
"id": "a37P2jiTLGZV",
"colab_type": "code",
"colab": {
"base_uri": "https://localhost:8080/",
"height": 1000
},
"outputId": "efc659eb-cc56-46ac-b4cf-20c4d8aa50d8"
},
"source": [
"search_term = input(\"Please Enter Search Query: \")\n",
"get_stmts_from_term(search_term,100000)"
],
"execution_count": 5,
"outputs": [
{
"output_type": "stream",
"text": [
"Please Enter Search Query: lipophagy\n"
],
"name": "stdout"
},
{
"output_type": "stream",
"text": [
"INFO: [2020-08-12 20:04:43] indra.sources.indra_db_rest.util - query: https://db.indra.bio/statements/from_papers\n",
"INFO: [2020-08-12 20:04:43] indra.sources.indra_db_rest.util - params: {'ev_limit': 10, 'best_first': True, 'max_stmts': [api-key], 'api_key': [api-key]}\n"
],
"name": "stderr"
},
{
"output_type": "execute_result",
"data": {
"text/plain": [
"[IncreaseAmount(CD36(), CEBPB()),\n",
" Phosphorylation(None, AMPK()),\n",
" Complex(phosphatidylethanolamine(), phosphatidylcholine()),\n",
" Inhibition(ATG7(), autophagy()),\n",
" Inhibition(metF(), niaD()),\n",
" Complex(Clathrin(), VPS27()),\n",
" Complex(SQSTM1(), FMN1()),\n",
" Complex(PNPLA2(), lipophagic protein ATG()),\n",
" IncreaseAmount((-)-epigallocatechin 3-gallate(), ATG7()),\n",
" Activation(ATG7(), CRTC2(muts: (S, 171, A))),\n",
" Activation(autophagy(), cell death()),\n",
" Inhibition(NR1H4(), response()),\n",
" Complex(LAMP1(), RAB10()),\n",
" Complex(ABHD5(), G0S2()),\n",
" Phosphorylation(3',5'-cyclic AMP(), LIPE()),\n",
" Activation(SQSTM1(), exocytosis()),\n",
" Complex(3',5'-cyclic AMP(), PKA downstream target proteins()),\n",
" Activation(TP53(), PGC1A1alpha()),\n",
" Activation(ASAH2(), metabolic process()),\n",
" IncreaseAmount(ethanol(), SQSTM1()),\n",
" Complex(cholesterol(), NPC1()),\n",
" IncreaseAmount(CQ(), triglyceride()),\n",
" Activation(BNIP3L(), CCCP()),\n",
" Inhibition(MAP1S(), autophagy()),\n",
" Activation(Thr-Thr(), NAFLD()),\n",
" Activation(ULK1(), ATG13()),\n",
" Inhibition(ATG14(), autophagy()),\n",
" Complex(PINK1(), PARL()),\n",
" Complex(FMN1(), RAB10()),\n",
" Activation(IPMK(), inflammatory response()),\n",
" Inhibition(PKM(), pyruvate kinase()),\n",
" Activation(okadaic acid(), FMN1()),\n",
" DecreaseAmount(MLX-3(), LIPM()),\n",
" Phosphorylation(CK2(), FUNDC1(), Y, 18),\n",
" Inhibition(CIDEC(), lipolysis()),\n",
" Complex(RAB(), SNAREs()),\n",
" Complex(POMC(), Agouti()),\n",
" Activation(hexadecanoic acid(), (-)-epigallocatechin 3-gallate()),\n",
" Activation(DNM2(), Leu-Asp-Ser()),\n",
" Inhibition(PNPLA2(), FMN1()),\n",
" Inhibition(Cyclin(), LC3II-B()),\n",
" Activation(SOCE(), 3',5'-cyclic AMP()),\n",
" Inhibition(cholesterol(), NR1H3()),\n",
" Activation(BECN1(), autophagy()),\n",
" Complex(STUB1(), TFE3()),\n",
" Activation(hexadecanoic acid(), autophagy()),\n",
" Activation(PTEN(), PRKN()),\n",
" Activation(FMN1(), LD-MVB platform()),\n",
" Activation(chenodeoxycholic acid(), NR1H4()),\n",
" Activation(2-[bis(2-hydroxyethyl)amino]ethanesulfonic acid(), CAT()),\n",
" Complex(FOXC2(), ARF1()),\n",
" Complex(RAB7A(), FYVE()),\n",
" Phosphorylation(PINK1(), PRKN()),\n",
" Activation(LPIN1(), SREBPs()),\n",
" Inhibition(RNAi(), SNARE()),\n",
" Complex(Npc2p(), raft-like domain()),\n",
" IncreaseAmount(ethanol(), triglyceride()),\n",
" Activation(pentapeptide(), PLIN3()),\n",
" DecreaseAmount(BAAT(), PNPLA2()),\n",
" DecreaseAmount(ethanol(), MTOR()),\n",
" Translocation(RAB5A(), None, membrane),\n",
" Complex(NPC2(), NPC1()),\n",
" Activation(SMPD1(), ab()),\n",
" DecreaseAmount(ethanol(), ATG7()),\n",
" Inhibition(dioscin(), sucrose()),\n",
" Complex(WIPI2(), MEF()),\n",
" IncreaseAmount(LEP(), LCLAT1()),\n",
" Complex(HDL(), MBTPS1()),\n",
" Activation(metformin(), AMPK()),\n",
" Activation(ethanol(), triglyceride()),\n",
" Phosphorylation(PINK1(), MFN2()),\n",
" Activation(ATG7(), ITGAM()),\n",
" Inhibition(RAB10(), EHD3()),\n",
" Translocation(FAS(), None, None),\n",
" Inhibition(lactose(), cholesterol()),\n",
" Phosphorylation(AMPK(), ELF4()),\n",
" DecreaseAmount(quercetin(), SLC17A5()),\n",
" Complex(dynactin(), dynein()),\n",
" Phosphorylation(None, EIF2AK2()),\n",
" Activation(NADH(), dioxygen()),\n",
" Complex(SOAT1(), LO()),\n",
" Activation(ethanol(), Reactive Oxygen Species()),\n",
" Inhibition(sirolimus(), triglyceride()),\n",
" Inhibition((-)-epigallocatechin 3-gallate(), Leu-Asp-Ser()),\n",
" Inhibition(resveratrol(), ethanol()),\n",
" Activation(Cyclin(), IK()),\n",
" Inhibition(ORAI1(), SOCE()),\n",
" DecreaseAmount(MTOR(), LC3-II()),\n",
" Inhibition(GW4064(), pirinixic acid()),\n",
" Inhibition(autophagy(), homeostatic process()),\n",
" Inhibition(S-butyl-DL-homocysteine (S,R)-sulfoximine(), glutathione()),\n",
" Activation(FOXO(), catabolism()),\n",
" Activation(UUO(), autophagy()),\n",
" Activation(TGFB1(), Leu-Asp-Ser()),\n",
" DecreaseAmount(PNPLA2(mods: (modification)), SQSTM1()),\n",
" Inhibition(endoplasmic reticulum(), proteolysis()),\n",
" Phosphorylation(None, lipase()),\n",
" Phosphorylation(SOCE(), LIPE()),\n",
" DecreaseAmount(ER-stress(), INSR()),\n",
" Activation(BSCL2(), phosphatidic acid()),\n",
" Complex(ATG16L1(), ATG12(), ATG5()),\n",
" Activation(PTEN(), E3_Ub_ligase()),\n",
" Activation(MTOR(), EIF4EBP1()),\n",
" Dephosphorylation(mTORC1(), ULK1/2()),\n",
" Inhibition(XL388(), mTORC1()),\n",
" Activation(AMPK(), glycolytic process()),\n",
" Complex(TFE3(), CLEAR elements()),\n",
" Inhibition(lipopolysaccharide(), TGFB()),\n",
" Complex(MAP1S(), CD74()),\n",
" Complex(ULK1(), MTOR()),\n",
" Complex(ATG12(), help()),\n",
" Inhibition(STX5(), Leu-Asp-Ser()),\n",
" Activation(tamoxifen(), SOCE()),\n",
" Activation(RPS6KB1(), SREBP family()),\n",
" IncreaseAmount(resveratrol(), acetyl-CoA()),\n",
" Activation(CREB(), CRTC2()),\n",
" Activation(ethanol(), PDE()),\n",
" Acetylation(None, Histone_H4(), K, 16),\n",
" Complex(CREB(), CRTC2(), NR1H4()),\n",
" Activation(TFE3(), GFP-LC3()),\n",
" Inhibition(INS(), PNPLA2()),\n",
" Activation(CRTC2(), CRTC2()),\n",
" Activation(RAB10(), SLC2A4()),\n",
" DecreaseAmount(SOCE(), UCP2()),\n",
" Translocation(PRKN(), None, mitochondrial outer membrane),\n",
" Translocation(NR1H3(), None, nucleus),\n",
" Activation(TOR(), localization()),\n",
" Activation(capsaicin(), cholesterol()),\n",
" Complex(ATG7(), ATG10()),\n",
" Complex(AUP1(), DENV NS4A/B()),\n",
" Complex(MAP1LC3(), ATG16L1(), FOXC2()),\n",
" Activation(CRTC2(), transcription, DNA-templated()),\n",
" Complex(RAB18(), PLIN2()),\n",
" IncreaseAmount(ORAI1(bound: [ADCY8, True]), 3',5'-cyclic AMP()),\n",
" Activation(LRPAP1(), lipophagy()),\n",
" Inhibition(X(), pH reduction()),\n",
" Phosphorylation(hexadecanoic acid(), EIF2AK2()),\n",
" Activation(TFE3(), triglyceride()),\n",
" Activation(MAP1S(), turnover()),\n",
" Activation(2-[bis(2-hydroxyethyl)amino]ethanesulfonic acid(), MnSOD()),\n",
" DecreaseAmount(sirolimus(), Reactive Oxygen Species()),\n",
" Inhibition(CREB(), NR1H4()),\n",
" IncreaseAmount(AGRP(), AGRP()),\n",
" IncreaseAmount(ORMDL3(), BECN1()),\n",
" Activation(FOXO(), autophagy()),\n",
" Inhibition(mTORC1(), autophagy()),\n",
" Inhibition((-)-epigallocatechin 3-gallate(), LC3-II()),\n",
" IncreaseAmount(Cyclin(), FASN()),\n",
" Activation(resveratrol(), apoptotic process()),\n",
" Activation(ethanol(), Rabs.45()),\n",
" IncreaseAmount(LRPAP1(), BAT Ucp1()),\n",
" Phosphorylation(CSK(), DNM2()),\n",
" Activation(caffeine(), TFEB()),\n",
" Activation(malonaldehyde(), S-adenosyl-L-methionine()),\n",
" Inhibition(GW4064(), HLA-DRB1()),\n",
" Inhibition(NR1H4(), TFEB()),\n",
" Phosphorylation(None, PRKN(), S, 65),\n",
" Inhibition(lysosomal hydrolases(), aluminium(3+)()),\n",
" Activation(NR0B2(), demethylase LSD1()),\n",
" Activation(metF(), autophagy()),\n",
" Activation(lipopolysaccharide(), TLR4()),\n",
" Activation(sorafenib(), AKT()),\n",
" Activation(dhCer desaturase(), ifc -KO()),\n",
" Inhibition(EIF4E(), translation()),\n",
" Inhibition(cytidylyltransferase(), Leu-Asp-Ser()),\n",
" DecreaseAmount(Cyclin(), Leu-Asp-Ser()),\n",
" IncreaseAmount(LRPAP1(), LC3-II()),\n",
" Activation(ORMDL3(), autophagy()),\n",
" Inhibition(endoplasmic reticulum(), STIM1()),\n",
" Inhibition(PP2A inhibitor(), LC3 flux()),\n",
" Translocation(mTORC1(), cytoplasm, None),\n",
" Activation(BAAT(), FMN1()),\n",
" Phosphorylation(None, AMPK(), T, 172),\n",
" Activation(niaD(), catabolism()),\n",
" Complex(TBC1D4(), CIDEC(), RAB8A()),\n",
" Activation(PRDX1(), SQSTM1()),\n",
" Activation(ethanol(), CYP2E1()),\n",
" Activation(TFEB(), CRTC2(muts: (S, 171, A))),\n",
" Activation(FOXO(), GLUL()),\n",
" Activation(niaD(), FOXO1()),\n",
" Activation(2-[bis(2-hydroxyethyl)amino]ethanesulfonic acid(), SQSTM1()),\n",
" Inhibition(KDM1A(), autophagy()),\n",
" Phosphorylation(None, FMN1()),\n",
" Activation(NR(), catabolism()),\n",
" IncreaseAmount(PPARA(), LC3-I()),\n",
" Complex(AMPK(), SIRT1(), IPMK()),\n",
" Inhibition(Leu-Asp-Ser(), Histone_H2B()),\n",
" Inhibition(Phosphatase(), PI3K()),\n",
" Inhibition(autophagy(), cell death()),\n",
" Activation(PNPLA2(), FAS()),\n",
" Activation(hexadecane(), BAAT()),\n",
" Inhibition(HMBS(), LD proteins()),\n",
" Activation(curcumin(), AMPK()),\n",
" Inhibition(LRPAP1(), FMN1()),\n",
" Activation(IP3R(), calcium(2+)()),\n",
" Complex(CIDEC(), PNPLA2()),\n",
" Activation(sirolimus(), autophagy()),\n",
" Activation(Latrunculin A(), Erg6p-GFP()),\n",
" Activation(autophagy(), homeostatic process()),\n",
" Activation(BP(), 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene()),\n",
" Phosphorylation(mTORC1(), TFEB(), S),\n",
" Inhibition(PPP2(), mTORC1()),\n",
" Activation(FGF21(), autophagy()),\n",
" Complex(RAB18(), RAB8A(), RAB10()),\n",
" Activation(CRTC2(), TFEB()),\n",
" DecreaseAmount(PNPLA2(), CDK4()),\n",
" Complex(BRAP(), FOXC2()),\n",
" Phosphorylation(AMPK(), BECN1()),\n",
" Activation(lipopolysaccharide(), ATG5()),\n",
" Inhibition(BAAT(), FMN1()),\n",
" Inhibition(PGC1alpha siRNA(), FFAs beta()),\n",
" Translocation(SQSTM1(), None, None),\n",
" Activation(PTEN(), sensor()),\n",
" Activation(caffeine(), autophagy()),\n",
" Complex(PNPLA2(), LAMP1(), LIPE()),\n",
" Complex(RXR(), NR1H4()),\n",
" Complex(TGFB1(), HK2()),\n",
" Inhibition(HDL(), autophagy()),\n",
" Inhibition(PLIN2(), autophagy()),\n",
" Activation(PNPLA2(), HDAC_III()),\n",
" Activation(ethanol(), apoptotic process()),\n",
" Complex(ULK1(), ULK()),\n",
" Activation(autophagy(), cellular senescence()),\n",
" Activation(PNPLA2(), autophagy()),\n",
" Activation(sorafenib(), apoptotic process()),\n",
" Inhibition(Proteasome(), autophagy()),\n",
" Activation(TFE3(), autophagy()),\n",
" Complex(FFAR2(), ATG8()),\n",
" Complex(FOXC2(), RAB7A()),\n",
" Activation(PNPLA2(), PPARA()),\n",
" Complex(cholesterol(), LAMP2()),\n",
" Dephosphorylation(PPP2(), TFEB()),\n",
" Activation(guanine(), GDP()),\n",
" Phosphorylation(None, CRMP1()),\n",
" Complex(GTP(), MADS3()),\n",
" Activation(RAB7A(), CTSB()),\n",
" Activation(3',5'-cyclic AMP(), F3()),\n",
" Complex(Clathrin(), vps27()),\n",
" Activation(TFEB(), AKT()),\n",
" Inhibition(quercetin(), triglyceride()),\n",
" Inhibition(PRDX1(), cholesterol()),\n",
" Inhibition(sirolimus(), Reactive Oxygen Species()),\n",
" Complex(RAB(), DNM2()),\n",
" Complex(CSK(), DNM2()),\n",
" DecreaseAmount(F11(), perilipin()),\n",
" Translocation(ATG5(), None, autophagosome membrane),\n",
" Phosphorylation(None, LIPE(), S, 660),\n",
" Complex(BECN1(), PIK3C3()),\n",
" Activation(CREB(), TFEB()),\n",
" Activation(HDL-S1P(), PI3K()),\n",
" Activation(N-acetyltransferase(), generation of precursor metabolites and energy()),\n",
" Inhibition(Z1001(), mTORC1()),\n",
" Dephosphorylation(Phosphatase(), FUNDC1(), S, 13),\n",
" Activation(endoplasmic reticulum(), ASAH2()),\n",
" Inhibition(mcpB(), APOB()),\n",
" Phosphorylation(None, ULK1(), S, 758),\n",
" Complex(ATG16L1(), FOXC2()),\n",
" Inhibition(PTEN(), PI3K()),\n",
" Activation(dioscin(), ACADM()),\n",
" Inhibition(SQSTM1(), triglyceride()),\n",
" Translocation(Leu-Asp-Ser(), None, lysosome),\n",
" Inhibition(ethanol(), autophagy()),\n",
" Activation(thapsigargin(), SOCE()),\n",
" Activation(resveratrol(), inflammatory response()),\n",
" Complex(Starch Binding Domain(), glycogen()),\n",
" Inhibition((-)-epigallocatechin 3-gallate(), Membrane Potential, Mitochondrial()),\n",
" Activation(2-[bis(2-hydroxyethyl)amino]ethanesulfonic acid(), STAT3()),\n",
" Complex(MAP1LC3(), PLIN2()),\n",
" Activation(ankaflavin(), AMPK()),\n",
" Complex(Mon1(), Rab5-GTP()),\n",
" Activation(mTORC1(), INS()),\n",
" Activation(TSPO(), ATP()),\n",
" Activation(ATG5(), autophagy()),\n",
" Activation(ATP(), autophagy()),\n",
" IncreaseAmount(TFE3(mods: (modification)), PPARGC1A()),\n",
" Inhibition(SNAP23(), Leu-Asp-Ser()),\n",
" Inhibition(LRPAP1(), BAAT()),\n",
" Complex(MAP1LC3(), FOXC2()),\n",
" Activation(HDAC6(), transport()),\n",
" Activation(class V ESCRT protein(), ESCRT III()),\n",
" Inhibition(lipase inhibitors(), glycolytic process()),\n",
" Inhibition(RAB7A(), EGFR()),\n",
" Activation(SQSTM1(), nuclear factor erythroid 2-related factor 2()),\n",
" Activation(NFkappaB(), SQSTM1()),\n",
" Activation(pentapeptide(), PLIN2()),\n",
" Activation(INS(), mTORC1()),\n",
" Activation(Cyclin(), autophagy()),\n",
" Activation(NR0B2(), Histone()),\n",
" Activation(CCZ1(bound: [Mon1, True]), RAB7A()),\n",
" Inhibition(sirolimus(), mTORC1()),\n",
" IncreaseAmount(thapsigargin(), PPARGC1A()),\n",
" Complex(phosphatidylethanolamine(), ATG14()),\n",
" Inhibition(ATGListatin(), LC3 punctae()),\n",
" Dephosphorylation(caffeine(), AKT()),\n",
" Activation(staurosporine(), autophagy()),\n",
" Inhibition(3-Methyladenine(), autophagy()),\n",
" Activation(ATG7(), LC3-I()),\n",
" Activation(PNPLA2(), PGC()),\n",
" Inhibition(RAB7A(), Leu-Asp-Ser()),\n",
" Inhibition(PPARA(), triglyceride()),\n",
" Phosphorylation(None, CSK()),\n",
" Activation(superoxide(), MitoSOX()),\n",
" Inhibition(FMN1(), autophagy()),\n",
" Phosphorylation(None, DNM2()),\n",
" Activation(perilipins(mods: (phosphorylation)), PNPLA2()),\n",
" IncreaseAmount(niaD(), LIPA()),\n",
" Activation(glucose(), pH reduction()),\n",
" Complex(RAB7A(), RAC1()),\n",
" Activation(Phosphatase(), APOB()),\n",
" Inhibition(SOCE(), FAO()),\n",
" Activation(okadaic acid(), cell death()),\n",
" Translocation(Leu-Asp-Ser(), None, None),\n",
" IncreaseAmount(CQ(), cholesterol()),\n",
" Inhibition(calcium(2+)(), STIM1()),\n",
" Phosphorylation(AKT(), TSC2()),\n",
" Activation(PPARA(), FGF21()),\n",
" Inhibition(malonaldehyde(), S-adenosyl-L-methionine()),\n",
" Inhibition(sirolimus(), CYP2E1()),\n",
" Activation(PPP2(), autophagy()),\n",
" IncreaseAmount(MTOR(), K04A8.5()),\n",
" Inhibition(LRPAP1(), MTOR()),\n",
" Inhibition(PINK1(), MFN2()),\n",
" Phosphorylation(PKA(), PLIN1()),\n",
" Activation(hormone(), oxidative phosphorylation()),\n",
" Dephosphorylation(3',5'-cyclic AMP(), CREB()),\n",
" Complex(MON1A(), Rab5-GTP()),\n",
" Activation(FOXO1(), astatine atom()),\n",
" Activation(Acetyl_CoA_synthetase(), FAS()),\n",
" Activation(TSC2(), ULK1()),\n",
" Activation(okadaic acid(), SOCE()),\n",
" Inhibition(cholesterol(), nuclear receptor subfamily 1()),\n",
" Translocation(PAH1(), None, membrane),\n",
" IncreaseAmount(CNR1(), PLIN2()),\n",
" Complex(PINK1(), PRKN()),\n",
" Activation(PFK158(), Leu-Asp-Ser()),\n",
" DecreaseAmount(MLX-3(), LIPJ()),\n",
" Activation(Dbi(), gamma-aminobutyric acid()),\n",
" Activation(potassium cyanide(), SPIN1()),\n",
" Inhibition(CCT_complex(), Leu-Asp-Ser()),\n",
" Activation(LPS with O-antigen(), isotretinoin()),\n",
" Activation(isoprenaline(), autophagy()),\n",
" Inhibition(GW4064(), TFEB()),\n",
" Complex(CD74(), FMN1()),\n",
" Complex(ATP(), ABCA1()),\n",
" Activation(isoprenaline(), glycerol()),\n",
" Inhibition(ethanol(), lysosomal enzymes()),\n",
" Complex(PLIN2(), cma(), NCIT:C17764()),\n",
" Activation(capsaicin(), TRPV1()),\n",
" Inhibition(CIDEC(), EGR1()),\n",
" Complex(RAB18(), FMN1()),\n",
" Phosphorylation(3,3',5-triiodo-L-thyronine(), PRKAA1()),\n",
" Activation(aluminium(3+)(), autophagy()),\n",
" Activation(LPS with O-antigen(), autophagy()),\n",
" Complex(AMPK(), IPMK()),\n",
" Activation(proteins(bound: [RAB10, True]), Leu-Asp-Ser()),\n",
" Activation(APOA1(), cholesterol()),\n",
" Phosphorylation(Reactive Oxygen Species(), PRKAA1()),\n",
" Inhibition(RUBCN(), BECN1()),\n",
" IncreaseAmount(PNPLA2(), LAMP1()),\n",
" Methylation(S-adenosyl-L-methionine(mods: (modification)), PPP2()),\n",
" Activation(pyruvic acid(), cell differentiation()),\n",
" Inhibition(resveratrol(), IL6()),\n",
" Inhibition(dioscin(), inflammatory response()),\n",
" Activation(SQSTM1(), cell death()),\n",
" Complex(AMPK(), SIRT1()),\n",
" Activation(Cyclin(), AMPK()),\n",
" Activation(PCID:101179(), lipophagy()),\n",
" Phosphorylation(None, Lipk()),\n",
" Complex(MAP1LC3(), ULK1(), ATG14()),\n",
" Inhibition(Leu-Asp-Ser(), Histone(muts: (H, 2, A))),\n",
" Activation(PLIN1(), CIDEC()),\n",
" Inhibition(sirolimus(), Cell Survival()),\n",
" Dephosphorylation(mTORC1(), ATG13()),\n",
" Activation(ATG13(), autophagy()),\n",
" Inhibition(3-methyladenine(), autophagy()),\n",
" Activation(S-adenosyl-L-methionine(), N/L()),\n",
" Activation(AMPK(), cell differentiation()),\n",
" DecreaseAmount(ethanol(), triglyceride()),\n",
" Complex(ATG16L1(), ATG5()),\n",
" Activation(Esm1p(), ESCRT III()),\n",
" Activation(cAMP-dependent(), LIPE()),\n",
" Complex(SCD(), FOXC2()),\n",
" Complex(RAS(), MADS3()),\n",
" Inhibition(Zinc(), CAMKK2()),\n",
" Inhibition(MAP1S(), amoxicillin()),\n",
" Phosphorylation(SRC(), DNM2()),\n",
" Ubiquitination(None, AUP1()),\n",
" Complex(CIDEC(), PLIN1()),\n",
" Dephosphorylation(None, LPIN1()),\n",
" DecreaseAmount(trans-piceid(), TFEB()),\n",
" Inhibition(S-adenosyl-L-methionine(), autophagy()),\n",
" IncreaseAmount(GW 7647(), LC3a mRNA()),\n",
" Inhibition(Reactive Oxygen Species(), ATP()),\n",
" Complex(FIS1(), TBC1D15()),\n",
" Activation(MTOR(), proteolysis()),\n",
" Activation(Leu-Asp-Ser(), FMN1()),\n",
" Phosphorylation(DNM2(mods: (phosphorylation)), SRC()),\n",
" Inhibition(small interfering RNA(), autophagy()),\n",
" Phosphorylation(PKA(), AOC3()),\n",
" Activation(GCG(), autophagy()),\n",
" Activation(PLIN2(), localization()),\n",
" Activation(autophagy(), cell differentiation()),\n",
" DecreaseAmount(CTSB(mods: (modification)), SQSTM1()),\n",
" IncreaseAmount(PPARA(), FGF21()),\n",
" Activation(PTH(), (S)-lactic acid()),\n",
" Inhibition(triglyceride(), hydrolase()),\n",
" Activation(FMN1(), Leu-Asp-Ser()),\n",
" Activation(RAB7A(), MAP1LC3()),\n",
" Activation(mTORC1(), SREBP()),\n",
" Activation(dynein-dynactin motors(), transport()),\n",
" Inhibition(inflammatory response(), phosphatidic acid()),\n",
" DecreaseAmount(ethanol(), SQSTM1()),\n",
" Activation(lipase(), autophagy()),\n",
" Inhibition(cobamide(), LDL-cholesterol()),\n",
" Inhibition(TOLLIP(), nuclear factor kappaB()),\n",
" Activation(PRKN(), apoptotic process()),\n",
" Activation(HIF1A(), VEGF()),\n",
" Complex(BECN1(), ULK1()),\n",
" Inhibition(caffeine(), TGF-beta effector protein()),\n",
" Inhibition(ethanol(), RAB7A()),\n",
" Activation(LPIN1(), PPARA()),\n",
" Inhibition(S-adenosyl-L-methionine(), catabolic process()),\n",
" Inhibition(VAMP4(), Leu-Asp-Ser()),\n",
" Inhibition(okadaic acid(), localization()),\n",
" Activation(PNPLA2(), triglyceride()),\n",
" Complex(VIM(), PRPH(), RAB7A()),\n",
" Dephosphorylation(None, FUNDC1(), S, 13),\n",
" Inhibition(ATGListatin(), localization()),\n",
" Activation(okadaic acid(), ATP()),\n",
" DecreaseAmount(tag(), Ldo45()),\n",
" Activation(GW4064(), CRTC2(muts: (S, 171, A))),\n",
" Inhibition(MAP1S(), Genomic Instability()),\n",
" Inhibition(chloroquine(), autophagy()),\n",
" Inhibition(LRPAP1(), BAT LD()),\n",
" DecreaseAmount(caffeine(), ACC()),\n",
" Activation(LAMP1(), cellular senescence()),\n",
" Activation(PTEN(), HSPB3()),\n",
" Inhibition(ethanol(), psrC()),\n",
" Activation(FMN1(), cell death()),\n",
" Inhibition(ligase(), NFE2L2()),\n",
" Activation(TFEB(), PPARG()),\n",
" Inhibition(RUBCN(), autophagy()),\n",
" Activation(phosphatidic acid(), NFE2L2()),\n",
" Inhibition(ESR1(), inflammatory response()),\n",
" Complex(MAP1LC3(), LIR(), lipase()),\n",
" Activation((R)-lipoic acid(), cell population proliferation()),\n",
" Inhibition(ammonia(), fatty acid()),\n",
" Activation(flavoprotein(), ACAD()),\n",
" Inhibition(PK-11195(), generation of precursor metabolites and energy()),\n",
" Complex(PPP2(), MTOR()),\n",
" Activation(RAB10(), FMN1()),\n",
" Activation(PI3K(), phosphatidylinositol phosphate()),\n",
" Phosphorylation(None, EIF4EBP1()),\n",
" Complex(triglyceride(), FOXC2()),\n",
" IncreaseAmount(ethanol(), SLC17A5()),\n",
" Inhibition(ethanol(), FMN1()),\n",
" Activation(BANF1(), FMN1()),\n",
" Activation(RAB10(), Leu-Asp-Ser()),\n",
" Inhibition(Cyclin(), AMPK()),\n",
" Complex(NCOR(), NCOR2()),\n",
" Inhibition(mTORC1(), biogenesis()),\n",
" DecreaseAmount(ethanol(), glutathione()),\n",
" IncreaseAmount(ethanol(), MTOR()),\n",
" Inhibition(ubenimex(), cell population proliferation()),\n",
" Activation(sensor(), autophagy()),\n",
" Inhibition(NR1H4(), puncta()),\n",
" Activation(NFE2L2(), homeostatic process()),\n",
" Inhibition(PRDX1(), LDL()),\n",
" IncreaseAmount(PNPLA2(), LC3II()),\n",
" Activation(CCZ1(), RAB7A()),\n",
" Complex(SQSTM1(), PLIN2()),\n",
" Inhibition(INS(), AKT()),\n",
" Inhibition(dinitrogen(), autophagy()),\n",
" IncreaseAmount(ethanol(), cholesterol()),\n",
" Phosphorylation(PKA(), LIPE()),\n",
" Activation(CREB(), autophagy()),\n",
" Activation(autophagy(), innate immune response()),\n",
" IncreaseAmount(metF(), LAMP1()),\n",
" Activation(IGF1(), RAB7A()),\n",
" Activation(mon1(), RAB7A()),\n",
" Activation(IRGM(), NAFLD()),\n",
" Inhibition(AMPK(), mTORC1()),\n",
" Activation(SIRT1 inhibitor(), Leu-Asp-Ser()),\n",
" Activation(Ldo proteins(), BSCL2()),\n",
" Inhibition(NGF(), NTRK1()),\n",
" IncreaseAmount(thapsigargin(), PPARA()),\n",
" Complex(LIPE(), LC3-II()),\n",
" IncreaseAmount(ethanol(), PINK1()),\n",
" Activation(pyruvic acid(), metabolic process()),\n",
" Activation(uncoupling protein-1(), BAAT()),\n",
" Inhibition(AZD3147(), mTORC1()),\n",
" Complex(VPS26A(), VPS35()),\n",
" Phosphorylation(None, CREB()),\n",
" Inhibition(aminoglutethimide(), cholesterol()),\n",
" Activation(Phosphatase(), INS()),\n",
" Activation(FOXO3(), autophagy()),\n",
" Inhibition(Eb(), SQSTM1()),\n",
" Complex(CCZ1(), Mon1()),\n",
" Complex(cholesterol(), NPC2()),\n",
" Inhibition(glucose(), INS())]"
]
},
"metadata": {
"tags": []
},
"execution_count": 5
}
]
}
]
}
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