Portal:IEM
From WikiPathways
This portal is set up to give an overview of all Inherited Metabolic Disorders (IMDs, also known as Inborn Errors of Metabolism (IEM), see 2021 classification) pathways. This portal is also featured in the latest NAR Database Issue on WikiPathways.
IMPORTANT: the current list of pathways is originally based on the currently published (2014) 4th edition of the book (ISBN 3642403360 (978-3642403361)) and being updated for the new fifth edition (DOI 10.1007/978-3-030-67727-5 and ISBN:978-3-030-67726-8) in a collaboration with the chapter authors.
Covered Pathways
| Chapter ed. 5 | Title | Links WP | Chapter ed. 4 | Status | Diseases: x from ch. ed. 4 (+y) from other ch. |
|---|---|---|---|---|---|
| 13 | Disorders of pyrimidine and purine metabolism | WP4225 and WP4224 | 41 | Approved (ed.5) | |
| 14 | Disorders of Nucleotide Metabolism | ||||
| 15 | Creatine disorders | WP5190 | 32 | Approved | |
| 16 | Disorders of glutathione metabolism | WP4518 | 42 | Approved | |
| 17 | Disorders of ammonia detoxification | WP4595 | 4 | Approved | |
| 18 | Disorders of amino acid transport | WP5029 | 6 | Approved | |
| 19 | Disorders of monoamine metabolism | WP4220 | 31 | Approved (ed.5) | 6, non missing |
| 20 | Disorders of phenylalanine and tetrahydrobiopterin metabolism | WP4156 | 1 | Approved (ed.5) | 8 (+2), non missing |
| 21 | Disorders of tyrosine metabolism | WP4506 | 2 | Approved (ed.5) | 5, non missing |
| 22 | Disorders of sulfur amino acid and sulfide metabolism | WP4292 | 3 | Approved | 7, non missing |
| 23 | Disorders of branched-chain amino acid metabolism | WP4686 | 7 | Approved | |
| 24 | Disorders of Beta and Gamma Amino Acids | Fig.24.2: WP4157 | 5 (Fig.5.3) | Approved (ed.5) | 2, non missing |
| 26 | Disorders of glycine metabolism | Fig.5.1:WP5028, Fig.5.4: WP5026 | 5 | In Progress | |
| 26 | Disorders of glycine metabolism | Fig.5.2: WP4688 | 5 | Approved | |
| 27 | Disorders of Lipoic Acid and Iron-Sulphur Protein Metabolism | ||||
| 28 | Disorders of cobalamin metabolism | WP4271 | 13 | Approved | |
| 29 | Disorders of folate metabolism | WP4259 and WP4288 | 10 | Approved | 9 (+3), non missing |
| 30 | Disorders of biotin metabolism | WP5031 | 14 | Approved | |
| 31 | Disorders of thiamine metabolism | WP4297 | 15 | Approved | |
| 32 | Disorders of riboflavin metabolism | WP5037 | 16 | Approved | |
| 33 | Disorders of Niacin, NAD, and Pantothenate Metabolism | ||||
| 34 | Vitamin B6 -Dependent and Responsive Disorders | WP4228 | 11 | Approved (ed.5) | 5, non missing |
| 35 | Disorders of molybdenum metabolism | WP4507 and WP4504 | 12 | Approved | |
| 36 | Disorders of copper , zinc and selenium metabolism | WP5189 | 39 | Approved | |
| 37 | Iron metabolism disorder | WP5172 | 40 | Approved | |
| 38 | Disorders of Manganese Metabolism | ||||
| 39 | Disorders of carbohydrate and glucose transport | Fig.18.3:WP5173, Fig.18.4: WP5178 | 18 | Approved | |
| 40 | Disorders of Pentose Phosphate Pathway and Polyol Metabolism | ||||
| 41 | Disorders Congenital Hyperinsulinism | ||||
| 42 | Disorders of pyruvate and Krebs cycle metabolism | WP4236 | 20 | Approved | |
| 43 | Disorders of Mitochondrial Carriers | ||||
| 44 | Isolated Mitochondrial Complex Deficiencies | ||||
| 45 | Disorders of Replication, Transcription and Translation of Mitochondrial DNA | ||||
| 46 | Disorders of Mitochondrial Homeostatis, Dynamics, Protein Import, and Quality Control | ||||
| 47 | Primary CoQ10 deficiencies | WP5037 | 16 | Approved | |
| 48 | Disorders of carnitine, fatty acid and fatty aldehyde metabolism | WP5123 | 17 | In Progress | |
| 49 | Disorders of Glycerol Metabolism | ||||
| 50 | Disorders of ketone body metabolism | Fig.23.1 and 23.2:WP5175, Fig.23.3: WP5195 | 23 | Approved | |
| 51 | Disorders of Complex Lipids | ||||
| 52 | Disorders of eicosanoid metabolism (including leukotrienes) | WP5171 | 38 | Approved | |
| 53 | Disorders of lipoprotein metabolism | WP4522 | 43 | Approved | |
| 54 | Cholesterol synthesis disorders | WP5193 | 36 | Approved | |
| 55 | Disorders of steroid metabolism | WP4523 and WP4524 | 37 | Approved | |
| 56 | Disorders of Bile acid synthesis (and biliary transport) | WP5176 | 34 | Approved | |
| 57 | Disorders of Heme metabolism | WP5169 | 33 | Approved | |
| 58 | Inherited Disorders of Bilirubin Metabolite | ||||
| 59 | Disorders of Autophagy | ||||
| 60 | Lysosomal storage disorders | WP4153 | 25 | Approved (ed.5) | 8, 8 unconnected |
| 61 | The Neuronal Ceroid Lipofuscinoses | no pathway diagram | |||
| 62 | Mucolipidoses, Multiple Sulfatase Deficiency, and Cathepsin K and C Deficiency | ||||
| 63 | Oligosaccharidoses and Sialic Acid Disorders | ||||
| 64 | The Mucopolysaccharidoses | ||||
| 65 | Disorders of oxalate metabolism | WP5166 | 28 | Approved | |
| 66 | Congenital disorders of N-linked and O-linked glycosylation | WP4521 | 30 | Approved | |
| 67 | Disorders of Oxalate Metabolism | ||||
| 68 | Congenital Disorders of Glycosylation | ||||
| 69 | Cerebral organic acidurias | WP4519 and WP5030 | 8 & 9 | Approved | |
| 70 | 3-Methylglutaconic Acidurias | ||||
| - | Disorders of phosphoinositide metabolism | WP4971 | NA | Approved | |
| - | Oxysterols derived from cholesterol | WP4545 | NA | Approved | |
| - | Mitochondrial oxidative phosphorylation | 22 | In Progress |
Information on Pathway Curation:
This Table provides an overview of which chapters have been covered by WikiPathways. Approved pathways are coloured blue; pathways which still need work (however are a part of the database) are coloured orange.
Tip:
Click on the arrows behind the Table headers to sort this table based on Chapter number (edition 4 and 5 available), title, WikiPathways reference and Curation Status.
Pathway Visualisations
View all digitized Pathways from the Physician's Guide to the Diagnosis, Treatment, and Follow-Up of Inherited Metabolic Diseases by Blau et al. (see it on Scholia.)
How to add a pathway to the portal
The list of Featured Pathways is not static and can be updated at any time. If you know of a pathway that should be added, please contact Denise Slenter.
Data Analysis
With the pathways from the Blau book (as well as with other pathways on WikiPathways), various data analysis approaches can be performed. You can find the relevant book chapter as Open Access regarding these data approaches here: Slenter, D.N., Kutmon, M., Willighagen, E.L. (2022). WikiPathways: Integrating Pathway Knowledge with Clinical Data. In: Blau, N., Dionisi Vici, C., Ferreira, C.R., Vianey-Saban, C., van Karnebeek, C.D.M. (eds) Physician's Guide to the Diagnosis, Treatment, and Follow-Up of Inherited Metabolic Diseases. Springer, Cham. DOI:10.1007/978-3-030-67727-5_73.
For the current overview of which pathways are covered and their status, see here.
To download all pathways tagged for Inborn Errors of Metabolsim as GPML, click here.
For example scripts (in R), please visit IEMPathwayAnalysis.
The Figure on the left shows an example of network analysis with Cytoscape, where known drug-target interactions from DrugBank using the CyTargetLinker app have been added to the purine metabolism pathway.
Featured Pathway
|
Classical pathway of steroidogenesis with glucocorticoid and mineralocorticoid metabolism (Homo sapiens) Image does not exist Classical pathway of steroidogenesis with glucocorticoid and mineralocorticoid metabolism |
| View all Featured Pathways for this Portal |
News
- Spring 2022: The new edition is published, including the chapter about this portal Open Access.
- Winter 2020: All images of the first 15 chapters are available on WikiPathways.
- Summer 2020: An overview of all covered chapter has been created on the main page
- Spring 2020: The Portal has been created
- Autumn 2019: Several chapters of the new book have already been digitized (but are embargoed)
