diff --git a/pathways/WP4932/WP4932.gpml b/pathways/WP4932/WP4932.gpml index 522c01c724..b684fd9f3f 100644 --- a/pathways/WP4932/WP4932.gpml +++ b/pathways/WP4932/WP4932.gpml @@ -1,135 +1,137 @@ - - 7q11.23 copy number variation syndrome (MIM 609757, also called Williams-Beuren region duplication syndrome, WBS duplication syndrome, Chromosome 7q11.23 duplication syndrome, or Somerville-van-der-Aa syndrome) is a copy number variation syndrome with a duplication in the region chr7:72,744,454-74,142,513 (GRCh37/hg19). The breakpoint is defined from Carolyn B Mervis 7q11.23 Duplication Syndrome in Gene Reviews PMID: 20301295. - - + + 7q11.23 copy number variation syndrome (MIM 609757, also called Williams-Beuren region duplication syndrome, WBS duplication syndrome, Chromosome 7q11.23 duplication syndrome, or Somerville-van-der-Aa syndrome) is a copy number variation syndrome with a duplication in the region chr7:72,744,454-74,142,513 (GRCh37/hg19). The breakpoint is defined from Carolyn B Mervis 7q11.23 Duplication Syndrome in Gene Reviews PMID: 20301295. + + + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + C16orf7 - + - + - + - + MT-ATP6 - - MT-ATP8 + + MT-ATP8 - + ATP5F1 - + ATP5G1 - + ATP5G2 - + ATP5G3 - + - + - + @@ -369,7 +371,7 @@ - + @@ -721,11 +723,11 @@ - + - + @@ -752,24 +754,24 @@ c80 - - + + e7b - - + + fe3 - - + + @@ -778,15 +780,15 @@ bfc a72 - - + + - - + + @@ -794,23 +796,23 @@ dc5 - - + + a4d - - + + - - + + @@ -818,46 +820,46 @@ bd9 - - + + f01 - - + + - - + + - - + + e89 - - + + de2 - - + + @@ -866,110 +868,110 @@ b8e cb5 - - + + a3f - - + + c43 - - + + - - + + e7b - - + + dc5 - - + + e02 - - + + f6b - - + + c61 - - + + - - + + - - + + eda - - + + - - + + fe3 - - + + @@ -977,56 +979,56 @@ c80 - - + + b9a - - + + f80 - - + + efd - - + + b41 - - + + fe3 - - + + e59 - - + + @@ -1034,100 +1036,100 @@ f02 - - + + - - + + - - + + - - + + bd9 - - + + c1f - - + + - - + + e27 - - + + - - + + - - + + b41 - - + + - - + + c1f - - - + + + @@ -1135,8 +1137,8 @@ c80 - - + + @@ -1144,94 +1146,94 @@ bf3 - - + + - - + + e00 - - + + e59 - - + + a8f - - + + cff - - + + e27 - - + + b42 - - + + c61 - - + + b4a - - + + e81 - - + + - - + + @@ -1239,100 +1241,100 @@ a5e fdb - - + + a36 - - + + dba - - + + e2e - - + + - - - - + + + + a85 - - + + af3 - - + + - - + + e2e - - + + - - + + - - + + - - + + - - + + @@ -1340,31 +1342,31 @@ e8d bbb - - + + b9e - - + + e59 - - + + - - + + @@ -1373,24 +1375,24 @@ c59 aa7 - - + + b91 - - + + fa3 - - + + @@ -1398,24 +1400,24 @@ e0a c12 - - + + c1f - - + + bb9 - - + + @@ -1424,62 +1426,62 @@ a8e a61 - - + + - - + + bd9 - - + + e81 - - + + b4a - - + + b4a - - + + - - + + c61 - - + + @@ -1487,63 +1489,63 @@ c61 - - + + eda - - + + eda - - + + eda - - + + c1f - - + + - - + + - - + + - - + + @@ -1553,8 +1555,8 @@ b8e cb5 - - + + @@ -1563,8 +1565,8 @@ b8e cb5 - - + + @@ -1573,16 +1575,16 @@ b8e cb5 - - + + b41 - - + + @@ -1590,99 +1592,99 @@ b41 - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + b91 - - + + - - + + @@ -1691,39 +1693,39 @@ e00 - - + + - - + + - - + + - - + + - - + + - - + + + diff --git a/pathways/WP5123/WP5123.gpml b/pathways/WP5123/WP5123.gpml index 05b9dac69a..caf335af96 100644 --- a/pathways/WP5123/WP5123.gpml +++ b/pathways/WP5123/WP5123.gpml @@ -1,5 +1,5 @@ - + Fatty Acids (FAs) consists of several chain lengths (short, medium and long chain), which all need to be converted to CoA-bound esters to cross the inner mitochondrial membrane. The long-chain lengths however also need additional carnitine esterification. Several diseases are linked to the proteins in this pathway, which can be categorized into four groups: 1. entry of long-chain FAs into mitochondria disorders; 2. intra-mitochondrial beta-oxidation membrane-bound proteins defects involving long-chain FAs; 3. intra-mitochondrial beta-oxidation matrix proteins defects involving short and medium-chain FAs; 4. impaired electron transfer to Oxidative phosphorylation (OXPHOS) system. @@ -7,7 +7,6 @@ Several diseases are linked to the proteins in this pathway, which can be catego This pathway has been inspired by Chapter 17 of the book of Blau (ISBN 3642403360 (978-3642403361)), edition 4 and build on top of the original [https://www.wikipathways.org/instance/WP368_r117795 'Mitochondrial long chain fatty acid beta-oxidation pathway']. Proteins on this pathway have targeted assays available via the [https://assays.cancer.gov/available_assays?wp_id=WP368 CPTAC Assay Portal] - test de7 d8e @@ -976,21 +975,57 @@ Proteins on this pathway have targeted assays available via the [https://assays. - - carnitine palmitoyltransferase I deficiency - DOID:0090129 - Disease - + + 11826276 + PubMed + Fatty acid oxidation disorders. + Annu Rev Physiol + 2002 + Rinaldo P + Matern D + Bennett MJ + fatty acid beta degradation pathway PW:0000738 Pathway Ontology + + carnitine palmitoyltransferase II deficiency + DOID:0060235 + Disease + + + NA + PubMed + Physician's Guide to the Diagnosis, Treatment, and Follow-Up of Inherited Metabolic Diseases, Chapter 17 + ISBN 978-3-642-40337-8 + 2014 + Blau, N. + Duran, M. + Gibson, K.M. + Donisi-Vici, C. + carnitine palmitoyltransferase I deficiency pathway PW:0002574 Pathway Ontology + + carnitine-acylcarnitine translocase deficiency + PW:0002506 + Pathway Ontology + + + carnitine palmitoyltransferase I deficiency + DOID:0090129 + Disease + + + fatty acid beta oxidation pathway + PW:0000738 + Pathway Ontology + 30850536 PubMed @@ -1007,47 +1042,11 @@ Proteins on this pathway have targeted assays available via the [https://assays. DOID:0111585 Disease - - carnitine palmitoyltransferase II deficiency - DOID:0060235 - Disease - classic metabolic pathway PW:0000002 Pathway Ontology - - 11826276 - PubMed - Fatty acid oxidation disorders. - Annu Rev Physiol - 2002 - Rinaldo P - Matern D - Bennett MJ - - - carnitine-acylcarnitine translocase deficiency - PW:0002506 - Pathway Ontology - - - fatty acid beta oxidation pathway - PW:0000738 - Pathway Ontology - - - NA - PubMed - Physician's Guide to the Diagnosis, Treatment, and Follow-Up of Inherited Metabolic Diseases, Chapter 17 - ISBN 978-3-642-40337-8 - 2014 - Blau, N. - Duran, M. - Gibson, K.M. - Donisi-Vici, C. - diff --git a/pathways/WP5180/WP5180.gpml b/pathways/WP5180/WP5180.gpml index 421d50e1a1..b79313f74d 100644 --- a/pathways/WP5180/WP5180.gpml +++ b/pathways/WP5180/WP5180.gpml @@ -1,10 +1,10 @@ - + DYRK1A (Dual-specificity tyrosine phosphorylation-regulated kinase 1A)(OMIM 600855) is a kinase whose gene is located at 21q22.13 and is highly conserved.It is composed of a nuclear targeting sequence, a protein kinase domain, a leucine zipper motif and a 13-consecutive-histidine repeat. The gene is located in the so-called "Down syndrome critical region" (DSCR), a region on chromosome 21 thought responsible for most phenotypic manifestations of Down syndrome. DYRK1A is involved in signaling pathways regulating cell proliferation in brain development. Amongst others, haploinsufficiency of DYRK1A, DYRK1A overexpression and interactions with alpha-synuclein are thought to be the main factors for the clinical phenotype. - + @@ -504,7 +504,7 @@ Earlier differentiation e4b - + @@ -806,7 +806,7 @@ Earlier differentiation - + @@ -1480,45 +1480,50 @@ this phosphorylation is required for DREAM complex formation - - 19218269 + + 25795597 PubMed - DYRK1A interacts with the REST/NRSF-SWI/SNF chromatin remodelling complex to deregulate gene clusters involved in the neuronal phenotypic traits of Down syndrome. - Hum Mol Genet - 2009 - Lepagnol-Bestel AM - Zvara A - Maussion G - Quignon F - Ngimbous B - Ramoz N - Imbeaud S - Loe-Mie Y - Benihoud K - Agier N - Salin PA - Cardona A - Khung-Savatovsky S - Kallunki P - Delabar JM - Puskas LG - Delacroix H - Aggerbeck L - Delezoide AL - Delattre O - Gorwood P - Moalic JM - Simonneau M + DYRK1A in neurodegeneration and cancer: Molecular basis and clinical implications. + Pharmacol Ther + 2015 + Abbassi R + Johns TG + Kassiou M + Munoz L - - 11518709 + + 23720711 PubMed - Protein kinase Dyrk1 activates cAMP response element-binding protein during neuronal differentiation in hippocampal progenitor cells. + The role of the hippo pathway in melanocytes and melanoma. + Front Oncol + 2013 + Kim JE + Finlay GJ + Baguley BC + + + 20167603 + PubMed + DYRK1A and DYRK3 promote cell survival through phosphorylation and activation of SIRT1. J Biol Chem - 2001 - Yang EJ - Ahn YS - Chung KC + 2010 + Guo X + Williams JG + Schug TT + Li X + + + 16733250 + PubMed + Phosphorylation of amphiphysin I by minibrain kinase/dual-specificity tyrosine phosphorylation-regulated kinase, a kinase implicated in Down syndrome. + J Biol Chem + 2006 + Murakami N + Xie W + Lu RC + Chen-Hwang MC + Wieraszko A + Hwang YW 15287745 @@ -1534,39 +1539,50 @@ this phosphorylation is required for DREAM complex formation Wang R Hwang YW - - - - DREAM complex - Wikipedia, The Free Encyclopedia. Retrieved 12:18, February 17, 2022, from https://en.wikipedia.org/w/index.php?title=DREAM_complex&oldid=1064901567 - 2022, January 10 - Wikipedia contributors - - - 15199138 + + intellectual disability + DOID:1059 + Disease + + + 19783418 PubMed - - - + Dynamic regulation of Notch signaling in neural progenitor cells. + Curr Opin Cell Biol + 2009 + Kageyama R + Ohtsuka T + Shimojo H + Imayoshi I - - 14593110 + + Down syndrome + DOID:14250 + Disease + + + Lewy body dementia + DOID:12217 + Disease + + + 11518709 PubMed - Phosphorylation of Ser640 in muscle glycogen synthase by DYRK family protein kinases. + Protein kinase Dyrk1 activates cAMP response element-binding protein during neuronal differentiation in hippocampal progenitor cells. J Biol Chem - 2004 - Skurat AV - Dietrich AD + 2001 + Yang EJ + Ahn YS + Chung KC - - 23720711 + + 23406382 PubMed - The role of the hippo pathway in melanocytes and melanoma. - Front Oncol + Alzheimer's Aβ42 and Aβ40 peptides form interlaced amyloid fibrils. + J Neurochem 2013 - Kim JE - Finlay GJ - Baguley BC + Gu L + Guo Z 33081032 @@ -1583,40 +1599,67 @@ this phosphorylation is required for DREAM complex formation Møller LB - microcephaly - DOID:10907 + Parkinson's disease + DOID:14330 Disease - - 15906374 + + 16671894 PubMed - Regulation of the proapoptotic activity of huntingtin interacting protein 1 by Dyrk1 and caspase-3 in hippocampal neuroprogenitor cells. - J Neurosci Res - 2005 - Kang JE - Choi SA - Park JB - Chung KC + dDYRK2 and Minibrain interact with the chromatin remodelling factors SNR1 and TRX. + Biochem J + 2006 + Kinstrie R + Lochhead PA + Sibbet G + Morrice N + Cleghon V - - Lewy body dementia - DOID:12217 - Disease - - - 27308401 + + 15199138 PubMed - DYRK1A: the double-edged kinase as a protagonist in cell growth and tumorigenesis. - Mol Cell Oncol - 2015 - 27308401 + + + + + + 19218269 PubMed - DYRK1A: the double-edged kinase as a protagonist in cell growth and tumorigenesis. - Mol Cell Oncol - 2015 - Fernández-Martínez P - Zahonero C - Sánchez-Gómez P + DYRK1A interacts with the REST/NRSF-SWI/SNF chromatin remodelling complex to deregulate gene clusters involved in the neuronal phenotypic traits of Down syndrome. + Hum Mol Genet + 2009 + Lepagnol-Bestel AM + Zvara A + Maussion G + Quignon F + Ngimbous B + Ramoz N + Imbeaud S + Loe-Mie Y + Benihoud K + Agier N + Salin PA + Cardona A + Khung-Savatovsky S + Kallunki P + Delabar JM + Puskas LG + Delacroix H + Aggerbeck L + Delezoide AL + Delattre O + Gorwood P + Moalic JM + Simonneau M + + + 15694837 + PubMed + Dual-specificity tyrosine-phosphorylated and regulated kinase 1A (DYRK1A) interacts with the phytanoyl-CoA alpha-hydroxylase associated protein 1 (PAHX-AP1), a brain specific protein. + Int J Biochem Cell Biol + 2005 + Bescond M + Rahmani Z 25795597 @@ -1629,75 +1672,54 @@ this phosphorylation is required for DREAM complex formation Kassiou M Munoz L - - 21536729 + + 27308401 PubMed - Sweet DREAMs for Hippo. - Genes Dev - 2011 - Dick FA - Mymryk JS - - - 11311120 + DYRK1A: the double-edged kinase as a protagonist in cell growth and tumorigenesis. + Mol Cell Oncol + 2015 + 27308401 PubMed - The kinase DYRK1A phosphorylates the transcription factor FKHR at Ser329 in vitro, a novel in vivo phosphorylation site. - Biochem J - 2001 - Woods YL - Rena G - Morrice N - Barthel A - Becker W - Guo S - Unterman TG - Cohen P + DYRK1A: the double-edged kinase as a protagonist in cell growth and tumorigenesis. + Mol Cell Oncol + 2015 + Fernández-Martínez P + Zahonero C + Sánchez-Gómez P - - 21777625 + + 14593110 PubMed - DYRK1A binds to an evolutionarily conserved WD40-repeat protein WDR68 and induces its nuclear translocation. - Biochim Biophys Acta - 2011 - Miyata Y - Nishida E + Phosphorylation of Ser640 in muscle glycogen synthase by DYRK family protein kinases. + J Biol Chem + 2004 + Skurat AV + Dietrich AD - - 25795597 - PubMed - DYRK1A in neurodegeneration and cancer: Molecular basis and clinical implications. - Pharmacol Ther - 2015 - Abbassi R - Johns TG - Kassiou M - Munoz L + + + + DREAM complex + Wikipedia, The Free Encyclopedia. Retrieved 12:18, February 17, 2022, from https://en.wikipedia.org/w/index.php?title=DREAM_complex&oldid=1064901567 + 2022, January 10 + Wikipedia contributors - - 19783418 + + 15906374 PubMed - Dynamic regulation of Notch signaling in neural progenitor cells. - Curr Opin Cell Biol - 2009 - Kageyama R - Ohtsuka T - Shimojo H - Imayoshi I + Regulation of the proapoptotic activity of huntingtin interacting protein 1 by Dyrk1 and caspase-3 in hippocampal neuroprogenitor cells. + J Neurosci Res + 2005 + Kang JE + Choi SA + Park JB + Chung KC - intellectual disability - DOID:1059 + Alzheimer's disease + DOID:10652 Disease - - 23406382 - PubMed - Alzheimer's Aβ42 and Aβ40 peptides form interlaced amyloid fibrils. - J Neurochem - 2013 - Gu L - Guo Z - 12138125 PubMed @@ -1713,54 +1735,14 @@ this phosphorylation is required for DREAM complex formation Wu G Wu D - - Alzheimer's disease - DOID:10652 - Disease - - - Down syndrome - DOID:14250 - Disease - - - 16733250 - PubMed - Phosphorylation of amphiphysin I by minibrain kinase/dual-specificity tyrosine phosphorylation-regulated kinase, a kinase implicated in Down syndrome. - J Biol Chem - 2006 - Murakami N - Xie W - Lu RC - Chen-Hwang MC - Wieraszko A - Hwang YW - - - 16671894 - PubMed - dDYRK2 and Minibrain interact with the chromatin remodelling factors SNR1 and TRX. - Biochem J - 2006 - Kinstrie R - Lochhead PA - Sibbet G - Morrice N - Cleghon V - - - Parkinson's disease - DOID:14330 - Disease - - - 15694837 + + 21536729 PubMed - Dual-specificity tyrosine-phosphorylated and regulated kinase 1A (DYRK1A) interacts with the phytanoyl-CoA alpha-hydroxylase associated protein 1 (PAHX-AP1), a brain specific protein. - Int J Biochem Cell Biol - 2005 - Bescond M - Rahmani Z + Sweet DREAMs for Hippo. + Genes Dev + 2011 + Dick FA + Mymryk JS 24904820 @@ -1778,16 +1760,35 @@ this phosphorylation is required for DREAM complex formation Bakulev V Bischof J - - 20167603 + + microcephaly + DOID:10907 + Disease + + + 11311120 PubMed - DYRK1A and DYRK3 promote cell survival through phosphorylation and activation of SIRT1. - J Biol Chem - 2010 - Guo X - Williams JG - Schug TT - Li X + The kinase DYRK1A phosphorylates the transcription factor FKHR at Ser329 in vitro, a novel in vivo phosphorylation site. + Biochem J + 2001 + Woods YL + Rena G + Morrice N + Barthel A + Becker W + Guo S + Unterman TG + Cohen P + + + 21777625 + PubMed + DYRK1A binds to an evolutionarily conserved WD40-repeat protein WDR68 and induces its nuclear translocation. + Biochim Biophys Acta + 2011 + Miyata Y + Nishida E - \ No newline at end of file + + diff --git a/pathways/WP5382/WP5382.gpml b/pathways/WP5382/WP5382.gpml index 6b2779d2bc..8a5cf92944 100644 --- a/pathways/WP5382/WP5382.gpml +++ b/pathways/WP5382/WP5382.gpml @@ -1,5 +1,5 @@ - + Regulation of TGFβ/Smad Signaling Pathway in Trabecular Meshwork (TM) cells. In this pathway, TGF-β binds to the TGF-β-type II receptor, inducing the activation of the TGF-β-type-I receptor. This induces the phosphorylation of Smad2/3 proteins which form a complex with Smad4. The translocation of this complex to the nucleus is facilitated by the TAZ protein. Once in the nucleous, it binds to SBEs (Smad Binding Elements), promoting the transcription of TGF-beta-response genes. The inhibition of this translocation instead occurs when phosphorylated TAZ protein interacts with 14-3-3 protein preventing the formation of complex TAZ-Smad. The translated ECM proteins are secreted by TM cells to the extracellular space. This pathway is based on Figure 4 of the publication “Mutual regulation of the Hippo/Wnt/LPA/TGF-β signaling pathways and their roles in glaucoma (Review)” by Xin Wang, Guoli Huai, Hailian Wang, Yuande Liu, Ping Qi, Wei Shi, Jie Peng, Hongji Yang, Shaoping Deng, and Yi Wang. @@ -33,7 +33,7 @@ This pathway is based on Figure 4 of the publication “Mutual regulation of the - + @@ -70,7 +70,7 @@ This pathway is based on Figure 4 of the publication “Mutual regulation of the - + @@ -461,6 +461,16 @@ This pathway is based on Figure 4 of the publication “Mutual regulation of the + + 22923731 + PubMed + Matrix control of transforming growth factor-β function. + J Biochem + 2012 + Horiguchi M + Ota M + Rifkin DB + 28769795 PubMed @@ -471,31 +481,6 @@ This pathway is based on Figure 4 of the publication “Mutual regulation of the Johnson KE Harrison CA - - 33894227 - PubMed - TGF beta -1, -2 and -3 in the modulation of fibrosis in the cornea and other organs. - Exp Eye Res - 2021 - Wilson SE - - - 29286147 - PubMed - Mutual regulation of the Hippo/Wnt/LPA/TGF‑β signaling pathways and their roles in glaucoma (Review). - Int J Mol Med - 2018 - Wang X - Huai G - Wang H - Liu Y - Qi P - Shi W - Peng J - Yang H - Deng S - Wang Y - 35954181 PubMed @@ -510,25 +495,13 @@ This pathway is based on Figure 4 of the publication “Mutual regulation of the PW:0000490 Pathway Ontology - - 24517218 - PubMed - The role of TGF-β2 and bone morphogenetic proteins in the trabecular meshwork and glaucoma. - J Ocul Pharmacol Ther - 2014 - Wordinger RJ - Sharma T - Clark AF - - - 22923731 + + 33894227 PubMed - Matrix control of transforming growth factor-β function. - J Biochem - 2012 - Horiguchi M - Ota M - Rifkin DB + TGF beta -1, -2 and -3 in the modulation of fibrosis in the cornea and other organs. + Exp Eye Res + 2021 + Wilson SE 24727033 @@ -541,6 +514,33 @@ This pathway is based on Figure 4 of the publication “Mutual regulation of the Downs JC O'Brien CJ + + 24517218 + PubMed + The role of TGF-β2 and bone morphogenetic proteins in the trabecular meshwork and glaucoma. + J Ocul Pharmacol Ther + 2014 + Wordinger RJ + Sharma T + Clark AF + + + 29286147 + PubMed + Mutual regulation of the Hippo/Wnt/LPA/TGF‑β signaling pathways and their roles in glaucoma (Review). + Int J Mol Med + 2018 + Wang X + Huai G + Wang H + Liu Y + Qi P + Shi W + Peng J + Yang H + Deng S + Wang Y + 35300422 PubMed diff --git a/pathways/WP5389/WP5389.gpml b/pathways/WP5389/WP5389.gpml index 29318d463b..017d433521 100644 --- a/pathways/WP5389/WP5389.gpml +++ b/pathways/WP5389/WP5389.gpml @@ -1,5 +1,5 @@ - + Adverse Outcome Pathway of DNA adduct formation leading to kidney failure. Stressors of this AOP include cisplatin and carboplatin. @@ -164,6 +164,12 @@ - + + + kidney disease + DOID:557 + Disease + + diff --git a/pathways/WP5391/WP5391.gpml b/pathways/WP5391/WP5391.gpml index 6f48a567fa..01b2f6114e 100644 --- a/pathways/WP5391/WP5391.gpml +++ b/pathways/WP5391/WP5391.gpml @@ -1,11 +1,11 @@ - + Representative anthocyanin biosynthetic pathway for red perilla (Perilla frutescens) c77 - + @@ -13,7 +13,7 @@ - + @@ -41,7 +41,7 @@ - + @@ -49,7 +49,7 @@ - + @@ -57,27 +57,27 @@ - + - + - + - + - + - + @@ -216,6 +216,11 @@ + + flavonoid biosynthetic pathway + PW:0000522 + Pathway Ontology + 36383440 PubMed @@ -233,11 +238,6 @@ Nakamura Y Bono H - - flavonoid biosynthetic pathway - PW:0000522 - Pathway Ontology -