datasets/README.md
In soderling-lab/geneLists: tools for mapping gene identifiers and a collection of gene lists in a universal format
Additional Information
Geisinger DBD Genes
A curated resource of human genes associated with ID, autism, ADHD,
schizophrenia, bipolar disorder, and epilepsy. This dataset includes
both loss of function and missense mutations associated with DBDs.
| ID/DD| Autism| Epilepsy| ADHD| Schizophrenia| Bipolar Disorder|
|-----:|------:|--------:|----:|-------------:|----------------:|
| 74| 287| 13| 215| 331| 70|
DisGeneNET DBD Genes
A database of gene-disease associations from public data sources
and the literature. Includes data from UniProt, CGI, ClinGen, Genomics England
Panel App, PsyGeNET, Orphanet, HPO, and CTD. Genes compiled using the
BeFree System are extracted from MEDLINE abstracts.
| autism| intellectual disability| attention deficit hyperactivity disorder| schizophrenia| bipolar disorder| epilepsy|
|------:|-----------------------:|----------------------------------------:|-------------:|----------------:|--------:|
| 433| 1279| 308| 1028| 513| 804|
SFARI ASD Genes
SFARI is an online database of human and animal genes associated with autism.
| Human Gene | Animal Gene|
|-----------:|-----------:|
| 859| 189|
University of Rochester Medical Center DBD Genes
The University of Rochester Medical Center (URMC)
Developmental Brain Disorders Database (DBDB) is a databse of
DBD-associated genes intended for use by clinician-scientists.
| autism| intellectual disability| epilepsy|
|------:|-----------------------:|--------:|
| 52| 239| 143|
Gene2Phenotype DBD Genes
G2P is an online database designed to facilitate the
development, validation, curation and distribution of large-scale,
evidence-based datasets for use in diagnostic variant filtering. Each G2P entry
associates an allelic requirement and a mutational consequence at a defined
locus with a disease entity. A confidence level and evidence link are assigned
to each entry. The Developmental Disease (DD) database used to identify genes
associated with autism, intellectual disability, and epilepsy was curated
by Helen V Firth and David FitzPatrick.
| autism| intellectual disability| epilepsy|
|------:|-----------------------:|--------:|
| 16| 126| 54|
Sanders et al., 2015. ASD Genes
Analysis of de novo CNVs (dnCNVs) from the full Simons Simplex
Collection (SSC) (N = 2,591 families) provides strong evidence
that de novo mutations are associated with ASD apart from the
risk for intellectual disability. Extending the transmission
and de novo association test (TADA) to include small de novo
deletions reveals 71 ASD risk loci, and 65 risk genes (FDR ≤ 0.1).
These genes were mapped to 67 homologous mouse ASD-genes.
| autism|
|------:|
| 67|
Satterstrom et al., 2020 ASD Genes
Satterstrom et al., present the largest exome sequencing study of autism spectrum
disorder (ASD) to date (n = 35,584 total samples, 11,986 with ASD). The authors
identify 102 risk genes (FDR<0.1). These risk genes appear to be expressed early in
brain development, and involved in neurodevelopmental and neuronal communication.
In cells from the human cortex, risk genes are enriched in excitatory and inhibitory
neuronal cell lineages.
| autism|
|------:|
| 96|
Wang et al., 2017 Epilepsy Genes
Genes associated with human epilepsies were compiled from the
literature and several online databases.
| Epilepsy Syndromes | Neurodevelopment| Epilepsy-Related| Potential| All|
|-------------------:|----------------:|----------------:|---------:|---:|
| 80| 222| 513| 251| 915|
Geladaki et al., 2019 HyperLopitDC
Geladaki et al., develop the LOPIT-DC method to identify the subcellular
localization of proteins in complex biological samples.
Velmeshev et al., 2019 ASD DEGs
Differentially expressed genes identified by single cell RNA
sequencing of Human ASD brain samples. Human genes were mapped to
433 mouse genes that are differentially expressed genes (DEGs).
|Cell Type | N Genes|
|:-----------------------|-------:|
|AST-FB DEGs | 14|
|AST-PP DEGs | 44|
|Endothelial DEGs | 55|
|IN-PV DEGs | 27|
|IN-SST DEGs | 26|
|IN-SV2C DEGs | 32|
|IN-VIP DEGs | 71|
|L2/3 DEGs | 91|
|L4 DEGs | 78|
|L5/6 DEGs | 8|
|L5/6-CC DEGs | 16|
|Microglia DEGs | 64|
|Neu-mat DEGs | 2|
|Neu-NRGN-I DEGs | 12|
|Neu-NRGN-II DEGs | 23|
|Oligodendrocytes DEGs | 13|
|OPC DEGs | 2|
|ASD DEGs | 433|
|ASD Up-regulated DEGs | 388|
|ASD Down-regulated DEGs | 190|
Velmeshev et al., 2019 Cell Types
Cell types defined by single cell RNA sequencing of human brains.
|Cell Type | Genes|
|:----------------|-----:|
|AST-FB | 2448|
|AST-PP | 5116|
|Endothelial | 1114|
|IN-PV | 1937|
|IN-SST | 2096|
|IN-SV2C | 1008|
|IN-VIP | 3259|
|L2/3 | 7024|
|L4 | 3528|
|L5/6 | 1727|
|L5/6-CC | 2343|
|Microglia | 1509|
|Neu-mat | 2148|
|Neu-NRGN-I | 1514|
|Neu-NRGN-II | 3586|
|Oligodendrocytes | 5767|
|OPC | 5333|
Koopman et al., 2019 SynGO Database
Compiled genes from the SynGO database.
Sharma et al., 2015 Mouse Brain Proteome
Sharma et al., performed high-resolution mass spectrometry proteomics
to obtain an in-depth profile of the mouse brain proteome. A
comparison of all proteins identified and with transcriptome data
indicates that a deep coverage of the total mouse brain proteome
was achieved. Below is a summary of brain region-specific
proteins (FE>10).
|Brain Region | Genes|
|:-------------------|-----:|
|Total Brain | 2872|
|Brainstem | 499|
|Cerebellum | 2241|
|Corpus Callosum | 3|
|Hippocampus | 358|
|Motor Cortex | 382|
|Olfactory Bulb | 799|
|Optic Nerve | 586|
|Striatum | 156|
|Thalamus | 1|
Uezu et al., 2016 iPSD Proteome
A proteome of the inhbitory post-synaptic density (iPSD) generated by
in vivo proximity proteomics. Summary of iPSD identified by Arhgef9,
Gephyrin, and InSyn1 iBioID:
| Arhgef9| Gphn| InSyn1| iPSD|
|-------:|----:|------:|----:|
| 74| 90| 85| 181|
Compiled iPSD Proteome
A inhibitory postsynaptic (iPSD) proteome compiled from 5 different studies.
| Heller et al., 2012| Kang et al., 2014| Loh et al., 2016| Nakamura et al., 2016| Uezu et al., 2016| All Studies|
|-------------------:|-----------------:|----------------:|---------------------:|-----------------:|-----------:|
| 18| 74| 38| 171| 181| 413|
Wilkinson Synaptic GAP/GEF Proteome
Proteome of synaptic GAPs and GEFs.
| Syngap1| Agap2| Kalrn|
|-------:|-----:|-----:|
| 124| 103| 53|
Iossifov et al., 2014 ASD Genes
310 mouse genes likely disrupting gene disrupting mutations in human
individuals with autism.
De Rubeis et al., 2014 ASD Genes
93 Autism associated genes.
Fromer et al., 2014 ASD Genes
419 genes
Additional Studies and DBD associated genes compiled by Fromer et al.,:
|Study |Reference | N Genes|
|:-----------------|:------------------------------------------------------------|-------:|
|arrabroadwave3ASD |ref^ | 58|
|deligt2012ID |ref | 55|
|girard2011SZ |ref | 14|
|gulsuner2013SZ |ref | 64|
|iossifov2012ASD |ref | 230|
|neale2012ASD |ref | 103|
|oroak2012ASD |ref | 167|
|rauch2012ID |ref | 69|
|sanders2012ASD |ref | 127|
|xu2012SZ |ref | 119|
^ ARRA Autism Sequencing Colloraboration
SynSysNet Synaptic Protein Tree
|Category | N Genes|
|:----------------------------------|-------:|
|post:CELL ADH TRANS SIGN | 131|
|post:CELL METABOLISM | 183|
|post:ENDOCYTOSIS | 22|
|post:EXCITABILITY | 33|
|post:EXOCYTOSIS | 25|
|post:GPCR SIGNALING | 30|
|post:INTRACELL SIGN TRANSDUC | 297|
|post:INTRACELLULAR TRAFFICKING | 47|
|post:ION BALANCE/TRANSPORT | 100|
|post:LGIC SIGNALING | 54|
|post:NEUROTRANSMITTER METABOLISM | 8|
|post:PEPTIDE/NEUROTROPHIN SIGNALS | 3|
|post:PROT CLUST | 103|
|post:RPSFB | 228|
|post:STRUCTURAL PLASTICITY | 174|
|post:TYR KINASE SIGN | 32|
|post:TYR KINASE SIGNALING | 9|
|post:UNKNOWN | 123|
|pre:CELL ADH TRANS SIGN | 104|
|pre:CELL METABOLISM | 4|
|pre:ENDOCYTOSIS | 105|
|pre:EXCITABILITY | 94|
|pre:EXOCYTOSIS | 186|
|pre:G-PROTEIN RELAY | 53|
|pre:GPCR SIGNALING | 87|
|pre:INTRACELL SIGN TRANSDUC | 230|
|pre:INTRACELLULAR TRAFFICKING | 132|
|pre:ION BALANCE/TRANSPORT | 22|
|pre:LGIC SIGNALING | 78|
|pre:NEUROTRANSMITTER METABOLISM | 42|
|pre:PEPTIDE/NEUROTROPHIN SIGNALS | 75|
|pre:PROT CLUST | 71|
|pre:STRUCTURAL PLASTICITY | 155|
|pre:UNKNOWN | 82|
|unspec:CELL ADH TRANS SIGN | 77|
|unspec:ENDOCYTOSIS | 55|
|unspec:EXCITABILITY | 58|
|unspec:EXOCYTOSIS | 119|
|unspec:G-PROTEIN RELAY | 105|
|unspec:GPCR SIGNALING | 17|
|unspec:INTRACELL SIGN TRANSDUC | 241|
|unspec:INTRACELLULAR TRAFFICKING | 84|
|unspec:ION BALANCE/TRANSPORT | 41|
|unspec:LGIC SIGNALING | 83|
|unspec:NEUROTRANSMITTER METABOLISM | 17|
|unspec:PROT CLUST | 117|
|unspec:STRUCTURAL PLASTICITY | 139|
|unspec:UNKNOWN | 100|
|post | 693|
|pre | 752|
|unspec | 602|
soderling-lab/geneLists documentation built on Sept. 6, 2021, 8:22 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Additional Information
Geisinger DBD Genes
A curated resource of human genes associated with ID, autism, ADHD, schizophrenia, bipolar disorder, and epilepsy. This dataset includes both loss of function and missense mutations associated with DBDs.
| ID/DD| Autism| Epilepsy| ADHD| Schizophrenia| Bipolar Disorder| |-----:|------:|--------:|----:|-------------:|----------------:| | 74| 287| 13| 215| 331| 70|
DisGeneNET DBD Genes
A database of gene-disease associations from public data sources and the literature. Includes data from UniProt, CGI, ClinGen, Genomics England Panel App, PsyGeNET, Orphanet, HPO, and CTD. Genes compiled using the BeFree System are extracted from MEDLINE abstracts.
| autism| intellectual disability| attention deficit hyperactivity disorder| schizophrenia| bipolar disorder| epilepsy| |------:|-----------------------:|----------------------------------------:|-------------:|----------------:|--------:| | 433| 1279| 308| 1028| 513| 804|
SFARI ASD Genes
SFARI is an online database of human and animal genes associated with autism.
| Human Gene | Animal Gene| |-----------:|-----------:| | 859| 189|
University of Rochester Medical Center DBD Genes
The University of Rochester Medical Center (URMC) Developmental Brain Disorders Database (DBDB) is a databse of DBD-associated genes intended for use by clinician-scientists.
| autism| intellectual disability| epilepsy| |------:|-----------------------:|--------:| | 52| 239| 143|
Gene2Phenotype DBD Genes
G2P is an online database designed to facilitate the development, validation, curation and distribution of large-scale, evidence-based datasets for use in diagnostic variant filtering. Each G2P entry associates an allelic requirement and a mutational consequence at a defined locus with a disease entity. A confidence level and evidence link are assigned to each entry. The Developmental Disease (DD) database used to identify genes associated with autism, intellectual disability, and epilepsy was curated by Helen V Firth and David FitzPatrick.
| autism| intellectual disability| epilepsy| |------:|-----------------------:|--------:| | 16| 126| 54|
Sanders et al., 2015. ASD Genes
Analysis of de novo CNVs (dnCNVs) from the full Simons Simplex Collection (SSC) (N = 2,591 families) provides strong evidence that de novo mutations are associated with ASD apart from the risk for intellectual disability. Extending the transmission and de novo association test (TADA) to include small de novo deletions reveals 71 ASD risk loci, and 65 risk genes (FDR ≤ 0.1). These genes were mapped to 67 homologous mouse ASD-genes.
| autism| |------:| | 67|
Satterstrom et al., 2020 ASD Genes
Satterstrom et al., present the largest exome sequencing study of autism spectrum disorder (ASD) to date (n = 35,584 total samples, 11,986 with ASD). The authors identify 102 risk genes (FDR<0.1). These risk genes appear to be expressed early in brain development, and involved in neurodevelopmental and neuronal communication. In cells from the human cortex, risk genes are enriched in excitatory and inhibitory neuronal cell lineages.
| autism| |------:| | 96|
Wang et al., 2017 Epilepsy Genes
Genes associated with human epilepsies were compiled from the literature and several online databases.
| Epilepsy Syndromes | Neurodevelopment| Epilepsy-Related| Potential| All| |-------------------:|----------------:|----------------:|---------:|---:| | 80| 222| 513| 251| 915|
Geladaki et al., 2019 HyperLopitDC
Geladaki et al., develop the LOPIT-DC method to identify the subcellular localization of proteins in complex biological samples.
Velmeshev et al., 2019 ASD DEGs
Differentially expressed genes identified by single cell RNA sequencing of Human ASD brain samples. Human genes were mapped to 433 mouse genes that are differentially expressed genes (DEGs).
|Cell Type | N Genes| |:-----------------------|-------:| |AST-FB DEGs | 14| |AST-PP DEGs | 44| |Endothelial DEGs | 55| |IN-PV DEGs | 27| |IN-SST DEGs | 26| |IN-SV2C DEGs | 32| |IN-VIP DEGs | 71| |L2/3 DEGs | 91| |L4 DEGs | 78| |L5/6 DEGs | 8| |L5/6-CC DEGs | 16| |Microglia DEGs | 64| |Neu-mat DEGs | 2| |Neu-NRGN-I DEGs | 12| |Neu-NRGN-II DEGs | 23| |Oligodendrocytes DEGs | 13| |OPC DEGs | 2| |ASD DEGs | 433| |ASD Up-regulated DEGs | 388| |ASD Down-regulated DEGs | 190|
Velmeshev et al., 2019 Cell Types
Cell types defined by single cell RNA sequencing of human brains.
|Cell Type | Genes| |:----------------|-----:| |AST-FB | 2448| |AST-PP | 5116| |Endothelial | 1114| |IN-PV | 1937| |IN-SST | 2096| |IN-SV2C | 1008| |IN-VIP | 3259| |L2/3 | 7024| |L4 | 3528| |L5/6 | 1727| |L5/6-CC | 2343| |Microglia | 1509| |Neu-mat | 2148| |Neu-NRGN-I | 1514| |Neu-NRGN-II | 3586| |Oligodendrocytes | 5767| |OPC | 5333|
Koopman et al., 2019 SynGO Database
Compiled genes from the SynGO database.
Sharma et al., 2015 Mouse Brain Proteome
Sharma et al., performed high-resolution mass spectrometry proteomics to obtain an in-depth profile of the mouse brain proteome. A comparison of all proteins identified and with transcriptome data indicates that a deep coverage of the total mouse brain proteome was achieved. Below is a summary of brain region-specific proteins (FE>10).
|Brain Region | Genes| |:-------------------|-----:| |Total Brain | 2872| |Brainstem | 499| |Cerebellum | 2241| |Corpus Callosum | 3| |Hippocampus | 358| |Motor Cortex | 382| |Olfactory Bulb | 799| |Optic Nerve | 586| |Striatum | 156| |Thalamus | 1|
Uezu et al., 2016 iPSD Proteome
A proteome of the inhbitory post-synaptic density (iPSD) generated by in vivo proximity proteomics. Summary of iPSD identified by Arhgef9, Gephyrin, and InSyn1 iBioID:
| Arhgef9| Gphn| InSyn1| iPSD| |-------:|----:|------:|----:| | 74| 90| 85| 181|
Compiled iPSD Proteome
A inhibitory postsynaptic (iPSD) proteome compiled from 5 different studies.
| Heller et al., 2012| Kang et al., 2014| Loh et al., 2016| Nakamura et al., 2016| Uezu et al., 2016| All Studies| |-------------------:|-----------------:|----------------:|---------------------:|-----------------:|-----------:| | 18| 74| 38| 171| 181| 413|
Wilkinson Synaptic GAP/GEF Proteome
Proteome of synaptic GAPs and GEFs.
| Syngap1| Agap2| Kalrn| |-------:|-----:|-----:| | 124| 103| 53|
Iossifov et al., 2014 ASD Genes
310 mouse genes likely disrupting gene disrupting mutations in human individuals with autism.
De Rubeis et al., 2014 ASD Genes
93 Autism associated genes.
Fromer et al., 2014 ASD Genes
419 genes
Additional Studies and DBD associated genes compiled by Fromer et al.,:
|Study |Reference | N Genes| |:-----------------|:------------------------------------------------------------|-------:| |arrabroadwave3ASD |ref^ | 58| |deligt2012ID |ref | 55| |girard2011SZ |ref | 14| |gulsuner2013SZ |ref | 64| |iossifov2012ASD |ref | 230| |neale2012ASD |ref | 103| |oroak2012ASD |ref | 167| |rauch2012ID |ref | 69| |sanders2012ASD |ref | 127| |xu2012SZ |ref | 119| ^ ARRA Autism Sequencing Colloraboration
SynSysNet Synaptic Protein Tree
|Category | N Genes| |:----------------------------------|-------:| |post:CELL ADH TRANS SIGN | 131| |post:CELL METABOLISM | 183| |post:ENDOCYTOSIS | 22| |post:EXCITABILITY | 33| |post:EXOCYTOSIS | 25| |post:GPCR SIGNALING | 30| |post:INTRACELL SIGN TRANSDUC | 297| |post:INTRACELLULAR TRAFFICKING | 47| |post:ION BALANCE/TRANSPORT | 100| |post:LGIC SIGNALING | 54| |post:NEUROTRANSMITTER METABOLISM | 8| |post:PEPTIDE/NEUROTROPHIN SIGNALS | 3| |post:PROT CLUST | 103| |post:RPSFB | 228| |post:STRUCTURAL PLASTICITY | 174| |post:TYR KINASE SIGN | 32| |post:TYR KINASE SIGNALING | 9| |post:UNKNOWN | 123| |pre:CELL ADH TRANS SIGN | 104| |pre:CELL METABOLISM | 4| |pre:ENDOCYTOSIS | 105| |pre:EXCITABILITY | 94| |pre:EXOCYTOSIS | 186| |pre:G-PROTEIN RELAY | 53| |pre:GPCR SIGNALING | 87| |pre:INTRACELL SIGN TRANSDUC | 230| |pre:INTRACELLULAR TRAFFICKING | 132| |pre:ION BALANCE/TRANSPORT | 22| |pre:LGIC SIGNALING | 78| |pre:NEUROTRANSMITTER METABOLISM | 42| |pre:PEPTIDE/NEUROTROPHIN SIGNALS | 75| |pre:PROT CLUST | 71| |pre:STRUCTURAL PLASTICITY | 155| |pre:UNKNOWN | 82| |unspec:CELL ADH TRANS SIGN | 77| |unspec:ENDOCYTOSIS | 55| |unspec:EXCITABILITY | 58| |unspec:EXOCYTOSIS | 119| |unspec:G-PROTEIN RELAY | 105| |unspec:GPCR SIGNALING | 17| |unspec:INTRACELL SIGN TRANSDUC | 241| |unspec:INTRACELLULAR TRAFFICKING | 84| |unspec:ION BALANCE/TRANSPORT | 41| |unspec:LGIC SIGNALING | 83| |unspec:NEUROTRANSMITTER METABOLISM | 17| |unspec:PROT CLUST | 117| |unspec:STRUCTURAL PLASTICITY | 139| |unspec:UNKNOWN | 100| |post | 693| |pre | 752| |unspec | 602|
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