Reference

All relevant information about the data implemented into the SysID-database can be found in the corresponding paper: Kochinke K, Zweier C, Nijhof B, Fenckova M, Cizek P, Honti F, Keerthikumar S, Oortveld MA, Kleefstra T, Kramer JM, Webber C, Huynen MA, Schenck A. “Systematic Phenomics Analysis Deconvolutes Genes Mutated in Intellectual Disability into Biologically Coherent Modules”. Am J Hum Genet. 2016 Jan 7;98(1):149-64. doi: 10.1016/j.ajhg.2015.11.024.

Supplemental Table S1: List of ID genes and related information: Complete catalog of 650 ID genes as of January 2014, including a short gene description and the human gene info.

Supplemental Table S2: List of fly screens and phenotypes: Complete catalog of ID gene orthologs screened for neuronal and wing-screen in Drosophila and their phenotypes (ID gene catalog as of mid 2010).


Citation Policy & Credits

If you chose to use this database for your work please cite:

Kochinke K, Zweier C, Nijhof B, Fenckova M, Cizek P, Honti F, Keerthikumar S, Oortveld MA, Kleefstra T, Kramer JM, Webber C, Huynen MA, Schenck A. “Systematic Phenomics Analysis Deconvolutes Genes Mutated in Intellectual Disability into Biologically Coherent Modules”. Am J Hum Genet. 2016 Jan 7;98(1):149-64. doi: 10.1016/j.ajhg.2015.11.024.

 

The linked sources we have utilized are:

Name Link
NCBI (National Center for Biotechnology Information): gene informaion http://www.ncbi.nlm.nih.gov/gene
Ensembl http://www.ensembl.org/index.html
HUGO Gene Nomenclature Committee (HGNC) http://www.genenames.org
Human protein Reference Database (hPRD) http://www.hprd.org
Gene Ontology Consortium http://geneontology.org
Online Mendelian Inheritance in Man (OMIM) http://www.ncbi.nlm.nih.gov/omim
Gene Reviews http://www.ncbi.nlm.nih.gov/books/NBK1116
Biological General Repository for Interaction Datasets (BioGRID) http://thebiogrid.org
BrainSpan Atlas of the developing human brain http://www.brainspan.org
Genotype-Tissue Expression Project (GTEx) http://www.gtexportal.org/home
Treefam: Database of animal gene trees http://www.treefam.org
Flybase: Database of Drosophila Genes & Genomes http://flybase.org
FlyAtlas: the Drosophila gene expression atlas http://www.flyatlas.org
Bloomington Drosophila Stock centre http://flystocks.bio.indiana.edu
Vienna Drosophila Stock Center (VDRC) http://stockcenter.vdrc.at/control/main

Please check the indicated websites/databases for their particular reference policies.

 

The assay used for the neuronal screen was published by: Schmidt, I., Thomas, S., Kain, P., Risse, B., Naffin, E., and Klambt, C. (2012). Kinesin heavy chain function in Drosophila glial cells controls neuronal activity. The Journal of neuroscience : the official journal of the Society for Neuroscience 32, 7466-7476, PMID: 22649226.

hPSD data were otbained from : Bayes, A., van de Lagemaat, L.N., Collins, M.O., Croning, M.D., Whittle, I.R., Choudhary, J.S., and Grant, S.G. (2011). Characterization of the proteome, diseases and evolution of the human postsynaptic density. Nature neuroscience 14, 19-21. PMID: 21170055.

 

Clinical application of SysID

The SysID gene catalog is utilized for diagnostic purposes by establishing gene sets for exome or panel sequencing at the Institute of Human Genetics, Erlangen, Germany.


Support

The database was supported by

  • The European Union’s FP7 large scale integrated network GenCoDys (HEALTH-241995) to C Webber, MA Huynen and A Schenck
  • VIDI and TOP grants (917-96-346, 912-12-109) from The Netherlands Organisation for Scientific Research (NWO) to A Schenck
  • the IZKF (Interdisziplinäres Zentrum für Klinische Forschung) Erlangen to C Zweier
  • DFG (Deutsche Forschungsgemeinschaft) grant ZW184/1-1 and -2 to C Zweier
  • ZonMw grant (NWO, 907-00-365) to T Kleefstra

News / Updates

Release 1.0: 2014-12-30: version used in SysID-paper (Download)

Release 1.1: 2015-01-30: updated to 680 and some changes within 650 ID genes

The "primary ID gene" and the "candidate ID gene" lists are updated every 3 to 4 months. The latest date is shown on the first page.


Help

For details on confidence criteria for ID gene list, bipartite classification of ID as well as data implemented in the SysID database see reference (link to reference above)

First steps: Browse our database by gene name, entrez ID or fly-gene specifications or by table or by clicking the symbols in the figure to get ready information on our bipartite classification system.

FAQs:
  • What is the difference between "primary ID genes" and "candidate ID genes"?

"Primary ID genes" are published ID genes that are confirmed by a sufficient number of patients with mutations and/or by sufficient clinical information. "Candidate ID genes" are ID genes that are published but do not yet fulfill criteria to be in the "primary ID gene" list. For detailed inclusion criteria see also the Reference above. Please note that clinical classes and accompanying phenotypes are only annotated for the "primary ID genes".

  • What does ‘limited confidence criterion’ in disease info and overview stand for?

    This column indicates, whether only a limited number of patients is available for this disorder, thus the clinical information is limited (ticked: true, no tick: false).

  • Why are some accompanying phenotype-symbols in brackets?

    The brackets indicate limited information/number on patients and it is therefore not clear if the accompanying phenotype is a common or typical aspect of the disorder.

  • What does the row ‘orthology relationship’ in the table ‘orthology’ mean?

    It indicates the orthology-relationship human-to-fly; not available means that no orthology is to be determined.

  • What do the different numbers in the Fly screen tables mean?

    Basically 0 = false (no hit), 1 = true (hit); for any lethality in neuronal screen: 1 = partial lethal (with survivors), 2 = total lethal (no survivors).

  • What does ‘flight performance evidence’ in neuronal screen mean?

    Here we indicated the overall tendency of the phenotype(s) over time: phenotypes get worse (= evidence progression); phenotype gets better (= evidence recovery); phenotype stays equal or no phenotype (no evidence).