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).
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:
|NCBI (National Center for Biotechnology Information): gene informaion||http://www.ncbi.nlm.nih.gov/gene|
|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|
|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.
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.
The database was supported by
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.
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.
"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".
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).
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.
It indicates the orthology-relationship human-to-fly; not available means that no orthology is to be determined.
Basically 0 = false (no hit), 1 = true (hit); for any lethality in neuronal screen: 1 = partial lethal (with survivors), 2 = total lethal (no survivors).
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).