Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28038678", "kind": "science-record", "revision": 6, "content_hash": "sha256:9af3478eff2644d44700c3f37e47095580b3303c67c30e94397716ccbb489210", "created_at": "2026-11-01T15:40:22Z", "updated_at": "2026-11-01T21:20:45Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive.", "doi": "10.1186/s13059-016-1118-6", "pmid": "28038678", "authors": ["Abhinav Nellore", "Andrew E Jaffe", "Jean-Philippe Fortin", "José Alquicira-Hernández", "Leonardo Collado-Torres", "Siruo Wang", "Robert A Phillips", "Nishika Karbhari", "Kasper D Hansen", "Ben Langmead", "Jeffrey T Leek"], "journal": "Genome biology", "year": 2016, "abstract": "BACKGROUND: Gene annotations, such as those in GENCODE, are derived primarily from alignments of spliced cDNA sequences and protein sequences. The impact of RNA-seq data on annotation has been confined to major projects like ENCODE and Illumina Body Map 2.0.\nRESULTS: We aligned 21,504 Illumina-sequenced human RNA-seq samples from the Sequence Read Archive (SRA) to the human genome and compared detected exon-exon junctions with junctions in several recent gene annotations. We found 56,861 junctions (18.6%) in at least 1000 samples that were not annotated, and their expression associated with tissue type. Junctions well expressed in individual samples tended to be annotated. Newer samples contributed few novel well-supported junctions, with the vast majority of detected junctions present in samples before 2013. We compiled junction data into a resource called intropolis available at http://intropolis.rail.bio . We used this resource to search for a recently validated isoform of the ALK gene and characterized the potential functional implications of unannotated junctions with publicly available TRAP-seq data.\nCONCLUSIONS: Considering only the variation contained in annotation may suffice if an investigator is interested only in well-expressed transcript isoforms. However, genes that are not generally well expressed and nonetheless present in a small but significant number of samples in the SRA are likelier to be incompletely annotated. The rate at which evidence for novel junctions has been added to the SRA has tapered dramatically, even to the point of an asymptote. Now is perhaps an appropriate time to update incomplete annotations to include splicing present in the now-stable snapshot provided by the SRA.", "claims": [{"id": "claim-method", "statement": "We then used the row-centered matrix A for PCA; that is, Aij=xij−x¯i.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28038678", "locator": "sections[19] \"Principal component analysis\" paragraph 2", "quote": "We then used the row-centered matrix A for PCA; that is, Aij=xij−x¯i."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The dataset is available from Figshare [41]. The code is also available from Figshare [42].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28038678", "locator": "sections[22] \"Availability of data and materials\" paragraph 2", "quote": "The dataset is available from Figshare [41]. The code is also available from Figshare [42]."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Aligning 21,504 publicly available SRA RNA-seq samples with Rail-RNA revealed 56,861 junctions observed in at least 1,000 samples that were absent from existing annotations.", "kind": "quantitative", "target": {"value": 18.6, "unit": "per cent", "tolerance": null, "source": "We found 56,861 junctions (18.6%) in at least 1000 samples that were not annotated, and their expression associated with tissue type."}, "evidence": [{"asset": "source:pmid:28038678", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "We aligned 21,504 Illumina-sequenced human RNA-seq samples from the Sequence Read Archive (SRA) to the human genome and compared detected exon-exon junctions with junctions in several recent gene annotations."}, {"asset": "source:pmid:28038678", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "We found 56,861 junctions (18.6%) in at least 1000 samples that were not annotated, and their expression associated with tissue type."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Aligning 21,504 publicly available SRA RNA-seq samples with Rail-RNA revealed 56,861 junctions observed in at least 1,000 samples that were absent from existing annotations.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:28038678"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5203714", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:28038678:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6d2309455e5520fb5056f5231fc690021aa8cdf2bae8a4cae2909f6f6775b0d1", "bytes": 780, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#Tab1", "version": null, "note": "Gene annotations from which exon-exon junctions were extracted and unioned to obtain a list of annotated junctions", "structure": {"pmcid": "PMC5203714", "section_index": 1, "section_title": "Background", "row_count": 19, "column_count": 3}, "table": {"label": "Table 1", "caption": "Gene annotations from which exon-exon junctions were extracted and unioned to obtain a list of annotated junctions", "rows": [["Gene annotation", "Number of junctions", "Reference"], ["hg19", "", ""], ["AceView", "395,410", "[12]"], ["CCDS", "174,337", "[43]"], ["GENCODE v19", "343,887", "[2]"], ["UCSC", "264,339", "[10]"], ["lincRNAs", "30,256", "[6]"], ["MGC", "160,388", "[44]"], ["RefSeq", "235,512", "[1]"], ["SIB", "414,422", "[45]"], ["Vega", "242,672", "[2]"], ["hg38", "", ""], ["CCDS", "178,775", "[43]"], ["GENCODE v24", "346,547", "[2]"], ["UCSC", "356,644", "[10]"], ["lincRNAs", "29,940", "[6]"], ["MGC", "169,302", "[44]"], ["RefSeq", "247,577", "[1]"], ["SIB", "433,606", "[45]"]], "row_count": 19, "column_count": 3, "numeric_cells": 36, "header_rows": 1, "locator": "section[1]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:28038678:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f7f3fe9215139384a5f555db47185cc9387c11a86139f27ce799e61ba469f14b", "bytes": 1508, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[1]#Tab2", "version": null, "note": "Top ten samples across the 21,504 analyzed in this paper in order of descending junction inclusion ratio D, as defined in the table", "structure": {"pmcid": "PMC5203714", "section_index": 7, "section_title": "Application to ALK isoform discovery", "row_count": 19, "column_count": 8}, "table": {"label": "Table 2", "caption": "Top ten samples across the 21,504 analyzed in this paper in order of descending junction inclusion ratio D, as defined in the table", "rows": [["Rank", "Sample (i.e., run)", "Project", "Description of sample", "Junction", "Junction", "Total junction", "D=(B-A)/C"], ["", "", "", "", "coverage A for ALK", "coverage B for ALK", "coverage C", ""], ["", "", "", "", "exons 1–19", "exons 20–29", "across ALK", ""], ["1", "SRR545713", "SRP007461", "NHEM.f_M2: normal human", "0", "139", "139", "1"], ["", "", "", "melanocyte", "", "", "", ""], ["1", "SRR396804", "SRP010166", "Non-small cell lung", "0", "172", "172", "1"], ["", "", "", "adenocarcinoma", "", "", "", ""], ["1", "SRR620100", "SRP017262", "Leukemia", "0", "108", "108", "1"], ["4", "SRR1289650", "SRP042031", "Macrophage", "1", "85", "86", "0.976"], ["5", "SRR1289651", "SRP042031", "Macrophage cultured", "1", "77", "78", "0.974"], ["", "", "", "with fibroblast", "", "", "", ""], ["6", "SRR545716", "SRP007461", "NHEM_M2: normal human", "2", "94", "96", "0.958"], ["", "", "", "melanocyte", "", "", "", ""], ["7", "SRR628586", "SRP017413", "Uveal melanoma", "12", "111", "123", "0.805"], ["8", "DRR016705", "DRP001919", "H2228, an EML4-ALK-expressing", "38", "285", "333", "0.765"], ["", "", "", "lung adenocarcinoma cell line", "", "", "", ""], ["9", "SRR545714", "SRP007461", "NHEM.f_M2: normal human", "14", "63", "77", "0.636"], ["", "", "", "melanocyte", "", "", "", ""], ["10", "ERR532612", "ERP006077", "Prostate tumor", "16", "53", "69", "0.536"]], "row_count": 19, "column_count": 8, "numeric_cells": 73, "header_rows": 3, "locator": "section[7]/table-wrap[1]#Tab2"}}], "gaps": []}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "principal_component_analysis", "specific": "pca", "label": "Principal component analysis", "dsl_operations": ["pca_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["wide_numeric_matrix"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "We then used the row-centered matrix A for PCA; 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Analysis of TRAP-seq samples All 15 mouse TRAP-seq samples were taken from the study S"], "order_basis": "paper_text_order:10498", "id": "assay:3"}, {"role": "analysis", "definition_id": "principal_component_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["pca_fit"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["We then used the row-centered matrix A for PCA; that is, Aij=xij−x¯i."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}