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Where to download gene list of human genome?

Where to download gene list of human genome?


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I am looking for a place where I can download a full gene list of human genome. Either by HGNC symbol or ensemble ID as long as it is usable on the consensusPathdatabase. Up until this point I have only found fasta files which include a bit too much information and unfortunately not in the format I would like. I am not in the biology field myself so if I am asking for something unreasonable call me out on it!

Reason for this is I am trying to stress test an application that uses the output tabular forms from the gene set analysis tool on consensusPathbase. The stress test on the entire human genome seemed to be the best option as a bigger data set than that will probably not occur.

Thanks in advance


The database you are looking for is ensembl [Yates (2016)].

Go here and chose Customise your download. There you can select a dataset (e.g. genes and then specify human genes - currently uses build GRCh38; you can also go the same way here to do the same for hg19/GRCh37).

After chosing your dataset, you can click on Attributes to specify what to include in your download (HGNC symbols, IDs, regions, GO terms, and a ton of other stuff), click on Filters to apply filters to your choices (only genes from a chromosome, region, and a ton of other stuff).

Then click Results and download your selection in a format of choice.

(Hint: click Count first and use it as a a sanity check to see if the number of selected genes fits your expectation.)


Where to download gene list of human genome? - Biology

The gene association files ingested from GO Consortium members are shown in the table below. Files are in the GO annotation file format and are compressed using the UNIX gzip utility. Please see the upstream resource information for further details on the annotation set. Any errors or omissions in annotations should be reported by writing to the GO Helpdesk.

Filtered Files

These files are taxon-specific and reflect the work of specific projects, primarily the model organisms database groups, to provide comprehensive, non-redundant annotation files for their organism. All the files in this table have been filtered using the annotation file QC pipeline. A major component to the filtering is the requirement that particular taxon IDs can only be included within the association files provided by specific projects the current list of authoritative groups and major model organisms can be found below.

Filtered Annotation File Downloads for 2021-06-16 release

Species/Database Entity type Annotations File
Species/Database Entity type Annotations File
Gallus gallus
EBI Gene Ontology Annotation Database (goa)
rna 2132 goa_chicken_rna.gaf (gzip)
Sus scrofa
EBI Gene Ontology Annotation Database (goa)
isoform 78385 goa_pig_isoform.gaf (gzip)
Dictyostelium discoideum
dictyBase (dictyBase)
n/a 64219 dictybase.gaf (gzip)
Mus musculus
Mouse Genome Informatics (mgi)
n/a 400701 mgi.gaf (gzip)
Aspergillus nidulans
Aspergillus Genome Database (aspgd)
n/a 640417 aspgd.gaf (gzip)
Solanaceae
Sol Genomics Network (sgn)
gene 1362 sgn.gaf (gzip)
Sus scrofa
EBI Gene Ontology Annotation Database (goa)
protein 132126 goa_pig.gaf (gzip)
Gallus gallus
EBI Gene Ontology Annotation Database (goa)
complex 25 goa_chicken_complex.gaf (gzip)
Danio rerio
Zebrafish Information Network (zfin)
n/a 183069 zfin.gaf (gzip)
Bos taurus
EBI Gene Ontology Annotation Database (goa)
rna 9974 goa_cow_rna.gaf (gzip)
Multi-species
Encyclopedia of E. coli metabolism (ecocyc)
n/a 53234 ecocyc.gaf (gzip)
Rattus norvegicus
Rat Genome Database (rgd)
n/a 374728 rgd.gaf (gzip)
Saccharomyces cerevisiae
Saccharomyces Genome Database (sgd)
n/a 104536 sgd.gaf (gzip)
Schizosaccharomyces pombe
PomBase (pombase)
n/a 41860 pombase.gaf (gzip)
Pseudomonas aeruginosa
Pseudomonas Genome Project (pseudocap)
n/a 3630 pseudocap.gaf (gzip)
Sus scrofa
EBI Gene Ontology Annotation Database (goa)
complex 13 goa_pig_complex.gaf (gzip)
Drosophila melanogaster
FlyBase (fb)
n/a 88267 fb.gaf (gzip)
Homo sapiens
EBI Gene Ontology Annotation Database (goa)
protein 554219 goa_human.gaf (gzip)
Caenorhabditis elegans
WormBase database of nematode biology (wb)
n/a 97568 wb.gaf (gzip)
Canis lupus familiaris
EBI Gene Ontology Annotation Database (goa)
isoform 75195 goa_dog_isoform.gaf (gzip)
Bos taurus
EBI Gene Ontology Annotation Database (goa)
protein 139347 goa_cow.gaf (gzip)
Multi-species
GeneDB (genedb)
n/a 6284 genedb_lmajor.gaf (gzip)
Canis lupus familiaris
EBI Gene Ontology Annotation Database (goa)
rna 14115 goa_dog_rna.gaf (gzip)
Homo sapiens
EBI Gene Ontology Annotation Database (goa)
complex 2082 goa_human_complex.gaf (gzip)
Bos taurus
EBI Gene Ontology Annotation Database (goa)
complex 12 goa_cow_complex.gaf (gzip)
Canis lupus familiaris
EBI Gene Ontology Annotation Database (goa)
complex 0 goa_dog_complex.gaf (gzip)
Bos taurus
EBI Gene Ontology Annotation Database (goa)
isoform 45658 goa_cow_isoform.gaf (gzip)
Multi-species
Reactome - a curated knowledgebase of biological pathways (reactome)
n/a 98980 reactome.gaf (gzip)
Gallus gallus
EBI Gene Ontology Annotation Database (goa)
isoform 29839 goa_chicken_isoform.gaf (gzip)
Sus scrofa
EBI Gene Ontology Annotation Database (goa)
rna 21926 goa_pig_rna.gaf (gzip)
Homo sapiens
EBI Gene Ontology Annotation Database (goa)
isoform 142412 goa_human_isoform.gaf (gzip)
Multi-species
Candida Genome Database (cgd)
n/a 356059 cgd.gaf (gzip)
Gallus gallus
EBI Gene Ontology Annotation Database (goa)
protein 104280 goa_chicken.gaf (gzip)
Canis lupus familiaris
EBI Gene Ontology Annotation Database (goa)
protein 124502 goa_dog.gaf (gzip)
Multi-species
GeneDB (genedb)
n/a 19244 genedb_tbrucei.gaf (gzip)
Arabidopsis thaliana
The Arabidopsis Information Resource (tair)
n/a 188515 tair.gaf (gzip)
Homo sapiens
EBI Gene Ontology Annotation Database (goa)
rna 45663 goa_human_rna.gaf (gzip)

Copyright © 1999-2020 the Gene Ontology (CC-BY 4.0)
Helpdesk • Citation/attribution • Terms of use
Member of the Open Biological and Biomedical Ontologies

The Gene Ontology Consortium is supported by a P41 grant from the National Human Genome Research Institute (NHGRI) [grant 5U41HG002273-14]. The Gene Ontology Consortium would like to acknowledge the assistance of many more people than can be listed here. Please visit the annotation contributors page for the full list.


Ontology files: Subsets

GO slims are subsets of terms in the ontology. GO subsets give a broad overview of the ontology content without the detail of the specific fine grained terms. More information in the GO subset guide.

Download GO subsets

The GO subsets in this list are maintained as part of the GO flat file. The files available below for download are generated by script from that file.

Subset name Maintainer File name OBO format OWL format json format
GO slim AGR subset Developed by GO Consortium for the Alliance of Genomes Resources goslim_agr obo owl json
Generic GO subset GO Consortium goslim_generic obo owl json
Aspergillus subset Aspergillus Genome Data goslim_aspergillus obo owl json
Candida albicans subset Candida Genome Database goslim_candida obo owl json
Drosophila subset FlyBase goslim_drosophila obo owl json
Chembl Drug Target subset ChEMBL goslim_chembl obo owl json
Metagenomics subset InterPro group goslim_metagenomic obo owl json
Mouse GO slim Mouse Genome Informatics goslim_mouse obo owl json
Plant subset The Arabidopsis Information Resource goslim_plant obo owl json
Protein Information Resource subset PIR goslim_pir obo owl json
Schizosaccharomyces pombe subset PomBase goslim_pombe obo owl json
Yeast subset Saccharomyces Genome Database goslim_yeast obo owl json

Download GO “anti-slims”

For internal checking purposes, GO maintains two “anti-slims”, terms to which annotations should not be made. “Anti-slim” terms should never be used when creating a subset.

Subset name Usage File name OBO format OWL format json format
Do not annotate The set of high level terms that are useful for grouping, but should have no direct annotations gocheck_do_not_annotate obo owl json
Do not manually annotate The set of high level terms that are useful for grouping, but should have no direct annotations except from automated tools gocheck_do_not_manually_annotate obo owl json


Where to download gene list of human genome? - Biology

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Sandwalk

This week marks the 20th anniversary of the publication of the first drafts of the human genome sequence. Science choose to celebrate the achievement with a series of articles that had little to say about the scientific discoveries arising out of the sequencing project one of the articles praised the opennesss of sequence data without mentioning that the journal had violated its own policy on openness by publishing the Celera sequence [The 20th anniversary of the human genome sequence: 1. Access to the data and the complicity of Science].

I've decided to post a few articles about the human genome beginning with one on finishing the sequence. In this post I'll summarize the latest data on the number of genes in the human genome.

The first drafts of the genome sequence predicted somewhere between 30,000 and 35,000 genes based largely on software predictions. In spite of what you might have read elsewhere, this number was very close to the predictions made by knowledgeable scientists dating back to the 1970s [False history and the number of genes].

We know more about protein-coding genes than noncoding genes. The number of predicted protein-coding genes dropped steadily for about 15 years following publication of the draft sequences but it is beginning to stabilize around 19,500 genes [How many protein-coding genes in the human genome?]. That number is likely to fall to about 19,000 in the future because there are hundreds of predicted protein-coding genes that are missing a protein There will never be an exact number because some people have more genes than others.

The number of noncoding genes is still up in the air. Here's a brief summary of the most likely numbers .

  • unique small RNAs: Humans have genes for a number of unique small RNAs such as the RNA component of RNAse P and the 7SL RNA of signal recognition particle. There are about 30 of these genes.
  • ribosomal RNA genes: There are mutliple copies of the large ribosomal RNA operon and multiple copies of 5S RNA genes. A good estimate of the average number in a typical human genome is about 300.
  • transfer RNA (tRNA) genes: There are at least several hundred tRNA genes in a typical genome. There are also hundreds of pseudogenes.
  • small nuclear RNAs (snRNAs) genes: Some of the main spliceosomal RNAs (U1, U2, U4, U5 and U6) are produced from a single gene but in other cases there are mutliple copies. There are a number of extra spliceosomal RNA genes such as U4atac and U7. The total number of snRNA genes is about 20.
  • small nucleolar RNA (snoRNA) genes: These are genes involved in modifying ribosomal RNAs. There are more than 100 snoRNA genes.
  • microRNA (miRNA) genes: Nobody knows exactly how many miRNA genes there are in the human genome. The predictions range from 100-1000 but the algorithms for detecting these genes aren't very good. It's likely that most of the predicted genes are pseudogenes. A good estimate is 100 miRNA genes.
  • short interfering RNA (siRNA) genes: This is the same situation as with miRNA genes. The best guess is 100 siRNA genes.
  • PIWI-interacting RNA (piRNA) genes: There are several thousand predicted piRNA genes in our genome but it's almost certain that most of them are nonfunctional. It's safe to assume there are about 100 functional genes in this category.
  • long noncoding RNA (lncRNA) genes: This is an extemely heterogeneous category consisting of RNAs that are at least 1000 nucleotides in length with, in most cases, no substantial open reading frame. Some lncRNAs have a function but these are rare. It's likely that there are no more than 1000 lncRNA genes and the remaing transcripts are junk RNA.

The total number of noncoding RNA genes comes to less than 2000 but I usually feel quite generous in estimating this number so let's say that there are about 5,000. If we round up the total number of protein-coding genes to 20,000 then I'm estimating that there are no more than 25,000 genes in our genome.

Most of the sequence databases list more genes and the "extra" genes are mostly noncoding genes for example, Ensembl estimates 23,997 noncding genes in the latest build (GRCh38.p13) [Human assembly and gene annotation]. About 17,000 of these genes are lncRNA genes but there's no evidence that these are functional genes. Until that evidence become available (I'm not holding my breath) we should stick with the best estimate of functional lncRNA genes [How many lncRNAs are functional?] [Functional RNAs?].

Image credit: The figure is from Palazzo and Lee (2015) - a must-read paper for those who are interested in following up on the number of noncoding genes.


Chromosomes

The DNA in a cell is not a single long molecule. It is divided into a number of segments of uneven lengths. At certain points in the life cycle of a cell, those segments can be tightly packed bundles known as chromosomes. During one stage, the chromosomes appear to be X-shaped.

Every fungus, plant, and animal has a set number of chromosomes. For example, humans have 46 chromosomes (23 pairs), rice plants have 24 chromosomes, and dogs have 78 chromosomes.


Role of the human genome in research

Since the 1980s there has been an explosion in genetic and genomic research. The combination of the discovery of the polymerase chain reaction, improvements in DNA sequencing technologies, advances in bioinformatics (mathematical biological analysis), and increased availability of faster, cheaper computing power has given scientists the ability to discern and interpret vast amounts of genetic information from tiny samples of biological material. Further, methodologies such as fluorescence in situ hybridization (FISH) and comparative genomic hybridization (CGH) have enabled the detection of the organization and copy number of specific sequences in a given genome.

Understanding the origin of the human genome is of particular interest to many researchers since the genome is indicative of the evolution of humans. The public availability of full or almost full genomic sequence databases for humans and a multitude of other species has allowed researchers to compare and contrast genomic information between individuals, populations, and species. From the similarities and differences observed, it is possible to track the origins of the human genome and to see evidence of how the human species has expanded and migrated to occupy the planet.


Where to download gene list of human genome? - Biology

  • All MGI Reports
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  • Deciphering the Mechanisms of Developmental Disorders (DMDD)
  • Contributed Data Sets
  • Community Links

For Mus musculus Build GRCm39 patch information and statistics, see The Genome Reference Consortium web site. MGI now incorporates strain genome data of de novo sequenced mouse strains from the Wellcome Sanger Institute's Mouse Genomes Project (MGP) and the European Bioinformatics Institute (EBI). Genome feature annotations are provided by the GENCODE consortium, the University of California Santa Cruz (UCSC) Genome Browser Group and the Mouse Genomes Project. Browse strain genome features using the Multiple Genome Viewer (MGV).

MGI contains information about mouse genes, DNA segments, cytogenetic markers and QTLs. Each record may include the marker symbol, name, other names or symbols and synonyms, nomenclature history, alleles, STSs, chromosomal assignment, centimorgan location, cytogenetic band, EC number (for enzymes), phenotypic classifications, human disease data, Gene Ontology (GO) terms, MGI accession IDs and supporting references. See Interpreting a Genes and Markers Summary and Interpreting Gene Details for more information about the content of the display of a marker record as it appears in the query results.

MGI contains a variety of maps and mapping data. Users can create graphical displays of genome features on the mouse genome using the JBrowse Genome Browser. A variety of types of Genetic Mapping Data are available from marker detail pages, including data from genetic linkage crosses, cytogenetic localization, recombinant inbred and recombinant congenic strains, and radiation hybrid mapping.


Maize (Zea mays) is the most produced (as measured by tonnes) staple crop world-wide and has been the focus of intense breeding efforts to improve agronomic traits for centuries. However, the genetic basis of numerous phenotypes is still unknown and genomic tools provide a valuable resource to accelerate breeding efforts. To facilitate breeding and research efforts in maize, we analyzed publicly available transcriptomic data for the reference maize inbred, B73, and developed the Maize Genomics Resource (MGR).

Transcriptomic data from the developmental B73 gene atlas and several B73 abiotic and biotic stress experiments (for complete list see here) were aligned to the AGPv4 B73 genome assembly and gene expression was quantified using the Zm00001d.1 gene annotation. Differential and co-expression analyses were conducted, and orthologous genes were characterized. The data was also deployed to the Bio-Analytic Resource for Plant Biology (BAR) eFP browser and new AGPv4 views were developed. The MGR consists of a set of search and query tools to quickly access this information via a BLAST server, genome browser, and gene report pages. Bulk data are also available for download.

This work was funded by the Department of Energy Great Lakes Bioenergy Research Center (DOE BER Office of Science DE-FC02-07ER64494), the National Science Foundation Plant Genome Research Program (IOS- 1546657), and the Michigan State University Foundation.

When using data and analyses from the Maize Genomic Resource (MGR), please cite the following publication: