I am having issues with KEGG pathway xml files. In short, when I run
pathview() files are being downloaded, but they are not in xml format and cannot be parsed so I get the following error:
Start tag expected, '<' not found
I tried updating XML and KEGGgraph packages, but the issue is still there.
I am using R version 3.6.0 and Bioconductor 3.9.
Any suggestions would be much appreciated, sorry if I missed a solution to this problem being already posted elsewhere.
For reference, this is what what I get for an 'xml' file:
ENTRY hsa04622 Pathway NAME RIG-I-like receptor signaling pathway - Homo sapiens (human) DESCRIPTION Specific families of pattern recognition receptors are responsible for detecting viral pathogens and generating innate immune responses. Non-self RNA appearing in a cell as a result of intracellular viral replication is recognized by a family of cytosolic RNA helicases termed RIG-I-like receptors (RLRs). The RLR proteins include RIG-I, MDA5, and LGP2 and are expressed in both immune and nonimmune cells. Upon recognition of viral nucleic acids, RLRs recruit specific intracellular adaptor proteins to initiate signaling pathways that lead to the synthesis of type I interferon and other inflammatory cytokines, which are important for eliminating viruses. CLASS Organismal Systems; Immune system PATHWAY_MAP hsa04622 RIG-I-like receptor signaling pathway NETWORK nt06133 RIG-I signaling (virus) nt06162 Hepatitis B virus (HBV) nt06163 Hepatitis C virus (HCV) nt06165 Epstein-Barr virus (EBV) nt06168 Herpes simplex virus 1 (HSV-1) nt06169 Measles virus (MV) nt06170 Influenza A virus (IAV) nt06263 Hepatocellular carcinoma ELEMENT N00469 RIG-I-IRF7/3 signaling pathway N00688 RIG-I-NFKB signaling pathway DISEASE H00290 Aicardi-Goutieres syndrome H00827 Brooke-Spiegler syndrome H00882 Cocoon syndrome H01746 STING-associated vasculopathy with onset in infancy ORGANISM Homo sapiens (human) [GN:hsa] GENE 23586 DDX58; DExD/H-box helicase 58 [KO:K12646] [EC:18.104.22.168] 64135 IFIH1; interferon induced with helicase C domain 1 [KO:K12647] [EC:22.214.171.124] 57506 MAVS; mitochondrial antiviral signaling protein [KO:K12648] 79132 DHX58; DExH-box helicase 58 [KO:K12649] [EC:126.96.36.199] 7187 TRAF3; TNF receptor associated factor 3 [KO:K03174] 10010 TANK; TRAF family member associated NFKB activator [KO:K12650] 64343 AZI2; 5-azacytidine induced 2 [KO:K12651] 9755 TBKBP1; TBK1 binding protein 1 [KO:K12652] 8517 IKBKG; inhibitor of nuclear factor kappa B kinase regulatory subunit gamma [KO:K07210] 29110 TBK1; TANK binding kinase 1 [KO:K05410] [EC:188.8.131.52] 9641 IKBKE; inhibitor of nuclear factor kappa B kinase subunit epsilon [KO:K07211] [EC:184.108.40.206] 3661 IRF3; interferon regulatory factor 3 [KO:K05411] 3665 IRF7; interferon regulatory factor 7 [KO:K09447] 3439 IFNA1; interferon alpha 1 [KO:K05414] 3440 IFNA2; interferon alpha 2 [KO:K05414] 3441 IFNA4; interferon alpha 4 [KO:K05414] 3442 IFNA5; interferon alpha 5 [KO:K05414] 3443 IFNA6; interferon alpha 6 [KO:K05414] 3444 IFNA7; interferon alpha 7 [KO:K05414] 3445 IFNA8; interferon alpha 8 [KO:K05414] 3446 IFNA10; interferon alpha 10 [KO:K05414] 3447 IFNA13; interferon alpha 13 [KO:K05414] 3448 IFNA14; interferon alpha 14 [KO:K05414] 3449 IFNA16; interferon alpha 16 [KO:K05414] 3451 IFNA17; interferon alpha 17 [KO:K05414] 3452 IFNA21; interferon alpha 21 [KO:K05414] 3456 IFNB1; interferon beta 1 [KO:K05415] 3467 IFNW1; interferon omega 1 [KO:K05440] 338376 IFNE; interferon epsilon [KO:K05442] 56832 IFNK; interferon kappa [KO:K05441] 8717 TRADD; TNFRSF1A associated via death domain [KO:K03171] 8772 FADD; Fas associated via death domain [KO:K02373] 8737 RIPK1; receptor interacting serine/threonine kinase 1 [KO:K02861] [EC:220.127.116.11] 841 CASP8; caspase 8 [KO:K04398] [EC:18.104.22.168] 843 CASP10; caspase 10 [KO:K04400] [EC:22.214.171.124] 1147 CHUK; component of inhibitor of nuclear factor kappa B kinase complex [KO:K04467] [EC:126.96.36.199] 3551 IKBKB; inhibitor of nuclear factor kappa B kinase subunit beta [KO:K07209] [EC:188.8.131.52] 4793 NFKBIB; NFKB inhibitor beta [KO:K02581] 4792 NFKBIA; NFKB inhibitor alpha [KO:K04734] 4790 NFKB1; nuclear factor kappa B subunit 1 [KO:K02580] 5970 RELA; RELA proto-oncogene, NF-kB subunit [KO:K04735] 7186 TRAF2; TNF receptor associated factor 2 [KO:K03173] [EC:184.108.40.206] 6885 MAP3K7; mitogen-activated protein kinase kinase kinase 7 [KO:K04427] [EC:220.127.116.11] 7189 TRAF6; TNF receptor associated factor 6 [KO:K03175] [EC:18.104.22.168] 4214 MAP3K1; mitogen-activated protein kinase kinase kinase 1 [KO:K04416] [EC:22.214.171.124] 5599 MAPK8; mitogen-activated protein kinase 8 [KO:K04440] [EC:126.96.36.199] 5602 MAPK10; mitogen-activated protein kinase 10 [KO:K04440] [EC:188.8.131.52] 5601 MAPK9; mitogen-activated protein kinase 9 [KO:K04440] [EC:184.108.40.206] 5600 MAPK11; mitogen-activated protein kinase 11 [KO:K04441] [EC:220.127.116.11] 6300 MAPK12; mitogen-activated protein kinase 12 [KO:K04441] [EC:18.104.22.168] 5603 MAPK13; mitogen-activated protein kinase 13 [KO:K04441] [EC:22.214.171.124] 1432 MAPK14; mitogen-activated protein kinase 14 [KO:K04441] [EC:126.96.36.199] 3576 CXCL8; C-X-C motif chemokine ligand 8 [KO:K10030] 7124 TNF; tumor necrosis factor [KO:K03156] 3592 IL12A; interleukin 12A [KO:K05406] 3593 IL12B; interleukin 12B [KO:K05425] 3627 CXCL10; C-X-C motif chemokine ligand 10 [KO:K12671] 7706 TRIM25; tripartite motif containing 25 [KO:K10652] [EC:188.8.131.52] 1540 CYLD; CYLD lysine 63 deubiquitinase [KO:K08601] [EC:184.108.40.206] 54941 RNF125; ring finger protein 125 [KO:K12170] [EC:220.127.116.11] 9636 ISG15; ISG15 ubiquitin like modifier [KO:K12159] 9474 ATG5; autophagy related 5 [KO:K08339] 9140 ATG12; autophagy related 12 [KO:K08336] 79671 NLRX1; NLR family member X1 [KO:K12653] 340061 TMEM173; transmembrane protein 173 [KO:K12654] 55593 OTUD5; OTU deubiquitinase 5 [KO:K12655] [EC:18.104.22.168] 80143 SIKE1; suppressor of IKBKE 1 [KO:K12656] 1654 DDX3X; DEAD-box helicase 3 X-linked [KO:K11594] [EC:22.214.171.124] 5300 PIN1; peptidylprolyl cis/trans isomerase, NIMA-interacting 1 [KO:K09578] [EC:126.96.36.199] 26007 TKFC; triokinase and FMN cyclase [KO:K00863] [EC:188.8.131.52 184.108.40.206 220.127.116.11] REFERENCE PMID:15208624 AUTHORS Yoneyama M, Kikuchi M, Natsukawa T, Shinobu N, Imaizumi T, Miyagishi M, Taira K, Akira S, Fujita T TITLE The RNA helicase RIG-I has an essential function in double-stranded RNA-induced innate antiviral responses. JOURNAL Nat Immunol 5:730-7 (2004) DOI:10.1038/ni1087 REFERENCE PMID:18272355 AUTHORS Takeuchi O, Akira S TITLE MDA5/RIG-I and virus recognition. JOURNAL Curr Opin Immunol 20:17-22 (2008) DOI:10.1016/j.coi.2008.01.002 REFERENCE PMID:19120475 AUTHORS Yoneyama M, Fujita T TITLE RNA recognition and signal transduction by RIG-I-like receptors. JOURNAL Immunol Rev 227:54-65 (2009) DOI:10.1111/j.1600-065X.2008.00727.x REFERENCE PMID:19539500 AUTHORS Nakhaei P, Genin P, Civas A, Hiscott J TITLE RIG-I-like receptors: sensing and responding to RNA virus infection. JOURNAL Semin Immunol 21:215-22 (2009) DOI:10.1016/j.smim.2009.05.001 REFERENCE PMID:18549796 AUTHORS Moore CB, Ting JP TITLE Regulation of mitochondrial antiviral signaling pathways. JOURNAL Immunity 28:735-9 (2008) DOI:10.1016/j.immuni.2008.05.005 REFERENCE PMID:19615405 AUTHORS Barral PM, Sarkar D, Su ZZ, Barber GN, DeSalle R, Racaniello VR, Fisher PB TITLE Functions of the cytoplasmic RNA sensors RIG-I and MDA-5: key regulators of innate immunity. JOURNAL Pharmacol Ther 124:219-34 (2009) DOI:10.1016/j.pharmthera.2009.06.012 REFERENCE PMID:19120476 AUTHORS Schlee M, Hartmann E, Coch C, Wimmenauer V, Janke M, Barchet W, Hartmann G TITLE Approaching the RNA ligand for RIG-I? JOURNAL Immunol Rev 227:66-74 (2009) DOI:10.1111/j.1600-065X.2008.00724.x REFERENCE PMID:18591413 AUTHORS Saito T, Gale M Jr TITLE Differential recognition of double-stranded RNA by RIG-I-like receptors in antiviral immunity. JOURNAL J Exp Med 205:1523-7 (2008) DOI:10.1084/jem.20081210 REFERENCE PMID:19076341 AUTHORS Kawai T, Akira S TITLE Toll-like receptor and RIG-I-like receptor signaling. JOURNAL Ann N Y Acad Sci 1143:1-20 (2008) DOI:10.1196/annals.1443.020 REFERENCE PMID:18439848 AUTHORS Michallet MC, Meylan E, Ermolaeva MA, Vazquez J, Rebsamen M, Curran J, Poeck H, Bscheider M, Hartmann G, Konig M, Kalinke U, Pasparakis M, Tschopp J TITLE TRADD protein is an essential component of the RIG-like helicase antiviral pathway. JOURNAL Immunity 28:651-61 (2008) DOI:10.1016/j.immuni.2008.03.013 REFERENCE PMID:18984593 AUTHORS Yoshida R, Takaesu G, Yoshida H, Okamoto F, Yoshioka T, Choi Y, Akira S, Kawai T, Yoshimura A, Kobayashi T TITLE TRAF6 and MEKK1 play a pivotal role in the RIG-I-like helicase antiviral pathway. JOURNAL J Biol Chem 283:36211-20 (2008) DOI:10.1074/jbc.M806576200 REFERENCE PMID:19224920 AUTHORS Mikkelsen SS, Jensen SB, Chiliveru S, Melchjorsen J, Julkunen I, Gaestel M, Arthur JS, Flavell RA, Ghosh S, Paludan SR TITLE RIG-I-mediated activation of p38 MAPK is essential for viral induction of interferon and activation of dendritic cells: dependence on TRAF2 and TAK1. JOURNAL J Biol Chem 284:10774-82 (2009) DOI:10.1074/jbc.M807272200 KO_PATHWAY ko04622 ///