# Find Pathway Names By Literature

Source: `R/findPathwaysByLiterature.R`
`findPathwayNamesByLiterature.Rd`

Retrieve list of pathway names containing the query citation.

    findPathwayNamesByLiterature(query)

## Arguments

query | The `character` string to search for, e.g., a PMID, title keyword or author name.

## Value

A `list` of lists

## Details

Note: there will be multiple listings of the same pathway name if copies exist for multiple species.

## Examples

    {
    findPathwayNamesByLiterature('19649250')
    findPathwayNamesByLiterature('smith')
    findPathwayNamesByLiterature('cancer')
    }#>   [1] "E3 ubiquitin ligases ubiquitinate target proteins"
    #>   [2] "Signaling by FGFR1"
    #>   [3] "Irinotecan Pathway"
    #>   [4] "Irinotecan Pathway"
    #>   [5] "Irinotecan Pathway"
    #>   [6] "Irinotecan Pathway"
    #>   [7] "Irinotecan Pathway"
    #>   [8] "Irinotecan Pathway"
    #>   [9] "RAF/MAP kinase cascade"
    #>  [10] "Energy dependent regulation of mTOR by LKB1-AMPK"
    #>  [11] "Hedgehog ligand biogenesis"
    #>  [12] "Signaling by FGFR2"
    #>  [13] "mTOR signalling"
    #>  [14] "Metastatic brain tumor"
    #>  [15] "Signaling by Rho GTPases"
    #>  [16] "Signaling by FGFR4"
    #>  [17] "ATM Signaling Pathway"
    #>  [18] "NRF2-ARE regulation"
    #>  [19] "Signaling by FGFR3"
    #>  [20] "DNA IR-Double Strand Breaks (DSBs) and cellular response via ATM"
    #>  [21] "Integrin-mediated Cell Adhesion"
    #>  [22] "Bladder Cancer"
    #>  [23] "ATM Signaling Pathway"
    #>  [24] "TP53 Regulates Metabolic Genes"
    #>  [25] "Overview of leukocyte-intrinsic Hippo pathway functions"
    #>  [26] "Transcriptional activation by NRF2"
    #>  [27] "Keap1-Nrf2"
    #>  [28] "Keap1-Nrf2"
    #>  [29] "Keap1-Nrf2"
    #>  [30] "Retinol metabolism"
    #>  [31] "Phytochemical activity on NRF2 transcriptional activation"
    #>  [32] "Integrin-mediated Cell Adhesion"
    #>  [33] "Keap1-Nrf2"
    #>  [34] "Keap1-Nrf2"
    #>  [35] "Keap1-Nrf2"
    #>  [36] "Metastatic brain tumor"
    #>  [37] "Parkinsons Disease Pathway"
    #>  [38] "Bladder Cancer"
    #>  [39] "DNA IR-damage and cellular response via ATR"
    #>  [40] "Parkinsons Disease Pathway"
    #>  [41] "DNA Damage Response"
    #>  [42] "miRNA Regulation of DNA Damage Response"
    #>  [43] "DNA Damage Response"
    #>  [44] "DNA damage response"
    #>  [45] "HDR through Homologous Recombination (HRR) or Single Strand Annealing (SSA)"
    #>  [46] "YAP1- and WWTR1 (TAZ)-stimulated gene expression"
    #>  [47] "DNA Damage/Telomere Stress Induced Senescence"
    #>  [48] "Signaling by ERBB2"
    #>  [49] "Signaling by PTK6"
    #>  [50] "NCAM signaling for neurite out-growth"
    #>  [51] "Other interleukin signaling"
    #>  [52] "Interleukin-3, Interleukin-5 and GM-CSF signaling"
    #>  [53] "Signaling by SCF-KIT"
    #>  [54] "Signaling by NTRK1 (TRKA)"
    #>  [55] "RNA interference"
    #>  [56] "Signaling by MET"
    #>  [57] "Signaling by VEGF"
    #>  [58] "Signaling by EGFR"
    #>  [59] "Fanconi Anemia Pathway"
    #>  [60] "Generic Transcription Pathway"
    #>  [61] "Phase II - Conjugation of compounds"
    #>  [62] "TCF dependent signaling in response to WNT"
    #>  [63] "Signaling by NTRK3 (TRKC)"
    #>  [64] "Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R)"
    #>  [65] "Oxidative Stress Induced Senescence"
    #>  [66] "Senescence-Associated Secretory Phenotype (SASP)"
    #>  [67] "Signaling by NTRK2 (TRKB)"
    #>  [68] "ESR-mediated signaling"
    #>  [69] "PIP3 activates AKT signaling"
    #>  [70] "Signaling by ERBB4"
    #>  [71] "PI Metabolism"
    #>  [72] "Signaling by Hippo"
    #>  [73] "TP53 Regulates Transcription of DNA Repair Genes"
    #>  [74] "Signaling by Leptin"
    #>  [75] "Pre-NOTCH Expression and Processing"
    #>  [76] "Oncogene Induced Senescence"
    #>  [77] "RET signaling"
    #>  [78] "Gastrin-CREB signalling pathway via PKC and MAPK"
    #>  [79] "Signaling by NOTCH3"
    #>  [80] "Interleukin-2 family signaling"
    #>  [81] "Fc epsilon receptor (FCERI) signaling"
    #>  [82] "Transcriptional regulation by RUNX1"
    #>  [83] "Signaling by Insulin receptor"
    #>  [84] "DAP12 interactions"
    #>  [85] "O-linked glycosylation"
    #>  [86] "Transcriptional regulation by RUNX2"
    #>  [87] "Signaling by PDGF"
    #>  [88] "RAB GEFs exchange GTP for GDP on RABs"
    #>  [89] "Aflatoxin B1 metabolism"
    #>  [90] "Aflatoxin B1 metabolism"
    #>  [91] "Regulation of sister chromatid separation at the metaphase-anaphase transition"
    #>  [92] "Type 2 papillary renal cell carcinoma"
    #>  [93] "exRNA mechanism of action and biogenesis"
    #>  [94] "Aflatoxin B1 metabolism"
    #>  [95] "Aflatoxin B1 metabolism"
    #>  [96] "Aflatoxin B1 metabolism"
    #>  [97] "Aflatoxin B1 metabolism"
    #>  [98] "Glycerophospholipid Biosynthetic Pathway"
    #>  [99] "Glycerophospholipid Biosynthetic Pathway"
    #> [100] "Cancer immunotherapy by PD-1 blockade"
    #> [101] "Chromosomal and microsatellite instability in colorectal cancer "
    #> [102] "Epithelial to mesenchymal transition in colorectal cancer"
    #> [103] "Apoptosis-related network due to altered Notch3 in ovarian cancer"
    #> [104] "Apoptosis-related network due to altered Notch3 in ovarian cancer"
    #> [105] "Small cell lung cancer"
    #> [106] "Mammary gland development pathway - Embryonic development (Stage 1 of 4)"
    #> [107] "TP53 Regulates Transcription of Cell Cycle Genes"
    #> [108] "Regulation of TP53 Expression and Degradation"
    #> [109] "Interleukin-15 signaling"
    #> [110] "Processing of Capped Intron-Containing Pre-mRNA"
    #> [111] "Asparagine N-linked glycosylation"
    #> [112] "TGF Beta Signaling Pathway"
    #> [113] "DNA methylation"
    #> [114] "Transforming Growth Factor (TGF) Beta Signaling Pathway"
    #> [115] "Mitotic G1-G1/S phases"
    #> [116] "Beta-catenin independent WNT signaling"
    #> [117] "Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate"
    #> [118] "TGF Beta Signaling Pathway"
    #> [119] "Protein ubiquitination"
    #> [120] "Pentose phosphate pathway"
    #> [121] "p53 pathway"
    #> [122] "Transforming Growth Factor (TGF) Beta Signaling Pathway"
    #> [123] "Inositol phosphate metabolism"
    #> [124] "Regulation of TP53 Activity through Phosphorylation"
    #> [125] "Nucleotide Excision Repair"
    #> [126] "Mismatch Repair"
    #> [127] "TET1,2,3 and TDG demethylate DNA"
    #> [128] "Caspase activation via Dependence Receptors in the absence of ligand"
    #> [129] "Transforming Growth Factor (TGF) Beta Signaling Pathway"
    #> [130] "Transforming Growth Factor (TGF) Beta Signaling Pathway"
    #> [131] "Ebola Virus Pathway on Host"
    #> [132] "NADPH regeneration"
    #> [133] "TGF Beta Signaling Pathway"
    #> [134] "Integrated Cancer pathway"
    #> [135] "Regulation of RUNX1 Expression and Activity"
    #> [136] "Signaling by Erythropoietin"
    #> [137] "Regulation of Hypoxia-inducible Factor (HIF) by oxygen"
    #> [138] "RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs)"
    #> [139] "PluriNetWork"
    #> [140] "S Phase"
    #> [141] "Rett syndrome causing genes"
    #> [142] "Interactions between immune cells and microRNAs in tumor microenvironment"
    #> [143] "MET in type 1 papillary renal cell carcinoma"
    #> [144] "Oxysterols derived from cholesterol"
    #> [145] "Senescence and Autophagy in Cancer"
    #> [146] "TGF-beta Receptor Signaling"
    #> [147] "Pathways in clear cell renal cell carcinoma"
    #> [148] "Integrated Cancer Pathway"
    #> [149] "Zinc homeostasis"
    #> [150] "PI3K-Akt Signaling Pathway"
    #> [151] "Tamoxifen metabolism"
    #> [152] "Tamoxifen metabolism"
    #> [153] "Folate Metabolism"
    #> [154] "Selenium Micronutrient Network"
    #> [155] "Vitamin B12 Metabolism"
    #> [156] "Selenium Micronutrient Network"
    #> [157] "Vitamin B12 Metabolism"
    #> [158] "Folate Metabolism"
    #> [159] "Mevalonate pathway"
    #> [160] "Fragile X Syndrome "
    #> [161] "Integrated Breast Cancer Pathway"
    #> [162] "Breast cancer pathway"
    #> [163] "Endometrial cancer"
    #> [164] "FABP4 in ovarian cancer"
    #> [165] "Senescence and Autophagy in Cancer"
    #> [166] "Deregulation of Rab and Rab Effector Genes in Bladder Cancer"
    #> [167] "Deregulation of Rab and Rab Effector Genes in Bladder Cancer"
    #> [168] "Non-small cell lung cancer"
    #> [169] "Fluoropyrimidine Activity"
    #> [170] "Fluoropyrimidine Activity"
    #> [171] "Tamoxifen metabolism"
    #> [172] "RAC1/PAK1/p38/MMP2 Pathway"
    #> [173] "ErbB Signaling Pathway"
    #> [174] "Integrated Breast Cancer Pathway"
    #> [175] "ErbB Signaling Pathway"
    #> [176] "TGF-beta Receptor Signaling"
    #> [177] "Neurodegeneration with brain iron accumulation (NBIA) subtypes pathway"
    #> [178] "Transport of bile salts and organic acids, metal ions and amine compounds"
    #> [179] "MicroRNA for Targeting Cancer Growth and Vascularization in Glioblastoma"
    #> [180] "MFAP5 effect on permeability and motility of endothelial cells via cytoskeleton rearrangement"
    #> [181] "Modified nucleosides derived from t-RNA as urinary cancer markers"
    #> [182] "Hereditary leiomyomatosis and renal cell carcinoma pathway"
    #> [183] "Mitotic G2-G2/M phases"
    #> [184] "RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function"
    #> [185] "Integrin alphaIIb beta3 signaling"
    #> [186] "Sphingolipid metabolism"
    #> [187] "Transcriptional regulation by RUNX3"
    #> [188] "Hedgehog 'on' state"
    #> [189] "Unfolded Protein Response (UPR)"
    #> [190] "RHO GTPases Activate Formins"
    #> [191] "Genotoxicity pathway"
    #> [192] "Sulfur amino acid metabolism"
    #> [193] "RHO GTPases Activate WASPs and WAVEs"
    #> [194] "WNT ligand biogenesis and trafficking"
    #> [195] "SUMOylation of transcription factors"
    #> [196] "Gap junction trafficking and regulation"
    #> [197] "Miscellaneous transport and binding events"
    #> [198] "Signaling by NOTCH4"
    #> [199] "Nuclear Receptors Meta-Pathway"
    #> [200] "Visual phototransduction"
    #> [201] "Chromatin organization"
    #> [202] "RAF-independent MAPK1/3 activation"
    #> [203] "Netrin-1 signaling"
    #> [204] "Abacavir transport and metabolism"
    #> [205] "Amino acid synthesis and interconversion (transamination)"
    #> [206] "Iron uptake and transport"
    #> [207] "Metabolism of polyamines"
    #> [208] "Activation of anterior HOX genes in hindbrain development during early embryogenesis"
    #> [209] "Degradation of the extracellular matrix"
    #> [210] "Nucleobase catabolism"
    #> [211] "Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3"
    #> [212] "Metabolism of folate and pterines"
    #> [213] "Neurotransmitter Release Cycle"
    #> [214] "Signaling by ROBO receptors"
    #> [215] "Surfactant metabolism"
    #> [216] "Transcriptional Regulation by MECP2"
    #> [217] "RHO GTPases activate PKNs"
    #> [218] "DNA Double Strand Break Response"
    #> [219] "MAPK6/MAPK4 signaling"
    #> [220] "Signaling by NOTCH2"
    #> [221] "tRNA processing in the nucleus"
    #> [222] "Glycosaminoglycan metabolism"
    #> [223] "Iron uptake and transport"
    #> [224] "Signaling by NOTCH1"
    #> [225] "PTEN Regulation"
    #> [226] "Neurotransmitter release cycle"
    #> [227] "miRNAs involved in DNA damage response"
    #> [228] "Antimicrobial peptides"
    #> [229] "NRF2 pathway"
    #> [230] "Neddylation"
    #> [231] "Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors"
    #> [232] "Phase I - Functionalization of compounds"
    #> [233] "Pancreatic adenocarcinoma pathway"
    #> [234] "Vitamin D Receptor Pathway"
    #> [235] "miRNA targets in ECM and membrane receptors"
    #> [236] "miRNAs involved in DNA damage response"
    #> [237] "Apoptosis Modulation and Signaling"
    #> [238] "Thyroxine (Thyroid Hormone) Production"
    #> [239] "Influenza A virus infection"
    #> [240] "FAS pathway and Stress induction of HSP regulation"
    #> [241] "Quercetin and Nf-kB/ AP-1 Induced Cell Apoptosis"
    #> [242] "Estrogen metabolism"
    #> [243] "Selenium Metabolism and Selenoproteins"
    #> [244] "Selenium metabolism Selenoproteins"
    #> [245] "Estrogen metabolism"
    #> [246] "Selenium metabolism Selenoproteins"
    #> [247] "Estrogen metabolism"
    #> [248] "Thyroxine (Thyroid Hormone) Production"
    #> [249] "Serotonin HTR1 Group and FOS Pathway"
    #> [250] "Quercetin and Nf-kB/ AP-1 Induced Cell Apoptosis"
    #> [251] "Eicosanoid metabolism via Cyclo Oxygenases (COX)"
    #> [252] "Eicosanoid metabolism via Lipo Oxygenases (LOX)"
    #> [253] "Fas Ligand (FasL) pathway and Stress induction of Heat Shock Proteins (HSP) regulation"
    #> [254] "Selenium Metabolism and Selenoproteins"
    #> [255] "Lipid Metabolism Pathway"
    #> [256] "NRF2 pathway"
    #> [257] "Malate-aspartate shuttle"
    #> [258] "Estrogen metabolism"
    #> [259] "Estrogen metabolism"
    #> [260] "Estrogen metabolism"
    #> [261] "Selenium metabolism Selenoproteins"
    #> [262] "Estrogen metabolism"
    #> [263] "Elongation of (very) long chain fatty acids"
    #> [264] "Apoptosis Modulation and Signaling"
    #> [265] "Eicosanoid metabolism via Cyclo Oxygenases (COX)"
    #> [266] "Eicosanoid metabolism via Lipo Oxygenases (LOX)"
    #> [267] "PI3K-AKT-mTOR signaling pathway and therapeutic opportunities"
    #> [268] "miRNA regulation of prostate cancer signaling pathways"
    #> [269] "miRNA regulation of p53 pathway in prostate cancer"
    #> [270] "Cancer immunotherapy by CTLA4 blockade"
    #> [271] "mir-193a and MVP in colon cancer metastasis"
    #> [272] "LncRNA involvement in canonical Wnt signaling and colorectal cancer"
    #> [273] "PDGFR-beta pathway"
    #> [274] "Influenza A virus infection"
    #> [275] "Genetic alterations of lung cancer"
    #> [276] "Netrin-UNC5B signaling Pathway"
    #> [277] "EGFR Tyrosine Kinase Inhibitor Resistance"
    #> [278] "Transcriptional regulation of pluripotent stem cells"
    #> [279] "Serotonin Receptor 4/6/7 and NR3C Signaling"
    #> [280] "Signaling by NODAL"
    #> [281] "GPVI-mediated activation cascade"
    #> [282] "Regulation of RUNX2 expression and activity"
    #> [283] "NoRC negatively regulates rRNA expression"
    #> [284] "Degradation of beta-catenin by the destruction complex"
    #> [285] "BMAL1:CLOCK,NPAS2 activates circadian gene expression"
    #> [286] "Glycerophospholipid biosynthesis"
    #> [287] "Fatty acyl-CoA biosynthesis"
    #> [288] "SUMOylation of intracellular receptors"
    #> [289] "Signaling by BMP"
    #> [290] "Regulated Necrosis"
    #> [291] "RHO GTPases activate IQGAPs"
    #> [292] "Interleukin-20 family signaling"
    #> [293] "TNF signaling"
    #> [294] "POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation"
    #> [295] "Gastric cancer network 2"
    #> [296] "Vasopressin regulates renal water homeostasis via Aquaporins"
    #> [297] "Transcriptional regulation of white adipocyte differentiation"
    #> [298] "Extracellular matrix organization"
    #> [299] "DNA Damage Reversal"
    #> [300] "Nanoparticle triggered autophagic cell death"
    #> [301] "Structural Pathway of Interleukin 1 (IL-1)"
    #> [302] "Deubiquitination"
    #> [303] "Interleukin-4 and Interleukin-13 signaling"
    #> [304] "Gene Silencing by RNA"
    #> [305] "Transcriptional activity of SMAD2/SMAD3:SMAD4 heterotrimer"
    #> [306] "Gamma carboxylation, hypusine formation and arylsulfatase activation"
    #> [307] "Metabolism of steroid hormones"
    #> [308] "Transcriptional Regulation by E2F6"
    #> [309] "Signaling by Activin"
    #> [310] "Liver steatosis AOP"
    #> [311] "SUMOylation of ubiquitinylation proteins"
    #> [312] "Regulation of TP53 Activity through Association with Co-factors"
    #> [313] "Serotonin Receptor 2 and STAT3 Signaling"
    #> [314] "Class I MHC mediated antigen processing &amp; presentation"
    #> [315] "Signaling by MST1"
    #> [316] "mir-124 predicted interactions with cell cycle and differentiation "
    #> [317] "Nicotinate metabolism"
    #> [318] "ATM Signaling Pathway"
    #> [319] "Serotonin Receptor 2 and ELK-SRF/GATA4 signaling"
    #> [320] "Interleukin-17 signaling"
    #> [321] "MyD88 dependent cascade initiated on endosome"
    #> [322] "TP53 Regulates Transcription of Cell Death Genes"
    #> [323] "Cellular hexose transport"
    #> [324] "tRNA modification in the nucleus and cytosol"
    #> [325] "Peroxisomal lipid metabolism"
    #> [326] "Transport of inorganic cations/anions and amino acids/oligopeptides"
    #> [327] "Toll-like Receptor Cascades"
    #> [328] "Class A/1 (Rhodopsin-like receptors)"
    #> [329] "Serotonin Receptor 2 and STAT3 Signaling"
    #> [330] "miR-517 relationship with ARCN1 and USP1"
    #> [331] "Codeine and Morphine Metabolism"
    #> [332] "H19 action Rb-E2F1 signaling and CDK-Beta-catenin activity"
    #> [333] "Serotonin Receptor 2 and STAT3 Signaling"
    #> [334] "Serotonin Receptor 2 and ELK-SRF/GATA4 signaling"
    #> [335] "Serotonin Receptor 4/6/7 and NR3C Signaling"
    #> [336] "Prostaglandin Synthesis and Regulation"
    #> [337] "Prader-Willi and Angelman Syndrome"
    #> [338] "Codeine and Morphine Metabolism"
    #> [339] "Aryl Hydrocarbon Receptor"
    #> [340] "Melatonin metabolism and effects"
    #> [341] "Toll-like Receptor Signaling related to MyD88"
    #> [342] "Aryl Hydrocarbon Receptor Netpath"
    #> [343] "Structural Pathway of Interleukin 1 (IL-1)"
    #> [344] "Renin - Angiotensin System"
    #> [345] "Gastric Cancer Network 2"
    #> [346] "Glycosylation and related congenital defects"
    #> [347] "TCA Cycle Nutrient Utilization and Invasiveness of Ovarian Cancer"
    #> [348] "TCA Cycle Nutrient Utilization and Invasiveness of Ovarian Cancer"
    #> [349] "MFAP5-mediated ovarian cancer cell motility and invasiveness"
    #> [350] "Gastric Cancer Network 1"
    #> [351] "Gastric Cancer Network 1"
    #> [352] "miR-509-3p alteration of YAP1/ECM axis"
    #> [353] "Simplified Interaction Map Between LOXL4 and Oxidative Stress Pathway"
    #> [354] "Alzheimers Disease"
    #> [355] "Tumor suppressor activity of SMARCB1"
    #> [356] "Regulation of Pgc1a expression by a Gsk3b-Tfeb signaling axis in skeletal muscle"
    #> [357] "Thyroid hormones production and their peripheral downstream signalling effects regarding congenital hypothyroidism"
    #> [358] "Head and Neck Squamous Cell Carcinoma"
    #> [359] "Sialic acid metabolism"
    #> [360] "Inhibition of exosome biogenesis and secretion by Manumycin A in CRPC cells"
    #> [361] "Threonine catabolism"
    #> [362] "SUMOylation of transcription cofactors"
    #> [363] "Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs)"
    #> [364] "MAP kinase activation"
    #> [365] "Neural Crest Cell Migration during Development"
    #> [366] "Cell migration and invasion through p75NTR"
    #> [367] "Neural Crest Cell Migration in Cancer"
    #> [368] "Regulation of mRNA stability by proteins that bind AU-rich elements"
    #> [369] "ATF4 activates genes"
    #> [370] "PI3K Cascade"
    #> [371] "SUMOylation of DNA damage response and repair proteins"