Question: Issue with xml files downloaded with `pathview()`
0
gravatar for anamaria
29 days ago by
anamaria0
London, United Kingdom
anamaria0 wrote:

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:3.6.4.13]
            64135  IFIH1; interferon induced with helicase C domain 1 [KO:K12647] [EC:3.6.4.13]
            57506  MAVS; mitochondrial antiviral signaling protein [KO:K12648]
            79132  DHX58; DExH-box helicase 58 [KO:K12649] [EC:3.6.4.13]
            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:2.7.11.10]
            9641  IKBKE; inhibitor of nuclear factor kappa B kinase subunit epsilon [KO:K07211] [EC:2.7.11.10]
            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:2.7.11.1]
            841  CASP8; caspase 8 [KO:K04398] [EC:3.4.22.61]
            843  CASP10; caspase 10 [KO:K04400] [EC:3.4.22.63]
            1147  CHUK; component of inhibitor of nuclear factor kappa B kinase complex [KO:K04467] [EC:2.7.11.10]
            3551  IKBKB; inhibitor of nuclear factor kappa B kinase subunit beta [KO:K07209] [EC:2.7.11.10]
            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:2.3.2.27]
            6885  MAP3K7; mitogen-activated protein kinase kinase kinase 7 [KO:K04427] [EC:2.7.11.25]
            7189  TRAF6; TNF receptor associated factor 6 [KO:K03175] [EC:2.3.2.27]
            4214  MAP3K1; mitogen-activated protein kinase kinase kinase 1 [KO:K04416] [EC:2.7.11.25]
            5599  MAPK8; mitogen-activated protein kinase 8 [KO:K04440] [EC:2.7.11.24]
            5602  MAPK10; mitogen-activated protein kinase 10 [KO:K04440] [EC:2.7.11.24]
            5601  MAPK9; mitogen-activated protein kinase 9 [KO:K04440] [EC:2.7.11.24]
            5600  MAPK11; mitogen-activated protein kinase 11 [KO:K04441] [EC:2.7.11.24]
            6300  MAPK12; mitogen-activated protein kinase 12 [KO:K04441] [EC:2.7.11.24]
            5603  MAPK13; mitogen-activated protein kinase 13 [KO:K04441] [EC:2.7.11.24]
            1432  MAPK14; mitogen-activated protein kinase 14 [KO:K04441] [EC:2.7.11.24]
            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:2.3.2.27]
            1540  CYLD; CYLD lysine 63 deubiquitinase [KO:K08601] [EC:3.4.19.12]
            54941  RNF125; ring finger protein 125 [KO:K12170] [EC:2.3.2.27]
            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:3.4.19.12]
            80143  SIKE1; suppressor of IKBKE 1 [KO:K12656]
            1654  DDX3X; DEAD-box helicase 3 X-linked [KO:K11594] [EC:3.6.4.13]
            5300  PIN1; peptidylprolyl cis/trans isomerase, NIMA-interacting 1 [KO:K09578] [EC:5.2.1.8]
            26007  TKFC; triokinase and FMN cyclase [KO:K00863] [EC:4.6.1.15 2.7.1.29 2.7.1.28]
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
///


pathview xml kegg • 71 views
ADD COMMENTlink modified 26 days ago by Luo Weijun1.5k • written 29 days ago by anamaria0
Answer: Issue with xml files downloaded with `pathview()`
0
gravatar for Luo Weijun
26 days ago by
Luo Weijun1.5k
United States
Luo Weijun1.5k wrote:

This does not look like an xml file, and it is not a file pathview downloads. To see what pathview download, try:
download.kegg(pathway="04622", species="hsa")
you will see two files starts with hsa04622 in your working directory, one of them is xml.

ADD COMMENTlink modified 26 days ago • written 26 days ago by Luo Weijun1.5k

Thank you Luo, your example made me realise my stupid mistake -- instead of KEGG id, I was passing the full pathway name to pathview() , e.g. "hsa04622 RIG-I-like receptor signaling pathway", but using just the 04622 or hsa04622 works as expected.

ADD REPLYlink written 23 days ago by anamaria0
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