Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues.

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Here we describe a new computational system, ASprofile, and its application to RNA-seq data from Illumina's Human Body Map project (>2.5 billion reads). Using the system, we identified putative alternative splicing events in 16 different human tissues, which provide a dynamic picture of splicing variation across the tissues. We detected 26,989 potential exon skipping events representing differences in splicing patterns among the tissues. A large proportion of the events (>60%) were novel, involving new exons (~3000), new introns (~16000), or both. When tracing these events across the sixteen tissues, only a small number (4-7%) appeared to be differentially expressed ('switched') between two tissues, while 30-45% showed little variation, and the remaining 50-65% were not present in one or both tissues compared. Novel exon skipping events appeared to be slightly less variable than known events, but were more tissue-specific. Our study represents the first effort to build a comprehensive catalog of alternative splicing in normal human tissues from RNA-seq data, while providing insights into the role of alternative splicing in shaping tissue transcriptome differences. The catalog of events and the ASprofile software are freely available from the Zenodo repository ( http://zenodo.org/record/7068; doi: 10.5281/zenodo.7068) and from our web site http://ccb.jhu.edu/software/ASprofile.", "claims": [{"id": "claim-method", "statement": "Novel events are depleted in ‘switches’ compared to known events (test of homogeneity, df=2, chi-square 274.7, p = 0.0).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:24555089", "locator": "sections[20] \"S7. Reproducibility of exon skipping event discovery with other assembly methods\" paragraph 10", "quote": "Novel events are depleted in ‘switches’ compared to known events (test of homogeneity, df=2, chi-square 274.7, p = 0.0)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "These data are publicly available as the Illumina Human Body Map project (EMBL accession ENA-ERP000546; ArrayExpress accession: E-MTAB-513; http://www.ebi.ac.uk/arrayexpress/browse.html?keywords=E-MTAB-513&expandefo=on).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:24555089", "locator": "sections[3] \"A global view of alternative splicing in the 16 tissues\" paragraph 2", "quote": "These data are publicly available as the Illumina Human Body Map project (EMBL accession ENA-ERP000546; ArrayExpress accession: E-MTAB-513; http://www.ebi.ac.uk/arrayexpress/browse.html?keywords=E-MTAB-513&expandefo=on)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:24555089"], "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": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:E-MTAB-513"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:E-MTAB-513"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:24555089", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.12688/f1000research.2-188.v2", "sha256": "sha256:a4e3691420db92594113397804bdd694b8328bdf3a8ba3c350eace9fe174e20b", "bytes": 53995, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.12688/f1000research.2-188.v2", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC3892928", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:E-MTAB-513", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=E-MTAB-513", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "E-MTAB-513", "version": null, "note": "These data are publicly available as the Illumina Human Body Map project (EMBL accession ENA-ERP000546; ArrayExpress accession: E-MTAB-513; http://www.ebi.ac.uk/arrayexpress/browse.html?keywords=E-MTAB-513&expandefo=on).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "These data are publicly available as the Illumina Human Body Map project (EMBL accession ENA-ERP000546; ArrayExpress accession: E-MTAB-513; http://www.ebi.ac.uk/arrayexpress/browse.html?keywords=E-MTAB-513&expandefo=on).", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": null, "resolution_checked_at": "2026-10-31T18:29:01Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:24555089:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8c3a4327c55a372f8bad6c575ea3a84333abd1578c6228401cbc3d8a19699e01", "bytes": 1546, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[1]#TS1", "version": null, "note": "Total number of RNA-seq reads from each of 16 human tissues.\"Mapped\" refers to the number of reads that had at least one and no more than ten alignments to the genome.", "structure": {"pmcid": "PMC3892928", "section_index": 17, "section_title": "Supplementary materials", "row_count": 18, "column_count": 4}, "table": {"label": "Table S1.", "caption": "Total number of RNA-seq reads from each of 16 human tissues.\"Mapped\" refers to the number of reads that had at least one and no more than ten alignments to the genome.", "rows": [["Tissue", "Reads", "Mapped", "Properly paired"], ["Adipose", "154,600,144", "138,872,338 (88.9%)", "76,196,138 (49.3%)"], ["Adrenal", "148,945,742", "133,883,290 (89.9%)", "78,356,524 (52.6%)"], ["Brain", "147,026,094", "134,791,012 (91.7%)", "87,153,922 (59.3%)"], ["Breast", "151,724,430", "135,987,146 (89.6%)", "78,111,468 (51.5%)"], ["Colon", "164,874,886", "150,966,150 (91.6%)", "83,026,962 (50.4%)"], ["Heart", "165,837,568", "155,841,749 (94.0%)", "102,600,102 (61.9%)"], ["Kidney", "160,794,674", "143,888,751 (89.5%)", "84,285,000 (52.4%)"], ["Liver", "160,097,246", "149,817,522 (93.6%)", "94,840,760 (59.2%)"], ["Lung", "158,593,810", "144,039,113 (90.8%)", "90,728,136 (57.2%)"], ["Lymph", "164,156,314", "146,044,267 (89.0%)", "89,437,520 (54.5%)"], ["Ovary", "161,892,520", "147,588,256 (91.2%)", "81,207,460 (50.2%)"], ["Prostate", "164,668,152", "150,477,990 (92.2%)", "94,643,390 (57.5%)"], ["Skeletal muscle", "164,222,278", "151,847,711 (91.6%)", "95,036,702 (57.9%)"], ["Testes", "163,672,398", "149,727,704 (91.5%)", "83,729,866 (51.2%)"], ["Thyroid", "163,825,774", "148,942,521 (90.9%)", "80,513,364 (49.1%)"], ["White blood cell", "162,434,296", "149,167,286 (91.8%)", "87,806,618 (54.1%)"], ["Total", "2,557,366,326", "2,333,252,527 (91.2%)", "1,387,673,932 (54.3%)"]], "row_count": 18, "column_count": 4, "numeric_cells": 51, "header_rows": 1, "locator": "section[17]/table-wrap[1]#TS1"}}, {"id": "asset:table:pmid:24555089:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:2bbc6dd107dc4d59be066f4a0cfaf20e57cf1afbcceeaa2549d307ad7659ebe3", "bytes": 534, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[18]/table-wrap[1]#TS2", "version": null, "note": "Performance of four transcript assembly programs in capturing exon skipping events from simulated RNA-seq data. Recall = TP/(TP+FN), Precision = TP/(TP+FP).", "structure": {"pmcid": "PMC3892928", "section_index": 18, "section_title": "S2. Evaluation of transcript assemblers in detecting exon skipping (ES) events", "row_count": 6, "column_count": 5}, "table": {"label": "Table S2.", "caption": "Performance of four transcript assembly programs in capturing exon skipping events from simulated RNA-seq data. Recall = TP/(TP+FN), Precision = TP/(TP+FP).", "rows": [["Exon skipping (ES)"], ["", "Predicted", "Correct", "Recall", "Precision"], ["Cufflinks", "632", "561", "0.42", "0.89"], ["IsoCEM", "940", "496", "0.37", "0.53"], ["SLIDE", "3022", "311", "0.23", "0.10"], ["Scripture", "1724", "1045", "0.78", "0.61"]], "row_count": 6, "column_count": 5, "numeric_cells": 16, "header_rows": 2, "locator": "section[18]/table-wrap[1]#TS2"}}, {"id": "asset:table:pmid:24555089:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:aeeb0bd53234b4a1458e70f3ea88078af804ab6855eea4c94c7ea7b063376472", "bytes": 1637, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[18]/table-wrap[2]#TS3", "version": null, "note": "Overview of results from the Cufflinks transcript assembly process.Cufflinks assembles short reads aligned to a genome into a set of transcript fragments (‘transfrags’ or ‘transcripts’ or ‘txpts’, below), grouped by locus (‘gene’).", "structure": {"pmcid": "PMC3892928", "section_index": 18, "section_title": "S2. Evaluation of transcript assemblers in detecting exon skipping (ES) events", "row_count": 17, "column_count": 8}, "table": {"label": "Table S3.", "caption": "Overview of results from the Cufflinks transcript assembly process.Cufflinks assembles short reads aligned to a genome into a set of transcript fragments (‘transfrags’ or ‘transcripts’ or ‘txpts’, below), grouped by locus (‘gene’).", "rows": [["Tissue", "Genes*", "Multi-exon", "Txpts/gene †", "Transfrags", "Single exon", "Multiexon", "Exons/txpt ‡"], ["Adrenal", "307,088", "23,135", "2.0", "357,774", "311,766", "46,008", "5.6"], ["Adipose", "134,348", "21,793", "1.5", "158,142", "126,207", "31,935", "6"], ["Brain", "239,971", "24,435", "1.8", "218,818", "238,497", "43,321", "6"], ["Breast", "191,620", "23,553", "1.6", "222,525", "185,869", "36,656", "5.5"], ["Colon", "116,723", "23,503", "1.3", "133,953", "103,071", "30,882", "5.1"], ["Heart", "149,951", "21,537", "1.5", "177,059", "144,829", "32,230", "6.5"], ["Kidney", "171,862", "24,000", "1.5", "197,742", "162,910", "34,832", "5.4"], ["Liver", "95,495", "21,228", "1.3", "110,116", "82,732", "27,384", "5"], ["Lung", "172,439", "25,176", "1.4", "194,640", "159,123", "35,517", "4.9"], ["Lymph", "188,709", "23,766", "1.5", "216,692", "179,938", "36,754", "4.9"], ["Ovary", "210,035", "22,949", "1.8", "252,081", "210,391", "41,690", "6.5"], ["Prostate", "161,526", "24,584", "1.4", "186,159", "150,732", "35,427", "5.5"], ["Skel_muscle", "95,684", "19,695", "1.2", "105,209", "82,359", "22,850", "4.7"], ["Testes", "220,459", "29,546", "1.6", "259,043", "212,894", "46,169", "5.9"], ["Thyroid", "187,169", "23,357", "1.8", "224,647", "184,751", "39,896", "6.3"], ["White_blood", "98,731", "19,943", "1.3", "113,656", "88,538", "25,118", "5.5"]], "row_count": 17, "column_count": 8, "numeric_cells": 112, "header_rows": 1, "locator": "section[18]/table-wrap[2]#TS3"}}, {"id": "asset:table:pmid:24555089:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:539dd38e336f162f897dfe70e84656c5f0e019d83b1a00a0ba6ec0810bcf8a26", "bytes": 1473, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[18]/table-wrap[3]#TS4", "version": null, "note": "Novel and known gene splice forms in the sixteen tissues, determined by comparison to the ENSEMBL v.61 annotation database using the program Cuffcompare.Cuffcompare compares each predicted transcript’s intron chain against those of the reference transcripts and classifies the transfrag as: ‘equal’ to a reference transcript, if their intron chains are identical; ‘contained’, if included in a reference transcript’s; or as a ‘new splice form’, if the intron chain has at least one splice junction in common with the reference transcripts (n.b., other Cuffcompare codes are not relevant and were omitted).", "structure": {"pmcid": "PMC3892928", "section_index": 18, "section_title": "S2. Evaluation of transcript assemblers in detecting exon skipping (ES) events", "row_count": 18, "column_count": 4}, "table": {"label": "Table S4.", "caption": "Novel and known gene splice forms in the sixteen tissues, determined by comparison to the ENSEMBL v.61 annotation database using the program Cuffcompare.Cuffcompare compares each predicted transcript’s intron chain against those of the reference transcripts and classifies the transfrag as: ‘equal’ to a reference transcript, if their intron chains are identical; ‘contained’, if included in a reference transcript’s; or as a ‘new splice form’, if the intron chain has at least one splice junction in common with the reference transcripts (n.b., other Cuffcompare codes are not relevant and were omitted).", "rows": [["Set", "Comparison to ENSEMBL v.61"], ["", "Full-length (Equal)", "Partial (Contained)", "New splice forms"], ["Adrenal", "5,705", "22,613", "22,592"], ["Adipose", "5,593", "22,293", "11,233"], ["Brain", "6,497", "20,673", "19,329"], ["Breast", "5,665", "24,190", "13,665"], ["Colon", "4,689", "28,715", "9,310"], ["Heart", "6,103", "17,614", "11,701"], ["Kidney", "5,501", "26,615", "11,775"], ["Liver", "4,483", "24,563", "7,692"], ["Lung", "4,958", "33,735", "12,346"], ["Lymph", "4,574", "33,682", "14,364"], ["Ovary", "7,017", "18,667", "18,048"], ["Prostate", "5,673", "27,183", "12,470"], ["Skel_muscle", "3,318", "33,999", "4,999"], ["Testes", "7,077", "23,648", "17,306"], ["Thyroid", "6,487", "21,098", "16,667"], ["White_blood", "4,568", "25,004", "6,533"]], "row_count": 18, "column_count": 4, "numeric_cells": 49, "header_rows": 2, "locator": "section[18]/table-wrap[3]#TS4"}}, {"id": "asset:table:pmid:24555089:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:de8ae29a5d8bfc0c7622fa2fe9a12f62d2c706920c9680f83377140fef0fddd5", "bytes": 631, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[18]/table-wrap[4]#TS5", "version": null, "note": "Numbers of candidate alternative splicing events found in the Illumina Human Body Map data, by type.", "structure": {"pmcid": "PMC3892928", "section_index": 18, "section_title": "S2. Evaluation of transcript assemblers in detecting exon skipping (ES) events", "row_count": 8, "column_count": 3}, "table": {"label": "Table S5.", "caption": "Numbers of candidate alternative splicing events found in the Illumina Human Body Map data, by type.", "rows": [["Event type", "Code", "Count"], ["Exon skipping (single exon)", "SKIP", "26,989"], ["Exon skipping (multiple exons)", "MSKIP", "13,814"], ["Alternative 5´ terminal exon*", "TSS", "97,399"], ["Alternative 3´ terminal exon*", "TTS", "45,609"], ["Intron retention (single intron)", "IR", "16,671"], ["Intron retention (multiple introns)", "MIR", "2,636"], ["Alternative exon boundaries", "AE", "22,767"]], "row_count": 8, "column_count": 3, "numeric_cells": 9, "header_rows": 1, "locator": "section[18]/table-wrap[4]#TS5"}}, {"id": "asset:table:pmid:24555089:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e90467926691c404cc961fde0507e217184f98799ad28b2d195d2a7ba0c96970", "bytes": 1441, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[19]/table-wrap[1]#TS6", "version": null, "note": "Comparison of co-located ES events among the 26,989 events discovered from the Illumina Human Body Map data and the 25,114 exon skipping (ES) events extracted from the Ensembl v.61 annotations. All – all events co-located within V bp; Loci – clusters of co-located events (each with a representative ‘anchor’); Var ( =All-Loci) – variations (not including ‘anchors’), representing potential mapping artifacts.", "structure": {"pmcid": "PMC3892928", "section_index": 19, "section_title": "S6. Potential effects of imprecise splice junctions on the exon skipping (ES) estimates", "row_count": 12, "column_count": 11}, "table": {"label": "Table S6.", "caption": "Comparison of co-located ES events among the 26,989 events discovered from the Illumina Human Body Map data and the 25,114 exon skipping (ES) events extracted from the Ensembl v.61 annotations. All – all events co-located within V bp; Loci – clusters of co-located events (each with a representative ‘anchor’); Var ( =All-Loci) – variations (not including ‘anchors’), representing potential mapping artifacts.", "rows": [["V", "Cufflinks (26,989 events)", "Ensembl 61 (25,114 events)", "% Diff", "Potential artifacts"], ["All", "Loci", "Var.", "%", "All", "Loci", "Var.", "%"], ["1", "647", "300", "347", "1.29", "90", "45", "45", "0.18", "1.10", "298"], ["2", "1271", "585", "686", "2.54", "143", "71", "72", "0.29", "2.26", "608"], ["3", "2394", "1153", "1241", "4.60", "530", "262", "268", "1.07", "3.53", "953"], ["4", "3079", "1476", "1603", "5.94", "724", "359", "365", "1.45", "4.49", "1210"], ["5", "3507", "1685", "1822", "6.75", "839", "412", "427", "1.70", "5.05", "1363"], ["6", "3803", "1832", "1971", "7.30", "894", "440", "454", "1.81", "5.49", "1483"], ["7", "3923", "1890", "2033", "7.53", "930", "456", "474", "1.89", "5.65", "1523"], ["8", "4003", "1929", "2074", "7.68", "959", "471", "488", "1.94", "5.74", "1549"], ["9", "4126", "1991", "2135", "7.91", "1020", "502", "518", "2.06", "5.85", "1578"], ["10", "4192", "2057", "2135", "7.91", "1068", "500", "568", "2.26", "5.65", "1524"]], "row_count": 12, "column_count": 11, "numeric_cells": 112, "header_rows": 2, "locator": "section[19]/table-wrap[1]#TS6"}}, {"id": "asset:table:pmid:24555089:7", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:673b401b227db41b41881138c6afa756e32b0d87b2ea333577ba5de274d5fd35", "bytes": 599, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[20]/table-wrap[1]#TS7", "version": null, "note": "Reproducibility of exon skipping (ES) discovery from transcripts assembled with different methods, and robustness with varying cutoffs (V bp) for the margin of error when comparing exon and intron boundaries.", "structure": {"pmcid": "PMC3892928", "section_index": 20, "section_title": "S7. Reproducibility of exon skipping event discovery with other assembly methods", "row_count": 6, "column_count": 5}, "table": {"label": "Table S7.", "caption": "Reproducibility of exon skipping (ES) discovery from transcripts assembled with different methods, and robustness with varying cutoffs (V bp) for the margin of error when comparing exon and intron boundaries.", "rows": [["Method", "ES events", "Found by other methods"], ["V=0", "V=5", "V=10"], ["Cufflinks", "2,934", "2,471", "2,480", "2,482"], ["IsoCEM", "1,486", "1,361", "1,364", "1,365"], ["SLIDE", "1,418", "860", "884", "895"], ["Scripture", "4,770", "2,984", "3,072", "3,096"]], "row_count": 6, "column_count": 5, "numeric_cells": 19, "header_rows": 2, "locator": "section[20]/table-wrap[1]#TS7"}}, {"id": "asset:table:pmid:24555089:8", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e9862890d9e7581d352da420851dca796ab58cdfb77b7b41222025c3f5e2a69b", "bytes": 608, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[20]/table-wrap[2]#TS9", "version": null, "note": "Summary of novel features by comparison to four annotation databases (CCDS, UCSC Genes, Ensembl v. 61, and H-DBAS).Exon and intron boundaries were compared allowing for a small difference (up to V=0, 5 and 10 bp). Values in bold are those reported in the main text.", "structure": {"pmcid": "PMC3892928", "section_index": 20, "section_title": "S7. Reproducibility of exon skipping event discovery with other assembly methods", "row_count": 5, "column_count": 4}, "table": {"label": "Table S9.", "caption": "Summary of novel features by comparison to four annotation databases (CCDS, UCSC Genes, Ensembl v. 61, and H-DBAS).Exon and intron boundaries were compared allowing for a small difference (up to V=0, 5 and 10 bp). 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