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RGD DISEASE ONTOLOGY - ANNOTATIONS

RGD uses the Human Disease Ontology (DO, https://disease-ontology.org/) for disease curation across species. RGD automatically downloads each new release of the ontology on a monthly basis. Some additional terms which are required for RGD's curation purposes but are not currently covered in the official version of DO have been added. As corresponding terms are added to DO, these custom terms are retired and the DO terms substituted in existing annotations and subsequently used for curation.

Term:commensal bacterial infectious disease
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Accession:DOID:0050339 term browser browse the term
Definition:A bacterial infectious disease that results_in infection by bacteria which are part of the normal human flora when one or more of the defense mechanisms designed to restrict them from the usually sterile internal tissues are breached by accident, by intent (surgery), or by an underlying metabolic or an infectious disorder. (DO)
Synonyms:primary_id: RDO:9002545



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chlamydia term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G CCR5 C-C motif chemokine receptor 5 ISO RGD PMID:16118671 RGD:8549760 NCBI chr 3:46,370,142...46,376,206
Ensembl chr 3:46,370,946...46,376,206
JBrowse link
G CD40 CD40 molecule ISO RGD PMID:20102413 RGD:5132268 NCBI chr20:46,118,314...46,129,858
Ensembl chr20:46,118,271...46,129,863
JBrowse link
G FOXP3 forkhead box P3 treatment IEP RGD PMID:30832593 RGD:38455984 NCBI chr  X:49,250,438...49,264,710
Ensembl chr  X:49,250,438...49,264,800
JBrowse link
G ICAM1 intercellular adhesion molecule 1 ISO mRNA:increased expression:lung (mouse) RGD PMID:19728926 RGD:4145507 NCBI chr19:10,271,120...10,286,615
Ensembl chr19:10,271,093...10,286,615
JBrowse link
G IDO1 indoleamine 2,3-dioxygenase 1 treatment IEP
ISO
mRNA:increased expression:lung (mouse) RGD PMID:30832593 PMID:31249813 RGD:38455984, RGD:39938856 NCBI chr 8:39,913,891...39,928,790
Ensembl chr 8:39,902,275...39,928,790
JBrowse link
G IFNG interferon gamma EXP CTD Direct Evidence: marker/mechanism CTD PMID:19203382 NCBI chr12:68,154,768...68,159,740
Ensembl chr12:68,154,768...68,159,740
JBrowse link
G IL13 interleukin 13 ISO RGD PMID:21573182 RGD:5684365 NCBI chr 5:132,656,522...132,661,110
Ensembl chr 5:132,656,263...132,661,110
JBrowse link
G IL17A interleukin 17A ISO associated with Bronchial Hyprractivity; mRNA:increased expression:lung RGD PMID:20228193 PMID:19812198 RGD:4888528, RGD:4889101 NCBI chr 6:52,186,375...52,190,638
Ensembl chr 6:52,186,375...52,190,638
JBrowse link
G MIR21 microRNA 21 ISO associated with asthma;RNA:increased expression:lung RGD PMID:27448447 RGD:41404696 NCBI chr17:59,841,266...59,841,337
Ensembl chr17:59,841,266...59,841,337
JBrowse link
G TGFB1 transforming growth factor beta 1 treatment IEP RGD PMID:30832593 RGD:38455984 NCBI chr19:41,330,323...41,353,922
Ensembl chr19:41,301,587...41,353,922
JBrowse link
G TNF tumor necrosis factor EXP CTD Direct Evidence: marker/mechanism CTD PMID:19203382 NCBI chr 6:31,575,565...31,578,336
Ensembl chr 6:31,575,565...31,578,336
JBrowse link
Chlamydia pneumonia term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G CD274 CD274 molecule ISO mRNA:increased expression:lung RGD PMID:26378990 RGD:41412180 NCBI chr 9:5,450,542...5,470,554
Ensembl chr 9:5,450,503...5,470,566
JBrowse link
G PDCD1 programmed cell death 1 ISO mRNA:increased expression:lung RGD PMID:26378990 RGD:41412180 NCBI chr 2:241,849,884...241,858,894
Ensembl chr 2:241,849,884...241,858,894
JBrowse link
G PIK3CD phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit delta severity ISO RGD PMID:29893841 RGD:40890270 NCBI chr 1:9,627,258...9,729,114
Ensembl chr 1:9,629,889...9,729,114
JBrowse link
gas gangrene term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G GSN gelsolin IEP protein:decreased expression:blood serum (human) RGD PMID:9142022 RGD:329333022 NCBI chr 9:121,201,483...121,332,842
Ensembl chr 9:121,207,794...121,332,843
JBrowse link
toxic shock syndrome term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G A2M alpha-2-macroglobulin treatment ISO RGD PMID:2424486 RGD:10046036 NCBI chr12:9,067,708...9,116,229
Ensembl chr12:9,067,664...9,116,229
JBrowse link
G ACE angiotensin I converting enzyme severity IAGP DNA:SNP, insertion/deletion:promoter, intron: (rs4291, rs4646994) RGD PMID:28336767 RGD:39939121 NCBI chr17:63,477,061...63,498,373
Ensembl chr17:63,477,061...63,498,380
JBrowse link
G ADK adenosine kinase ISO RGD PMID:8207212 RGD:6482670 NCBI chr10:74,151,221...74,709,290
Ensembl chr10:74,151,202...74,709,963
JBrowse link
G ADM adrenomedullin ISO RGD PMID:17318497 PMID:17766482 RGD:1625310, RGD:1642599 NCBI chr11:10,305,073...10,307,397
Ensembl chr11:10,305,073...10,307,397
JBrowse link
G ADRB2 adrenoceptor beta 2 disease_progression
treatment
IAGP
IDA
DNA:polymorphism: :rs1042717(human) RGD PMID:19850944 PMID:16076286 RGD:8548487, RGD:8548529 NCBI chr 5:148,826,611...148,828,623
Ensembl chr 5:148,826,611...148,828,623
JBrowse link
G AGER advanced glycosylation end-product specific receptor ISO RGD PMID:21270403 RGD:6767566 NCBI chr 6:32,180,969...32,184,253
Ensembl chr 6:32,180,968...32,184,322
JBrowse link
G AQP1 aquaporin 1 (Colton blood group) EXP CTD Direct Evidence: marker/mechanism CTD PMID:24028651 NCBI chr 7:30,911,853...30,925,516
Ensembl chr 7:30,911,853...30,925,517
JBrowse link
G C5AR1 complement C5a receptor 1 EXP CTD Direct Evidence: marker/mechanism CTD PMID:18063050 NCBI chr19:47,307,477...47,322,066
Ensembl chr19:47,290,023...47,322,066
JBrowse link
G CCKBR cholecystokinin B receptor ISO mRNA:increased expression:myocardium RGD PMID:15948246 RGD:2311332 NCBI chr11:6,259,838...6,272,127
Ensembl chr11:6,259,806...6,272,127
JBrowse link
G CCL2 C-C motif chemokine ligand 2 disease_progression IEP RGD PMID:28834779 RGD:14995949 NCBI chr17:34,255,285...34,257,203
Ensembl chr17:34,255,274...34,257,208
JBrowse link
G CD274 CD274 molecule severity IEP protein:increased expression:serum
protein:increased expression:lymphocyte, mononcyte
RGD PMID:29702526 PMID:26063974 RGD:40822808, RGD:41410786 NCBI chr 9:5,450,542...5,470,554
Ensembl chr 9:5,450,503...5,470,566
JBrowse link
G ELANE elastase, neutrophil expressed treatment ISO RGD PMID:18323746 RGD:10450579 NCBI chr19:852,303...856,243
Ensembl chr19:851,014...856,247
JBrowse link
G ENO2 enolase 2 ISO proteiin:increased expression:serum RGD PMID:17083782 RGD:2293748 NCBI chr12:6,914,580...6,923,697
Ensembl chr12:6,913,745...6,923,698
JBrowse link
G F2 coagulation factor II, thrombin severity IEP protein:decreased expression:blood plasma (human) RGD PMID:2788582 RGD:40822807 NCBI chr11:46,719,213...46,739,506
Ensembl chr11:46,719,196...46,739,506
JBrowse link
G FANCC FA complementation group C ISO RGD PMID:17404312 RGD:11045879 NCBI chr 9:95,099,054...95,317,709
Ensembl chr 9:95,099,054...95,426,796
JBrowse link
G GC GC vitamin D binding protein EXP CTD Direct Evidence: marker/mechanism CTD PMID:17852808 NCBI chr 4:71,741,693...71,805,520
Ensembl chr 4:71,741,696...71,804,041
JBrowse link
G GRK2 G protein-coupled receptor kinase 2 IEP mRNA:decreased expression:polymorphonuclear leukocyte RGD PMID:24465168 RGD:126848796 NCBI chr11:67,266,473...67,286,556
Ensembl chr11:67,266,473...67,286,556
JBrowse link
G HLA-DRA major histocompatibility complex, class II, DR alpha disease_progression IEP
EXP
associated with Burns
CTD Direct Evidence: marker/mechanism
CTD
RGD
PMID:28771573 PMID:17568330 PMID:15644645 RGD:5490160, RGD:5490203 NCBI chr 6:32,439,887...32,445,046
Ensembl chr 6:32,439,878...32,445,046
JBrowse link
G HLA-DRB1 major histocompatibility complex, class II, DR beta 1 IEP mRNA:decreased expression:blood RGD PMID:15644645 RGD:5490203 NCBI chr 6:32,578,775...32,589,848
Ensembl chr 6:32,577,902...32,589,848
JBrowse link
G HMOX1 heme oxygenase 1 ISO RGD PMID:18208666 RGD:4145362 NCBI chr22:35,381,096...35,394,207
Ensembl chr22:35,380,361...35,394,214
JBrowse link
G HSPA1B heat shock protein family A (Hsp70) member 1B susceptibility IAGP associated wit community-acquired pneumonia;DNA:SNP: :1267A>G (human) RGD PMID:12771604 RGD:5147601 NCBI chr 6:31,827,738...31,830,254
Ensembl chr 6:31,827,738...31,830,254
JBrowse link
G IDO1 indoleamine 2,3-dioxygenase 1 severity IEP protein:increased activity, increased expression:plasma, heart (human) RGD PMID:21765346 RGD:39939075 NCBI chr 8:39,913,891...39,928,790
Ensembl chr 8:39,902,275...39,928,790
JBrowse link
G IFNG interferon gamma IEP protein:increased expression:plasma RGD PMID:25403265 RGD:38455982 NCBI chr12:68,154,768...68,159,740
Ensembl chr12:68,154,768...68,159,740
JBrowse link
G IL10 interleukin 10 severity
onset
IDA
ISO
IEP
protein:increased expression:lung (mouse)
protein:increased expression:plasma
RGD PMID:12117955 PMID:12117955 PMID:28659355 PMID:25403265 PMID:7593621 RGD:1598471, RGD:1598471, RGD:40890272, RGD:38455982, RGD:11049456 NCBI chr 1:206,767,602...206,772,494
Ensembl chr 1:206,767,602...206,774,541
JBrowse link
G IL19 interleukin 19 IEP protein:increased expression:serum RGD PMID:18246602 RGD:5037232 NCBI chr 1:206,770,773...206,842,981
Ensembl chr 1:206,770,764...206,842,981
JBrowse link
G IL1B interleukin 1 beta severity ISO protein:increased expression:lung (mouse) RGD PMID:28659355 RGD:40890272 NCBI chr 2:112,829,751...112,836,779
Ensembl chr 2:112,829,751...112,836,816
JBrowse link
G IL1RN interleukin 1 receptor antagonist treatment
susceptibility
IMP
IAGP
human gene in a mouse model
associated with Precursor Cell Lymphoblastic Leukemia-Lymphoma;DNA:polymorphism::
RGD PMID:15516267 PMID:23014359 RGD:8551736, RGD:11522756 NCBI chr 2:113,099,360...113,134,014
Ensembl chr 2:113,099,315...113,134,016
JBrowse link
G IL20RA interleukin 20 receptor subunit alpha ISO mRNA:increased expression:multiple RGD PMID:18246602 RGD:5037232 NCBI chr 6:136,999,971...137,044,965
Ensembl chr 6:136,999,971...137,045,180
JBrowse link
G IL20RB interleukin 20 receptor subunit beta ISO mRNA:increased expression:multiple RGD PMID:18246602 RGD:5037232 NCBI chr 3:136,957,983...137,011,085
Ensembl chr 3:136,946,230...137,011,085
JBrowse link
G IL27 interleukin 27 ISO protein, mRNA:increased expression:blood serum, spleen (mouse) RGD PMID:20435892 RGD:126790535 NCBI chr16:28,499,362...28,506,834
Ensembl chr16:28,499,362...28,512,051
JBrowse link
G IL6 interleukin 6 treatment ISO RGD PMID:2124237 RGD:11060276 NCBI chr 7:22,727,200...22,731,998
Ensembl chr 7:22,725,884...22,732,002
JBrowse link
G MBL2 mannose binding lectin 2 susceptibility IAGP associated with acute pyelonephritis;DNA:SNPs, missense mutations, haplotypes:promoter, cds:multiple RGD PMID:17202308 RGD:6903268 NCBI chr10:52,765,380...52,772,784
Ensembl chr10:52,765,380...52,772,784
JBrowse link
G MC2R melanocortin 2 receptor ISO protein:increased expression:liver (rat) RGD PMID:2822467 RGD:6484558 NCBI chr18:13,882,044...13,915,707
Ensembl chr18:13,882,044...13,915,707
JBrowse link
G MIF macrophage migration inhibitory factor ISO RGD PMID:17381395 PMID:17565848 RGD:4891013, RGD:1641978 NCBI chr22:23,894,383...23,895,223
Ensembl chr22:23,894,383...23,895,227
JBrowse link
G MIR155 microRNA 155 IEP RGD PMID:29979224 RGD:21081538 NCBI chr21:25,573,980...25,574,044
Ensembl chr21:25,573,980...25,574,044
JBrowse link
G MIR21 microRNA 21 exacerbates
ameliorates
ISO RGD PMID:28437377 PMID:31189875 RGD:41404641, RGD:41404698 NCBI chr17:59,841,266...59,841,337
Ensembl chr17:59,841,266...59,841,337
JBrowse link
G MIR494 microRNA 494 severity IEP RGD PMID:30783439 RGD:150527846 NCBI chr14:101,029,634...101,029,714
Ensembl chr14:101,029,634...101,029,714
JBrowse link
G MT-ND1 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 susceptibility IAGP associated with Burns; DNA:missense mutation:cds:m.4216T>C (human) RGD PMID:19487983 RGD:5148017 NCBI chr MT:3,307...4,262
Ensembl chr MT:3,307...4,262
JBrowse link
G NFKBIA NFKB inhibitor alpha treatment ISO RGD PMID:11961112 RGD:126928137 NCBI chr14:35,401,513...35,404,749
Ensembl chr14:35,401,079...35,404,749
JBrowse link
G NOS2 nitric oxide synthase 2 ISO
EXP
CTD Direct Evidence: marker/mechanism CTD
RGD
PMID:8745224 PMID:16601845 RGD:1580268 NCBI chr17:27,756,766...27,800,529
Ensembl chr17:27,756,766...27,800,529
JBrowse link
G NPPC natriuretic peptide C IEP protein:increased expression:plasma RGD PMID:8117275 RGD:1642297 NCBI chr 2:231,921,809...231,926,396
Ensembl chr 2:231,921,809...231,926,396
JBrowse link
G OGG1 8-oxoguanine DNA glycosylase ISO RGD PMID:15677345 RGD:8657146 NCBI chr 3:9,749,952...9,783,108
Ensembl chr 3:9,749,944...9,788,219
JBrowse link
G PARP1 poly(ADP-ribose) polymerase 1 ISO RGD PMID:12445868 RGD:10414070 NCBI chr 1:226,360,691...226,408,093
Ensembl chr 1:226,360,210...226,408,154
JBrowse link
G PDCD1 programmed cell death 1 severity IEP protein:increased expression:serum
protein:increased expression:lymphocyte, mononcyte
RGD PMID:29702526 PMID:26063974 RGD:40822808, RGD:41410786 NCBI chr 2:241,849,884...241,858,894
Ensembl chr 2:241,849,884...241,858,894
JBrowse link
G PIK3CD phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit delta severity ISO RGD PMID:28659355 RGD:40890272 NCBI chr 1:9,627,258...9,729,114
Ensembl chr 1:9,629,889...9,729,114
JBrowse link
G PLAUR plasminogen activator, urokinase receptor ISO RGD PMID:20693875 RGD:6484122 NCBI chr19:43,646,095...43,670,169
Ensembl chr19:43,646,095...43,670,547
JBrowse link
G PROC protein C, inactivator of coagulation factors Va and VIIIa treatment ISO
IDA
RGD PMID:19320827 PMID:21850534 RGD:11100015, RGD:11100041 NCBI chr 2:127,418,427...127,429,242
Ensembl chr 2:127,418,427...127,429,242
JBrowse link
G PTX3 pentraxin 3 IEP protein:increased expression:plasma (human) RGD PMID:30687307 RGD:38508896 NCBI chr 3:157,436,850...157,443,633
Ensembl chr 3:157,436,850...157,443,633
JBrowse link
G REN renin exacerbates IEP protein:increased activity:blood plasma (human) RGD PMID:31723628 RGD:125097502 NCBI chr 1:204,154,819...204,166,337
Ensembl chr 1:204,154,819...204,190,324
JBrowse link
G SELL selectin L ISO protein:increased expression:plasma RGD PMID:19375498 RGD:5685700 NCBI chr 1:169,690,667...169,711,620
Ensembl chr 1:169,690,665...169,711,702
JBrowse link
G SERPINC1 serpin family C member 1 treatment IDA RGD PMID:16732381 RGD:1599323 NCBI chr 1:173,903,800...173,917,327
Ensembl chr 1:173,903,800...173,917,327
JBrowse link
G SERPINE1 serpin family E member 1 susceptibility IAGP associated with Pneumonia; DNA:polymorphism:promoter:rs1799768 (human) RGD PMID:20429897 RGD:4144828 NCBI chr 7:101,127,104...101,139,247
Ensembl chr 7:101,127,104...101,139,247
JBrowse link
G SERPINF1 serpin family F member 1 severity IEP protein:decreased expression:plasma (human) RGD PMID:6158114 RGD:36174004 NCBI chr17:1,762,060...1,777,565
Ensembl chr17:1,762,029...1,777,565
JBrowse link
G SERPING1 serpin family G member 1 treatment IDA RGD PMID:8172580 RGD:8661646 NCBI chr11:57,597,685...57,614,848
Ensembl chr11:57,597,387...57,619,171
JBrowse link
G SFTPB surfactant protein B IAGP associated with Pneumonia;DNA:polymorphism: :1580C>T (human) RGD PMID:15190959 RGD:4143404 NCBI chr 2:85,657,307...85,668,741
Ensembl chr 2:85,657,314...85,668,741
JBrowse link
G SOCS1 suppressor of cytokine signaling 1 severity ISO RGD PMID:19469017 RGD:150573701 NCBI chr16:11,254,417...11,256,204
Ensembl chr16:11,254,417...11,256,204
JBrowse link
G TBXA2R thromboxane A2 receptor treatment ISO RGD PMID:7816742 RGD:11059599 NCBI chr19:3,594,507...3,606,875
Ensembl chr19:3,594,507...3,606,875
JBrowse link
G TFPI tissue factor pathway inhibitor treatment IDA RGD PMID:11776329 RGD:11062085 NCBI chr 2:187,464,230...187,554,435
Ensembl chr 2:187,464,230...187,565,760
JBrowse link
G THPO thrombopoietin IEP protein:increased expression:serum: RGD PMID:20467749 RGD:10449021 NCBI chr 3:184,371,935...184,379,688
Ensembl chr 3:184,371,935...184,381,968
JBrowse link
G TNF tumor necrosis factor treatment ISO
EXP
protein:increased expression:peritoneal macrophage, cell surface (rat)
CTD Direct Evidence: marker/mechanism
CTD
RGD
PMID:20054000 PMID:2213560 PMID:12622907 RGD:10449465, RGD:1598936 NCBI chr 6:31,575,565...31,578,336
Ensembl chr 6:31,575,565...31,578,336
JBrowse link
G TREM1 triggering receptor expressed on myeloid cells 1 IEP mRNA:decreased expression:polymorphonuclear leukocyte RGD PMID:24465168 RGD:126848796 NCBI chr 6:41,267,385...41,286,682
Ensembl chr 6:41,267,100...41,286,682
JBrowse link
G ZC3H12A zinc finger CCCH-type containing 12A ISO RGD PMID:23422584 RGD:39938961 NCBI chr 1:37,474,580...37,484,377
Ensembl chr 1:37,474,580...37,484,377
JBrowse link
trachoma term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G CXCL8 C-X-C motif chemokine ligand 8 susceptibility IAGP DNA:SNP:promoter:g.-251A>T (rs4073) (human) RGD PMID:20015396 RGD:150520200 NCBI chr 4:73,740,569...73,743,716
Ensembl chr 4:73,740,519...73,743,716
JBrowse link
G HLA-B major histocompatibility complex, class I, B IAGP DNA:polymorphism:cds:HLA-B*14 (human, Tanzanian) RGD PMID:18824733 RGD:7364877 NCBI chr 6:31,353,875...31,357,179
Ensembl chr 6:31,353,872...31,367,067
JBrowse link
G IL10 interleukin 10 no_association
severity
IEP
IAGP
protein:increased expression:tear
DNA:SNP:promoter:−1082G>A (human)
DNA:SNP:promoter:−819T>C, −592A>C (human)
DNA:SNP, haplotype:promoter:−1082G>A (human)
DNA:haplotype: :
RGD PMID:18628987 PMID:11023480 PMID:11023480 PMID:15789056 PMID:17947295 RGD:7365037, RGD:7365085, RGD:7365085, RGD:7365072, RGD:7365053 NCBI chr 1:206,767,602...206,772,494
Ensembl chr 1:206,767,602...206,774,541
JBrowse link
G IL17A interleukin 17A IEP mRNA:increased expression:conjunctiva (human) RGD PMID:21911461 RGD:9068420 NCBI chr 6:52,186,375...52,190,638
Ensembl chr 6:52,186,375...52,190,638
JBrowse link
G TNF tumor necrosis factor IAGP DNA:SNP, haplotypes:promoter:−308G>A (human) RGD PMID:17330135 RGD:8548830 NCBI chr 6:31,575,565...31,578,336
Ensembl chr 6:31,575,565...31,578,336
JBrowse link
Trachomatous Trichiasis term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G COL1A1 collagen type I alpha 1 chain IEP mRNA:decreased expression:tarsal conjunctiva (human) RGD PMID:20375326 RGD:8552676 NCBI chr17:50,184,101...50,201,631
Ensembl chr17:50,184,101...50,201,632
JBrowse link
Whipple disease term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G CD163 CD163 molecule IEP protein:increased expression:duodenum, macrophage (human) RGD PMID:19664628 RGD:149735573 NCBI chr12:7,470,811...7,503,777
Ensembl chr12:7,470,811...7,503,893
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  disease 151016
    disease by infectious agent 8266
      Bacterial Infections and Mycoses 2031
        bacterial infectious disease 1646
          commensal bacterial infectious disease 74
            Lemierre's syndrome 0
            Ritter's disease + 0
            actinobacillosis 0
            actinomycosis + 1
            chlamydia + 18
            gas gangrene 1
            inclusion conjunctivitis 0
            pertussis + 0
            toxic shock syndrome 62
            trachoma + 6
paths to the root