Proc. Article 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. Due to the continuous increase of data deposited in genomic repositories, a revision and analysis of their content is recommended. The data sets were created by exporting the data from each relative table of GeneBase as a spreadsheet. How has the classification of all protein-coding genes been done? Integr Org Biol. 2023 BioMed Central Ltd unless otherwise stated. The lists below constitute a complete list of all known human protein-coding genes. and JavaScript. 2004. 2023 Feb;55(2):209-220. doi: 10.1038/s41588-022-01276-9. The funding sources had no role in the design of this study and collection, analysis, and interpretation of data and in writing the manuscript. If you continue, we'll assume that you are happy to receive all cookies. Protein-coding genes: 559 to 629 Article 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. Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, BO, Italy, Allison Piovesan,Francesca Antonaros,Lorenza Vitale,Pierluigi Strippoli,Maria Chiara Pelleri&Maria Caracausi, You can also search for this author in In: Abdurakhmonov IY, editor. Estimates of the current updates are closer to 20,000 protein-coding genes, as well as an expanding number of functional, non-coding RNA sequences. Chromosome 11, which contains a little over 4% of our building blocks, is incredibly critical to our olfactory system as 40% of the 856 olfactory receptor genes in our body are clustered here. We are profoundly grateful to the Fondazione Umano Progresso, Milano, Italy for their fundamental support to our research on trisomy 21 and to this study. Non-coding RNA genes: 165 to 404 In order to make a protein, a molecule closely related to DNA called ribonucleic acid (RNA) first copies the code within DNA. Pseudogenes: 703 to 933. Pseudogenes: 373 to 481. Brief Bioinform. Finally, we confirm that there are no human introns shorter than 30 bp. Article The genome sequence is an organism's blueprint: the set of instructions dictating its biological traits. eCollection 2022. 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. 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. Go to interactive expression cluster page. This acrocentric chromosome measures 95 megabases long, and accounts for 3.5% of the human DNA. This article is an index of lists of human genes. However, rather than an intron excised via canonical splicing, this is a 26-nucleotide segment known to be removed in particular circumstances by a completely different mechanism, an excision mediated by the endonuclease inositol-requiring enzyme 1 (IRE1) [9]. Dismiss. BMC Res Notes 12, 315 (2019). Pseudogenes: 666 to 839. 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. Search human. Piovesan, A., Antonaros, F., Vitale, L. et al. https://doi.org/10.1186/s13104-019-4343-8, DOI: https://doi.org/10.1186/s13104-019-4343-8. protein-L-isoaspartate (D-aspartate) O-methyltransferase: 5: 20: PCNA: 113: proliferating cell nuclear antigen: 12: 67: PDGFB: 47: platelet-derived growth factor beta . Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. Now, let's filter to get only protein-coding genes, group by the ensembl gene ID, summarize to count how many transcripts are in each gene, inner join that result back to the original gene list, so we can select out only the gene, number of transcripts, symbol, and description, mutate the description column so that it isn't so wide that it'll break the display, arrange the returned data . 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. Co-authors David Sweetser, MD, PhD, and Lauren Briere, MS, CGC, narrowed the search to a single nucleotide variant in the gene MIR145, a microRNA gene. In the current release, we collected and curated 2507 unique human genes, including 2267 protein-coding and 240 non-coding genes from comprehensive manual examination of 10,960 PubMed article abstracts. Actually, apart from three introns estimated to be of 13bp long due to NCBI Gene Gene Table artifacts [5], there is one unique intron smaller than 30bp, intron 14 of XBP1 gene, in these data. A tour through the most studied genes in biology reveals some surprises. The UDN has allowed us to delve much deeper, beyond standard clinical testing. The https:// ensures that you are connecting to the 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 description of each field is included in the first row of the spreadsheet table. 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. 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]. -, Cunningham F, Achuthan P, Akanni W, Allen J, Amode MR, Armean IM, Bennett R, Bhai J, Billis K, Boddu S, et al. Summary. Protein-coding genes: 1,024 to 1,085 official website and that any information you provide is encrypted The human genome is conventionally divided into the "coding" genome, which generates the ~20,000 annotated human protein coding genes, and the "dark" genome, which does not encode. J. Clin. For this, for each gene in a TCGA cohort, the FPKM values were averaged per cohort. It is broadly suspected that a large fraction of these entries is simply spurious ORFs, because they show no evidence of evolutionary conservation. Science 244, 217221 (1989). Cell. 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. Finally, for each cell line, gene log2 fold changes were sorted from high to low, followed by the GSEA of the TCGA cohort elevated genes against the sorted gene list. Natl Acad. Produces many zinc based proteins, such as ZBTB43 and ZNF79. 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. The protein expression data from 44 normal human tissue types is derived from antibody-based protein profiling using conventional and multiplex immunohistochemistry. Protein-coding genes: 1,224 to 1,327 The red circles connected to each tissue name indicates the number of tissue enriched genes associated with that particular tissue. Below is a list of articles on human chromosomes, each of which contains an incomplete list of genes located on that chromosome. "There are 3000 human . We use cookies to enhance the usability of our website. Protein-coding genes: 215 to 256 Pseudogenes: 590 to 738. Nucleic Acids Res. 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) This optimistic trend culminated with ~ 550 new gene function . Here, a consensus z-score above 1 or below -1 was considered significant. Google Scholar. At 181 million base pairs, chromosome 5 is the fifth largest human chromosome, accounting for 6% of the total. 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. In humans, these genes and accompanying molecules are coiled tightly inside 23 pairs of structures called chromosomes. Also, DESeq2 normalized expression values were centered per gene as suggested. In 3 sisters with isolated pituitary hormone deficiency (CPHD7; 618160), Argente et al. 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/. "One reason for this might be that practically all genetic testing performed today focuses on protein coding genes. Invest. Pseudogenes: 288 to 379. Non-coding RNA genes: 244 to 881 This section of the Human Protein Atlas focuses on the expression profiles in human tissues of genes both on the mRNA and protein level. This can be served as a reference for cell line selection for in vitro experiments when studying a specific cancer type. 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. Pseudogenes: 180 to 207. TABLE 9.5 HUMAN GENOME AND HUMAN GENE STATISTICS SIZE OF GENOME COMPONENTS Mitochondrial genome Nuclear genome Euchromatic component . 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. Several miRNA variants from different populations are known to be associated with an increased risk of rheumatoid arthritis (RA). 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. -, Piovesan A, Vitale L, Pelleri MC, Strippoli P. Universal tight correlation of codon bias and pool of RNA codons (codonome): the genome is optimized to allow any distribution of gene expression values in the transcriptome from bacteria to humans. Provided by the Springer Nature SharedIt content-sharing initiative. 2023 Jan 20;9(3):eabq5072. Careers. Eye Retina Heart Skeletal muscle Smooth muscle Adrenal gland Parathyroid gland Thyroid gland Pituitary gland Lung Bone marrow Protein-coding genes: 1,961 to 2,093 Genome Res. 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 comprehensive catalog of functional elements in the human and mouse genomes provides a powerful resource for research into mammalian biology and mechanisms of human diseases. Symp. Genes that make proteins are called protein-coding genes. Search model organisms. Google Scholar. 2685 5610 8170 2764 861 Elevated in brain Elevated in other but expressed in brain Low tissue specificity but expressed in brain Not detected in . Epub 2012 Jun 18. 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.. Genes here can impact the space between eyes and thickness of the lower lip. This sex chromosome (allosome) is only present in males. The UCSC genome browser database: 2019 update. We wish to sincerely thank Matteo and Elisa Mele and family; the community of Dozza (BO), Italy: Comitato Arzdore di Dozza, Parrocchia di Dozza and Pro-Loco di Dozza as well as the Costa family and Lem Market Alimentari Srl for their support to our research. Correlation tests were used to identify relationships between gene length and other gene and protein characteristics. Article Cookies policy. Protein-coding genes: 739 to 822 The cell lines were then ranked based on Spearmans () and NES from high to low, respectively. California Privacy Statement, Examples: HI0934, Rv3245c, ECs2657/ECs2658 Advances in the Exon-Intron Database (EID). Biol Direct. Non-coding RNA genes: 277 to 993 Both types of genes can produce non-coding transcripts, but non-coding RNA genes do not produce protein-coding transcripts. . Piovesan A, Caracausi M, Ricci M, Strippoli P, Vitale L, Pelleri MC. Finally, we confirm that there are no human introns shorter than 30 bp. Genes contain nucleotides strands containing instructions on how to generate protein or RNA molecules. 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/. Yoshida H, Matsui T, Yamamoto A, Okada T, Mori K. XBP1 mRNA is induced by ATF6 and spliced by IRE1 in response to ER stress to produce a highly active transcription factor. MCP and MC supervised the project. Protein-coding genes: 1,124 to 1,199 The downloading, parsing and import of gene entries are described in more detail in the software public documentation. PMC Around 27.9% of the nucleotide sequences inside exhibit no protein encoding. 2015;22:495503. Piovesan A, Caracausi M, Antonaros F, Pelleri MC, Vitale L. Database (Oxford). The authors declare that they have no competing interests. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Further analysis of transcriptome data and clinical data from cancer patients showed that recurrently p53-regulated lncRNAs are associated with patient survival. Open Access Considering only upregulated DEGs or. The cell line cancer enriched and group enriched genes are displayed in the interactive plot below, in which clicking on the red and orange circles results in gene lists for the corresponding enriched and group enriched genes, respectively. Click to obtain the corresponding list of genes. Humans have about 20,000 protein-coding genes but scientists still know remarkably little about most of the proteins they encode. USA 90, 19771981 (1993). Click on a cluster or Go to interactive expression cluster page to view an interactive UMAP and details about all cluster annotations. 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. [5] [6] [7] Mammalian mitochondrial ribosomal proteins are encoded by nuclear genes and help in protein synthesis within the mitochondrion. 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 nucleotides in chromosome 3 accounts for 6.5% of our DNA, with over 200 million base pairs. Pseudogenes: 574 to 785. CAS Python scripts provided with the software were run for the initial data pre-processing. In addition, data can be exported in other formats and imported in other applications (database management systems, statistical software, genomic tools) for further analysis.