human protein coding genes list

17 January 2023, Mammalian Genome CAS A gene is a string of DNA that encodes the information necessary to make a protein, which then goes on to perform some function within our cells. 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. The three main human databases (GENCODE/Ensembl, RefSeq, UniProtKB) contain a total of 22,210 protein-coding genes but only 19,446 of these genes are found in all three databases. Google Scholar. The track includes both protein-coding genes and non-coding RNA genes. Part of Genomics. PMC Article Protein-coding genes: 1,024 to 1,085 The genes in chromosome 2 span 242 million nucleotide base pairs, which also amounts to about 8% of the human DNA. The clustering of 19023 genes expressed in tissues resulted in 89 expression clusters, which have been manually annotated to describe common features in terms of function and specificity. The UDN has allowed us to delve much deeper, beyond standard clinical testing. The primary growth genes for cell divisions, which makes them vulnerable to cancers. 2018;46:D8D13. Pseudogenes: 736 to 911. If two predicted genes have been merged to form a new gene, both OLNs are indicated, separated by a slash. In an additional analysis of the 2415 protein-coding genes differentially expressed over time, we performed an ORA enrichment of genes related to immune functions. Non-coding RNA genes: 165 to 404 2001;107:88191. Mouse-over reveals the number of genes in each of the three categories. eCollection 2023 Mar 14. A number of 2685 genes are classified as brain elevated and 202 genes were only detected in the brain. Pseudogenes: 761 to 902. The results are presented as an interactive UMAP plot in which mouse-over displays general information for the clusters and the clicking on a cluster will display more information and plots regarding that specific cluster, as well as, a clickable list of all clusters. Non-coding RNA genes: 277 to 993 Here we review the main computational pipelines used to generate the human reference protein-coding gene sets. Explore the proteomes of specific tissues and organs, The Human Protein Atlas project is funded, protein localization in tissues at a single-cell level, if a gene is enriched in a particular tissue (specificity), which genes have a similar expression profile across tissues (expression cluster). 5, 15131523 (1991). Haeussler M, Zweig AS, Tyner C, Speir ML, Rosenbloom KR, Raney BJ, Lee CM, Lee BT, Hinrichs AS, Gonzalez JN, et al. Hum Mol Genet. 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. "There are 3000 human proteins whose function is unknown," says Wood. The funding sources had no role in the design of this study and collection, analysis, and interpretation of data and in writing the manuscript. Hum Mol Genet. Before Pseudogenes: 180 to 207. PubMed Gene Status; AAR2: updated: AASS: updated: AATF: updated: ABCC1: updated: ABHD17A: updated: ABO pending: ACAD9: updated: ACADM: updated: ACBD5: updated: 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. PubMedGoogle Scholar. This site needs JavaScript to work properly. By using this website, you agree to our Pseudogenes: 247 to 333. Clipboard, Search History, and several other advanced features are temporarily unavailable. Deng, H. et al. (2018)). Data in the Transcripts.xlsx table include the same first five types of information provided in the Genes.xlsx table, plus RefSeq GenBank accession number for each transcript, length in bp of the whole transcript as well as of its 5 untranslated region UTR, coding sequence (CDS) and 3 UTR, number of exons and coding exons for that transcript, derived from the GeneBaseTranscripts table. Then, for each TCGA cohort, Spearmans was calculated between the averaged FPKM values and the nTPM values of the disease-matched cell lines based on the common 19,760 protein-coding genes. Identification of minimal eukaryotic introns through GeneBase, a user-friendly tool for parsing the NCBI Gene databank. In: Abdurakhmonov IY, editor. We use cookies to enhance the usability of our website. Enzymes . The position of the longest intron is related to biological functions in some human genes. statement and Human protein-coding genes and gene feature statistics in 2019. These data might also be used in comparative genomic studies when compared to similar data sets generated from different species to uncover specific and significant differences in genome and gene organization. Here, a consensus z-score above 1 or below -1 was considered significant. Non-coding RNA genes: 138 to 608 Protein-coding genes: 739 to 822 Non-coding RNA genes: 246 to 830 Pseudogenes: 590 to 738 Chromosome 9 accounts for between 4% and 4.5% of our DNA cells. Pseudogenes: 539 to 682. 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 lncRNA sequence is 2,913 nucleotides long and is found in Homo sapiens. 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]. Epub 2023 Jan 20. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, et al. Fellowships for FA and MC have been funded by the Fondazione Umano Progresso DIMES N. 3997 24-11-2015, and individual donations acknowledged above. 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. Klatzmann, D. et al. ISSN 0028-0836 (print). All rights reserved. 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) [5] [6] [7] Mammalian mitochondrial ribosomal proteins are encoded by nuclear genes and help in protein synthesis within the mitochondrion. 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. Database. https://doi.org/10.1186/s13104-019-4343-8, DOI: https://doi.org/10.1186/s13104-019-4343-8. Gene expression data were processed in the same way as for PROGENy analysis. Search human. This article is an index of lists of human genes. doi: 10.1093/iob/obac008. Bookshelf Science 244, 217221 (1989). Accessibility 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. Following the opening of the data sets in a spreadsheet application, users have easy access to the whole set of current reviewed/validated data about human nuclear protein-coding genes. Due to the continuous increase of data deposited in genomic repositories, a revision and analysis of their content is recommended. The concept is that genes that have an elevated expression in a TCGA cohort can be considered as the cohort signature, and their high expression should be reflected by cell line models. Genes contain nucleotides strands containing instructions on how to generate protein or RNA molecules. Piovesan, A., Antonaros, F., Vitale, L. et al. It is one of the only two allosome chromosomes (gender-determining chromosomes) in the human body. We aim to name protein-coding genes based on a key normal function of the gene product. and transmitted securely. Symp. Nucleic Acids Res. 2015;22:495503. Pseudogenes: 365 to 502. Protein-coding genes: 1,124 to 1,199 Article Correlation analysis based on mRNA expression levels of human genes in cancer tissue and the clinical outcome for almost 8000 cancer patients is presented in a gene-centric manner. Correlation tests were used to identify relationships between gene length and other gene and protein characteristics. 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. After that, for every cell line, we calculated the fold change of every gene relative to the disease baseline expression, followed by the log2 transformation of the fold change. 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. Nature 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. J Cell Physiol. All authors critically discussed the final manuscript. The Human Protein Atlas project is funded. Protein coding genes. 2001;409:860921. Nucleic Acids Res. Klatzmann, D. et al. Unable to load your collection due to an error, Unable to load your delegates due to an error. Nucleic Acids Res. Members of this family maint ain homeostasis by neutralizing overexpressed proteinase activity through their function as suicide substrates. The availability of the data sets presented here allows a ready update of main parameters about human genome, often cited in textbooks or reports without a source accounting for a rigorous method for extracting this information. All authors agreed both to be personally accountable for the authors own contributions and to ensure that questions related to the accuracy or integrity of any part of the work, even ones in which the author was not personally involved, are appropriately investigated, resolved, and the resolution documented in the literature. PubMed Central PubMedGoogle Scholar, Dolgin, E. The most popular genes in the human genome. Protein-coding genes: 996 to 1,111 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. How has the pathway and cytokine analysis been done? Acidic ribosomal proteins, called A-proteins (acidic) or P-proteins (phosphorylated acidic), such as RPLP2, are generally present in multiple copies on the ribosome and have isoelectric points in the range of pH 3 to 5, in contrast to most ribosomal proteins, which are single copy and basic. Finally, these data might be useful to design experiments for poorly characterized human genome regions, as in, for example, our current annotation effort of the recently defined highly restricted Down Syndrome critical region (HR-DSCR), which to date does not contain known genes [17], or to study transcription mechanisms such as alternative splicing or nonsense-mediated messenger RNA decay. Cell 42, 93104 (1985). protein-L-isoaspartate (D-aspartate) O-methyltransferase: 5: 20: PCNA: 113: proliferating cell nuclear antigen: 12: 67: PDGFB: 47: platelet-derived growth factor beta . Sci. Protein-coding genes: 727 to 769 [Analysis, identification and correction of some errors of model refseqs appeared in NCBI Human Gene Database by in silico cloning and experimental verification of novel human genes]. Proc. AB451389 - Homo sapiens EEF1A2 mRNA for eukaryotic translation elongation factor 1 . Pseudogenes: 568 to 654. the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Only about 1 percent of DNA is made up of protein-coding genes; the other 99 percent is noncoding. The data are updated as of January 2019, 3years after the last published analysis of human gene features [6] and pre-filtered according to public annotation about the review or validation of the records to ensure reliability of the data. AP and PS designed the study, collected the data and performed the analysis. Sci Rep. 2018;8:2977. Bethesda, MD 20894, Web Policies Google Scholar. Federal government websites often end in .gov or .mil. Dismiss. The UMAP was generated by clustering genes based on expression patterns. The two initial human genome papers reported 31,000 [ 2] and 26,588 protein-coding genes [ 3 ], and when the more . Gao Y, Wang F, Wang R, Kutschera E, Xu Y, Xie S, Wang Y, Kadash-Edmondson KE, Lin L, Xing Y. Sci Adv. doi: 10.1016/j.ygeno.2013.02.009. 2019;47:D74551. To test this, for the 27 cell line cancer types, gene expression was averaged per disease, resulting in the mean expression for each of the 27 cell line cancer types. Non-coding RNA genes: 483 to 1,158 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. Google Scholar. The result of the cluster analysis is presented as a UMAP based on gene expression, where each cluster has been summarized as colored areas containing most of the cluster genes. For this, for each gene in a TCGA cohort, the FPKM values were averaged per cohort. 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. Friedrich, G. & Soriano, P. Genes Dev. https://doi.org/10.1038/d41586-017-07291-9, DOI: https://doi.org/10.1038/d41586-017-07291-9. Cookies policy. 2023 BioMed Central Ltd unless otherwise stated. For example, based on current genome annotations, there is one human SERPINA1 gene with five mouse homologs, presumably due to gene duplication in the mouse lineage. How was the similarity of the cell lines to the corresponding TCGA cancer cohorts analysed? Due to the continuous increase of data deposited in genomic repositories, their content revision and analysis is recommended. GeneBase 1.1: a tool to summarize data from NCBI gene datasets and its application to an update of human gene statistics. The Cell Lines section contains information on genome-wide RNA expression profiles of human protein-coding genes in human cell lines. Introduction: MicroRNAs (miRNAs) are small non-coding RNAs that play a key role in post-transcriptional modulation of individual genes' expression. The three data tables Genes.xlsx, Transcripts.xlsx and Gene_Table.xlsx have been released in the public repository Open Science Framework and they can be freely downloaded at the address: https://osf.io/mhda7/. The orange circles indicate the number of genes with enriched expression in a group of tissues, connected by lines. Nucleic Acids Res. Follow the Python code link for information about updates to the list of genes on these pages. Ezkurdia I, Juan D, Rodriguez JM, Frankish A, Diekhans M, Harrow J, Vazquez J, Valencia A, Tress ML. More surprisingly, until about the year 2000, the fastest growing groups of human genes in the newly added literature were those that have never/rarely been reported about in previous years. 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). Protein-coding genes: 583 to 820 2017;232:75970. KJ901729 - Synthetic construct Homo sapiens clone ccsbBroadEn_11123 CCL25 gene, encodes complete protein. Protein-coding genes: 45 to 73 High-throughput sequencing technologies and bioinformatic tools significantly expanded our knowledge about ncRNAs, highlighting their key role in gene regulatory networks, through their capacity to interact with coding and non-coding RNAs, DNAs and . In order to provide a curated set of updated statistics regarding human nuclear protein-coding genes and transcripts through GeneBase 1.1 Human, we considered only NCBI Gene records retrieved bysearching for protein-coding gene type, with REVIEWED or VALIDATED RefSeq gene status, with at least one REVIEWED or VALIDATED transcript, excluding records annotated as not in current annotation release records (Genome_Annotation_Status field). Appended below is the summary of each of the chromosomes. Next the team showed that the same proportion of human protein-coding genes remain a mystery. Produces many zinc based proteins, such as ZBTB43 and ZNF79. Mitchell, J. Filtering by the Yes annotation allows the retrieval of a non-redundant set of exons, coding exons and introns, respectively. 2006 Jun;7(2):178-85. doi: 10.1093/bib/bbl003. The various subproteomes can be explored in this interactive database including numerous catalogs of protein-coding genes with detailed information regarding expression and localization of the corresponding proteins. The downloading, parsing and import of gene entries are described in more detail in the software public documentation. In 2008, a draft of the complete human proteome was released from UniProtKB/Swiss-Prot: the approximately 20,000 putative human protein-coding genes were represented by one UniProtKB/Swiss-Prot entry each, tagged with the keyword 'Complete proteome' (now obsolete) and later linked to proteome identifier UP000005640.. In the meantime, to ensure continued support, we are displaying the site without styles 2018;46:D813. Internet Explorer). Kapustin Y, Souvorov A, Tatusova T, Lipman D. Splign: algorithms for computing spliced alignments with identification of paralogs. It is possible to use calculation and statistical functions of the spreadsheet to analyze the data in any direction. Comparison with previous reports reveals substantial change in the number of known nuclear protein-coding genes (now 19,116), the protein-coding non-redundant transcriptome space [now 59,281,518 base pair (bp), 10.1% increase], the number of exons (now 562,164, 36.2% increase) due to a relevant increase of the RNA isoforms recorded. Epub 2023 Jan 12. Finally, a new classification has been introduced in which genes are clustered based on similarity in expression across the cell lines. Protein-coding genes: 988 to 1,036 Figure 1: Human species page. government site. Non-coding RNA genes: 55 to 122 (2018)). This is a preview of subscription content, access via your institution. A genome-wide expression analysis of 1055 human cell lines, including 985 cancer cell lines, was performed using RNA-seq with early-split samples as duplicates. 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. doi: 10.1093/nar/gkx1095. Cell 70, 431442 (1992). Pseudogenes: 590 to 738. Nature 551, 427431 (2017). 2023 Feb;55(2):209-220. doi: 10.1038/s41588-022-01276-9. J. Clin. In humans, these genes and accompanying molecules are coiled tightly inside 23 pairs of structures called chromosomes. -, Haeussler M, Zweig AS, Tyner C, Speir ML, Rosenbloom KR, Raney BJ, Lee CM, Lee BT, Hinrichs AS, Gonzalez JN, et al. Caracausi M, Piovesan A, Vitale L, Pelleri MC. "One reason for this might be that practically all genetic testing performed today focuses on protein coding genes. "Finishing the Euchromatic Sequence of the Human Genome," Nature 431, 931-945.] The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. 83, 21252130 (1989). Unauthorized use of these marks is strictly prohibited. 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 specificity, distribution and expression clusters. A. et al. On the other hand, a genetic element could be transcribed, and thus identified as a functional gene, only under particular conditions such as a developmental stage, a disease or the exposure to specific stresses or drugs. 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. National Center for Biotechnology Information, highly restricted Down Syndrome critical region. 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. Ensembl 2019. FOIA CAS This protein inhibits the neutrophil-derived proteinases neutrophil elastase, cathepsin G, and proteinase-3 and thus protects tissues from damage at inflammatory . 8600 Rockville Pike Protein-coding genes: 1,961 to 2,093 The nucleotides in chromosome 3 accounts for 6.5% of our DNA, with over 200 million base pairs. ADS Despite containing only up to 5.0% of the bodys DNA, chromosome 8 is quite important as over 8% of its genes are specialists in brain development. Measuring around 191 megabases in length, chromosome 4 contains 186 million base pairs, or 6% of our DNA. Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes. A tour through the most studied genes in biology reveals some surprises. Non-coding RNA genes: 251 to 1,046 AP and PS wrote the manuscript draft. 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. Gene disorders here are linked to diseases such as autism, EhlersDanlos syndrome and variants of dementia. DNA Res. Protein-coding genes: 790 to 886 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. The 83 million base pairs in chromosome 17 (almost 3%) plays a vital role in the development of physiological balance and generation of internal organs. All underlying images of immunohistochemistry stained normal tissues are available together with knowledge-based annotation of protein expression levels. Annotated by 9 databases (GeneCards, MalaCards, Ensembl/GENCODE, NONCODE, Ensembl, HGNC, LNCipedia, Expression Atlas, RefSeq). Non-coding RNA genes: 148 to 515 TNF - Encodes tumour necrosis factor, an immune molecule that has been a major drug target for inflammatory disease. The transcript abundance of each protein-coding gene was estimated using the average TPM value of the individual samples for each cell line. Genetic code variants [ edit] Google Scholar. Tu Q, Cameron RA, Worley KC, Gibbs RA, Davidson EH. Protein-coding genes: 862 to 984 ISTOCK, BLACKJACK3D T he human genome may contain more protein-coding genes than prior analyses suggested. Up to 50 of the genes in chromosome 18 are involved in birth defects, so it is not a particularly popular chromosome. Open Access Anyone you share the following link with will be able to read this content: Sorry, a shareable link is not currently available for this article. Non-coding RNA genes: 325 to 1,199 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. Open Access A total of 155 protein-coding genes mapped to the GO term "regulation of immune system process"; 85 genes from C1, 32 genes from C3 and 38 genes from C5. and JavaScript. Piovesan A, Caracausi M, Ricci M, Strippoli P, Vitale L, Pelleri MC. Below is a list of articles on human chromosomes, each of which contains an incomplete list of genes located on that chromosome. Nature 381, 661666 (1996). Non-coding RNA genes: 318 to 1,202 2023 Jan 10;13:1085139. doi: 10.3389/fgene.2022.1085139. It is broadly suspected that a large fraction of these entries is simply spurious ORFs, because they show no evidence of evolutionary conservation. 2019;47:D853D858. The protein encoded by this gene is a member of the serpin family of proteinase inhibitors. Anyone you share the following link with will be able to read this content: Sorry, a shareable link is not currently available for this article. We first performed a protein-centric transcriptomics scan to define a revised set of human secreted proteins (secretome) based on 19,670 protein-coding genes predicted by Ensembl ().For each protein-coding gene, all protein isoforms (splice variants) were annotated on the basis of the presence of a signal peptide, transmembrane regions, or both, and each protein isoform was classified as being . 1. Article The unfolding of these instructions is initiated by the transcription of the DNA into RNA sequences. Following validation by the software Splign [8], we confirm that there are no human (and possibly of any species) introns shorter than 30bp (Table2). 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]. 2014;23:586678. 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). Protein-coding genes: 1,194 to 1,292 Manage cookies/Do not sell my data we use in the preference centre. Non-coding RNA genes: 355 to 1,207 Maddon, P. J. et al. The .gov means its official.