https://doi.org/10.1038/d41586-017-07291-9, DOI: https://doi.org/10.1038/d41586-017-07291-9. The three most widely used human gene catalogs [Ensembl ( 4 ), RefSeq ( 5 ), and Vega ( 6 )] together contain a total of 24,500 protein-coding genes. The funding sources had no role in the design of this study and collection, analysis, and interpretation of data and in writing the manuscript. Protein-coding genes: 739 to 822 PCR: PCR is used to measure gene expression. The human genome began with the assumption that our genome contains 100,000 protein-coding genes, and estimates published in the 1990s revised this number slightly downward, usually reporting values between 50,000 and 100,000. doi: 10.1093/dnares/dsv028. doi: 10.1093/nar/gkx1095. PMC The expression for all protein-coding genes in all major tissues and organs in the human body can be explored in this interactive database, including numerous catalogs of proteins expressed in a tissue-restricted manner. Natl Acad. List of human protein-coding genes page 4 covers genes SLC22A7-ZZZ3 NB: Each list page contains 5000 human protein-coding genes, sorted alphanumerically by the HGNC -approved gene symbol. Using GeneBase, a software with a graphical interface able to import and elaborate National Center for Biotechnology Information (NCBI) Gene database entries, we provide tabulated spreadsheets updated to 2019 about human nuclear protein-coding gene data set ready to be used for any type of analysis about genes, transcripts and gene organization. This can be served as a reference for cell line selection for in vitro experiments when studying a specific cancer type. Using GeneBase, a software with a graphical interface able to import and elaborate National Center for Biotechnology Information (NCBI) Gene database entries, we provide tabulated spreadsheets updated to 2019 about human nuclear protein-coding gene data set ready to be used for any type of analysis about genes, transcripts and gene organization. GENCODE - Human Release 43 Human Release 43 (GRCh38.p13) Statistics of this release More information about this assembly (including patches, scaffolds and haplotypes) Go to GRCh37 version of this release GTF / GFF3 files Fasta files Metadata files MeSH NB: Each list page contains 5000 human protein-coding genes, sorted alphanumerically by the, Learn how and when to remove this template message, List of human protein-coding genes page 1, List of human protein-coding genes page 2, List of human protein-coding genes page 3, List of human protein-coding genes page 4, Entrez-Cross Database Query Search System, https://en.wikipedia.org/w/index.php?title=Lists_of_human_genes&oldid=1095516146, This page was last edited on 28 June 2022, at 20:15. PubMed Central Non-coding RNA genes: 323 to 622 The spreadsheets we provide allow the immediate identification of key features of genes or gene elements by simply filtering or ordering the data sets, the access to mRNA data already split to highlight 5 UTR, CDS and 3 UTR and an easy export or import of the data for any further analysis, as for instance general descriptive statistics for human nuclear protein-coding genes and mRNAs, exons, coding-exons and introns summarized here. Dismiss. A-proteins have hydrophobic amino acid compositions . For complete list, see the link in the infobox on the right. This sex chromosome (allosome) is only present in males. Chromosome 1 (human) Chromosome 2 (human) Chromosome 3 (human) Chromosome 4 (human) Chromosome 5 (human) Chromosome 6 (human) Chromosome 7 (human) Chromosome 8 (human) Chromosome 9 (human) Chromosome 10 (human) Epub 2023 Jan 12. Genomics. Nucleic Acids Res. The two initial human genome papers reported 31,000 [ 2] and 26,588 protein-coding genes [ 3 ], and when the more . Bookshelf Kapustin Y, Souvorov A, Tatusova T, Lipman D. Splign: algorithms for computing spliced alignments with identification of paralogs. On the cell line category specific pages, which are accessed by clicking on the piechart or the colored boxes on the Cell Line section page, plots showing the cancer-related pathway (PROGENy) and cytokine (CytoSig) activity relative to the average expression of all analyzed cell lines as the baseline are displayed. 2023 Jan 10;13:1085139. doi: 10.3389/fgene.2022.1085139. Haeussler M, Zweig AS, Tyner C, Speir ML, Rosenbloom KR, Raney BJ, Lee CM, Lee BT, Hinrichs AS, Gonzalez JN, et al. Introduction: MicroRNAs (miRNAs) are small non-coding RNAs that play a key role in post-transcriptional modulation of individual genes' expression. Accounting for just one and a half percent of the human genome, chromosome 21 is infamous for its role in Down syndrome. Funded by the National Human Genome Research Institute (NHGRI), the ENCODE Project set out to systematically identify and catalog all functional elements parts of the genetic blueprint that may be crucial in directing how our cells function present in our DNA. Members of this family maint ain homeostasis by neutralizing overexpressed proteinase activity through their function as suicide substrates. https://doi.org/10.1038/d41586-017-07291-9. The 985 cancer cell lines were analyzed for their representability of the corresponding TCGA disease cohorts. 83, 21252130 (1989). Nucleic Acids Res. "Finishing the Euchromatic Sequence of the Human Genome," Nature 431, 931-945.] ESPRESSO: Robust discovery and quantification of transcript isoforms from error-prone long-read RNA-seq data. Both types of genes can produce non-coding transcripts, but non-coding RNA genes do not produce protein-coding transcripts. For instance, it would easily become possible to explore hypotheses about the correlation of structural details of human nuclear protein-coding genes to their level of expression, exploiting quantitative descriptions of the human transcriptome [13], or to the dosage of metabolites related to enzyme proteins, exploiting quantitative representations of human metabolome in health and disease [14]. In order to make a protein, a molecule closely related to DNA called ribonucleic acid (RNA) first copies the code within DNA. protein-L-isoaspartate (D-aspartate) O-methyltransferase: 5: 20: PCNA: 113: proliferating cell nuclear antigen: 12: 67: PDGFB: 47: platelet-derived growth factor beta . Nucleic Acids Res. Researchers often turn to model organisms to understand the complex molecular mechanisms of the human body. Protein-coding genes: 45 to 73 Here we provide a tabulated set of data about human nuclear protein-coding genes (genes, transcripts and gene features such as exons, coding portion of the exons and introns) derived from advanced parsing of NCBI Gene web site offered in a standard, ready-to-use spreadsheet format. List of human protein-coding genes page 2 covers genes EPHA2-MTNR1B List of human protein-coding genes page 3 covers genes MTO1-SLC22A6 List of human protein-coding genes page 4 covers genes SLC22A7-ZZZ3 NB: Each list page contains 5000 human protein-coding genes, sorted alphanumerically by the HGNC-approved gene symbol. -. Mouse-over reveals the number of genes in each of the three categories. Protein-coding genes: 215 to 256 When the first draft of the human genome sequence published in 2001, there were approximately 30,000-40,000 protein-coding sequences. A genome-wide classification of the protein-coding genes with regard to cell line distribution across all cancer cell lines as well as specificity across 27 cancer types has been performed using between-sample normalized data (nTPM). All the currently (alive/live qualification) available human nuclear gene entries were downloaded from NCBI Gene web site on January 5th, 2019 using the following text query: Homo sapiens [Organism] AND source_genomic [properties] AND alive [property]. The length of the bars visualizes the number of elevated genes in each tissue compared to the tissue with the maximum amount of elevated genes (brain). Open Access Finally the two ranking lists were combined, and cell lines were reordered according to their average rank. Nucleic Acids Res. Humans have about 20,000 protein-coding genes but scientists still know remarkably little about most of the proteins they encode. Comprehensive multi-omic profiling of somatic mutations in malformations of cortical development. Pseudogenes: 574 to 785. 2013;14:R36. These data allowed us to identify novel regulators of cambium activities and many non-coding RNAs that may tune the expression of protein-coding genes. A well-known limit of genome browsers is that the large amount of genome and gene data is not organized in the form of a searchable database, hampering full management of numerical data and free calculations. The transcriptomics analysis covers 1055 human cell lines, corresponding to 27 cancer types, one non-cancerous group and one uncategorised group of cellines, and includes classification based on . -, Haeussler M, Zweig AS, Tyner C, Speir ML, Rosenbloom KR, Raney BJ, Lee CM, Lee BT, Hinrichs AS, Gonzalez JN, et al. Pelleri MC, Cicchini E, Locatelli C, Vitale L, Caracausi M, Piovesan A, Rocca A, Poletti G, Seri M, Strippoli P, et al. One of the most interesting diseases caused by genetic disorders in chromosome 12 is stuttering or stammering. Pseudogenes: 703 to 933. 2018;46:D8D13. Science 244, 217221 (1989). By default, the decoupleR was executed using the top performer methods benchmarked (i.e., mlm for multivariate linear model, ulm for univariate linear model, and wsum for weighted sum) and the results were integrated to obtain a consensus z-score to represent the pathway activity. The best assembled were COX1, COX3, and ND4L, as they have collected more than 90% of the protein-coding-gene length. Protein-coding genes: 1,124 to 1,199 Search human. This section of the Human Protein Atlas focuses on the expression profiles in human tissues of genes both on the mRNA and protein level. 2003, 460464 (2003). 2023 Jan 20;9(3):eabq5072. Click "View all genes" to view a table of human genes. Part of If two predicted genes have been merged to form a new gene, both OLNs are indicated, separated by a slash. Chung C, Yang X, Bae T, Vong KI, Mittal S, Donkels C, Westley Phillips H, Li Z, Marsh APL, Breuss MW, Ball LL, Garcia CAB, George RD, Gu J, Xu M, Barrows C, James KN, Stanley V, Nidhiry AS, Khoury S, Howe G, Riley E, Xu X, Copeland B, Wang Y, Kim SH, Kang HC, Schulze-Bonhage A, Haas CA, Urbach H, Prinz M, Limbrick DD Jr, Gurnett CA, Smyth MD, Sattar S, Nespeca M, Gonda DD, Imai K, Takahashi Y, Chen HH, Tsai JW, Conti V, Guerrini R, Devinsky O, Silva WA Jr, Machado HR, Mathern GW, Abyzov A, Baldassari S, Baulac S; Focal Cortical Dysplasia Neurogenetics Consortium; Brain Somatic Mosaicism Network; Gleeson JG. In the absence of functional data, protein-coding genes may be named in the following ways: Based on recognized structural domains and motifs encoded by the gene (e.g. Non-coding RNA genes: 355 to 1,207 The genes in chromosome 2 span 242 million nucleotide base pairs, which also amounts to about 8% of the human DNA. It is expected that cell lines showing high concordance to the matched TCGA cancer type should present high log2 fold changes of the elevated genes of that TCGA cohort relative to the disease baseline expression. eCollection 2023 Mar 14. Springer Nature. Gao Y, Wang F, Wang R, Kutschera E, Xu Y, Xie S, Wang Y, Kadash-Edmondson KE, Lin L, Xing Y. Sci Adv. KJ901729 - Synthetic construct Homo sapiens clone ccsbBroadEn_11123 CCL25 gene, encodes complete protein. Extensive annotations were added to aid identification of differentially expressed genes, potential gene editing sites, and non-coding gene . This article is an index of lists of human genes. doi: 10.1126/sciadv.abq5072. Genes that make proteins are called protein-coding genes. 28S ribosomal protein L42, mitochondrial is a protein that in humans is encoded by the MRPL42 gene. We use cookies to enhance the usability of our website. Comparison with a previous report of 3years ago [6], which in turn demonstrated important differences with the first analysis of the human genome sequence [10, 11], reveals some substantial changes in relevant parameters such as the number of known, characterized nuclear protein-coding genes (from 18,255 to 19,116), thus now approaching a limit theorized 5years ago [12]; the protein-coding non-redundant transcriptome space (from 53,827,863 to 59,281,518bp, with an increase of 10.1%); number of exons (from 412,641 to 562,164, plus 36.2%, when this number is not collapsed to eliminate redundant exons appearing in more than one mRNA) due to a relevant increase of the number of mRNA isoforms recorded. If you hold your mouse over a symbol, the corresponding organ will be highlighted in the human figure. The .gov means its official. Read more about the different categories of elevated expression here. Maddon, P. J. et al. Chromosome 13, with 3% of the bodys mapped human genome, is usually blamed for childhood obesity and delay in speech development. The human genome is a complete set of nucleic acid sequences for humans, encoded as DNA within the 23 chromosome pairs in cell nuclei and in a small DNA molecule found within individual mitochondria.These are usually treated separately as the nuclear genome and the mitochondrial genome. The assemblage of genes ND5 and ND6 was the worst of all, for which the length was 16% and 27% of the length of the whole gene, respectively. Pseudogenes: 633 to 819. 17 January 2023, Mammalian Genome Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. On average 10% of these genes are located in genomic regions unannotated by 12 other gene catalogs. Cunningham F, Achuthan P, Akanni W, Allen J, Amode MR, Armean IM, Bennett R, Bhai J, Billis K, Boddu S, et al. The genome-wide RNA expression profiles of human protein-coding genes in 18 single cell immune cell types are presented covering various B-cells, T-cells, NK-cells, monocytes, granulocytes and dendritic cells. Non-coding RNA genes: 245 to 973 Protein-coding genes: 862 to 984 "If people like our gene list, then maybe a . Although more than 90% of protein-coding genes in mouse have a 1:1 orthology relationship with a gene in human or rat, we also represent many-to-many 'orthology' relationships. Main summarized data derived from the analysis of our updated and standard-formatted data sets are also provided here, while the data tables remain available for human genome studies. Unmasking the biological function and regulatory mechanism of NOC2L: a novel inhibitor of histone acetyltransferase, Progress towards completing the mutant mouse null resource, Estrogen receptor- signaling in post-natal mammary development and breast cancers, p53 in ferroptosis regulation: the new weapon for the old guardian, Understudied proteins: opportunities and challenges for functional proteomics, An open invitation to the Understudied Proteins Initiative, Sign up for Nature Briefing: Translational Research. Pseudogenes: 545 to 693. Thanks to the mapping of the human genome by bodies such as the Human Genome Project, we now understand the size, variant, function and distribution of the genes inside these chromosomes. Appended below is the summary of each of the chromosomes. The similarity between cell lines and the corresponding TCGA cohort was estimated by two different approaches: For all 1055 analyzed cell lines, the activity of a total of 14 cancer-related pathways were inferred using the PROGENy, a package that relies on biological data mining of publicly available data to obtain cancer-related pathway responsive genes for human and mouse (Schubert M et al. At that time, Consortium researchers had confirmed the existence of 19,599 protein-coding genes in the human genome and identified another 2,188 DNA segments that are predicted to be protein-coding genes. (2018)). You can filter the table results by gene type to show only protein-coding or non-coding genes, or search within the list of human genes by gene name or protein name. Here, RNA-seq profiles of cell lines generated by the HPA (n = 69) and the Cancer Cell Line Encyclopedia (CCLE 2019; n = 1019) were integrated, with the 33 common cell lines averaged for their gene expression. Maria Chiara Pelleri. In addition, data can be exported in other formats and imported in other applications (database management systems, statistical software, genomic tools) for further analysis. Google Scholar. Use of a fluorescent probe which will bind to the target DNA if present (e. a specific gene's reverse transcribed mRNA). The RNA expression levels were determined for all protein-coding genes (n = 20090) across the 1055 human cell lines and the results are presented on the gene summary page of the Cell Lines section as exemplified in the figure below. To calculate the relative pathways activities across all cell lines, the normalized values were centered by subtracting the mean value per gene. Protein-coding genes: 516 to 555 Does the Pachytene Checkpoint, a Feature of Meiosis, Filter Out Mistakes in Double-Strand DNA Break Repair and as a side-Effect Strongly Promote Adaptive Speciation? Voshall A, Moriyama EN. Here they are listed below in order of frequency (1 = most highly researched): TP53 - Encodes the tumour-suppressor protein p53, which is mutated in up to half of all human cancers. A curated database of candidate human ageing-related genes and genes associated with longevity and/or ageing in model organisms. NCBI Resource Coordinators. Human protein-coding genes and gene feature statistics in 2019, https://doi.org/10.1186/s13104-019-4343-8, http://creativecommons.org/licenses/by/4.0/, http://creativecommons.org/publicdomain/zero/1.0/. Non-coding RNA genes: 242 to 1,052 The description of each field is included in the first row of the spreadsheet table. Strittmatter, W. J. et al. 2019;47:D853D858. 99.4% of the bodys euchromatic DNA is located in chromosome 20. Epub 2012 Jun 18. statement and Eye Retina Heart Skeletal muscle Smooth muscle Adrenal gland Parathyroid gland Thyroid gland Pituitary gland Lung Bone marrow (2021)). Identification of minimal eukaryotic introns through GeneBase, a user-friendly tool for parsing the NCBI Gene databank. London: IntechOpen; 2018. p. 1536. Internet Explorer). Sci. eCollection 2022. Non-coding RNA genes: 271 to 1,060 Disclaimer. In addition, based on biological data mining, for each cell line, the relative activity of 14 cancer-related pathways and 43 cytokines were inferred and presented to characterize the phenotype of the cell line. Database resources of the national center for biotechnology information. If you continue, we'll assume that you are happy to receive all cookies. Morgan, T. H. Science 32, 120122 (1910). It is broadly suspected that a large fraction of these entries is simply spurious ORFs, because they show no evidence of evolutionary conservation. Measures about 78 megabases in length and contains around 2.7% of our genetic library. Non-coding RNA genes: 299 to 894 USA 90, 19771981 (1993). Nucleic Acids Res. Homo sapiens (human) long intergenic non-protein coding RNA 32 (LINC00032) sequence is a product of NONHSAG051958.2, E, LINC00032, lnc-EQTN-1, ENSG00000291187.1 genes. The colored bars represent number of genes with elevated expression in the associated tissue divided into tissue enriched (red), group enriched (orange) or tissue enhanced (purple) categories according to the transcriptomics based specificity classification. In addition, following analysis based on the relationships between different data tables provided by the database at the core of the GeneBase tool, we provide the results in the simple form of a spreadsheet table, providing three data sets ready to be used for any type of analysis of the data about nuclear protein-coding genes, transcripts and gene organization (exons, coding exons and introns). Privacy Pseudogenes: 1,113 to 1,426. Friedrich, G. & Soriano, P. Genes Dev. Piovesan, A., Antonaros, F., Vitale, L. et al. Before Genome Biol. Pseudogenes: 666 to 839. The protein expression data from 44 normal human tissue types is derived from antibody-based protein profiling using conventional and multiplex immunohistochemistry. if a gene is enriched in cellines from a particular cancer type (specificity), which genes have a similar expression profile across the cell lines (expression cluster), the catalogue of genes elevated in each of the cell lines, which cell line has the most consistent expression profile to its corresponding TCGA disease cohort (i.e., the best cell lines for cancer study), cancer-related pathway and cytokine activity of each cell line, (i) classify the gene expression specificity in different cancer types and the distribution across all cell lines, (ii) evaluate the consistency between the cell lines and the corresponding TCGA disease cohort, (iii) estimate the cancer-related pathway (PROGENy) and cytokine (CytoSig) activity (with non-protein-coding genes included for calculation), (iv) find the highest correlating genes and further to classify all genes according to their cell line-specific expression. Following validation by the software Splign [8], we confirm that there are no human (and possibly of any species) introns shorter than 30bp (Table2). and transmitted securely. Several miRNA variants from different populations are known to be associated with an increased risk of rheumatoid arthritis (RA). Manage cookies/Do not sell my data we use in the preference centre. The activity of 43 CytoSig cytokines was inferred based on the gene expression profile of the 1055 cell lines by the package CytoSig (Jiang P et al. Google Scholar. Baker, S. J. et al. It is also not too different from chromosome 9 found in baboons and macaques. Protein-coding genes: 795 to 912 A well-known limit of genome browsers [1,2,3] is that the large amount of data they provide about human genome and genes is not organized in the form of a searchable database [4], hampering a full management of numerical data and free calculations on data subsets. Also, DESeq2 normalized expression values were centered per gene as suggested. Pseudogenes: 539 to 682. The primary growth genes for cell divisions, which makes them vulnerable to cancers. (i) Spearmans correlation coefficient () between every cancer cell line and its corresponding TCGA cohorts was estimated at the gene level. The Human Protein Atlas project is funded. Non-coding RNA genes: 165 to 404 A genomic coordinate list of these protein-coding genes is available as Table S1. Genes contain nucleotides strands containing instructions on how to generate protein or RNA molecules. Protein-coding genes: 417 to 496
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