{"data":{"id":"10.6084/m9.figshare.1493050.v1","type":"dois","attributes":{"doi":"10.6084/m9.figshare.1493050.v1","prefix":"10.6084","suffix":"m9.figshare.1493050.v1","identifiers":[],"alternateIdentifiers":[],"creators":[{"name":"Lebovitz, Chandra B","nameType":"Personal","givenName":"Chandra B","familyName":"Lebovitz","affiliation":[],"nameIdentifiers":[]},{"name":"A Gordon Robertson","affiliation":[],"nameIdentifiers":[]},{"name":"Goya, Rodrigo","nameType":"Personal","givenName":"Rodrigo","familyName":"Goya","affiliation":[],"nameIdentifiers":[]},{"name":"Jones, Steven J","nameType":"Personal","givenName":"Steven J","familyName":"Jones","affiliation":[],"nameIdentifiers":[]},{"name":"Morin, Ryan D","nameType":"Personal","givenName":"Ryan D","familyName":"Morin","affiliation":[],"nameIdentifiers":[]},{"name":"Marra, Marco A","nameType":"Personal","givenName":"Marco A","familyName":"Marra","affiliation":[],"nameIdentifiers":[]},{"name":"Gorski, Sharon M","nameType":"Personal","givenName":"Sharon M","familyName":"Gorski","affiliation":[],"nameIdentifiers":[]}],"titles":[{"title":"Cross-cancer profiling of molecular alterations within the human autophagy interaction network"}],"publisher":"Taylor \u0026 Francis","container":{},"publicationYear":2015,"subjects":[{"subject":"Plant Biology"},{"subject":"FOS: Biological sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Biological sciences","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"Cancer"},{"subject":"Marine Biology"},{"subject":"Developmental Biology"},{"subject":"Mathematics"},{"subject":"FOS: Mathematics","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Mathematics","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"Biological Sciences"},{"subject":"Immunology"},{"subject":"FOS: Clinical medicine","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Clinical medicine","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"Earth and Environmental Sciences"},{"subject":"Molecular Biology"},{"subject":"Genetics"},{"subject":"Cell Biology"}],"contributors":[],"dates":[{"date":"2015-09-02","dateType":"Created"},{"date":"2020-08-25","dateType":"Updated"},{"date":"2015","dateType":"Issued"}],"language":null,"types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Dataset","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[{"relationType":"IsSupplementTo","relatedIdentifier":"10.1080/15548627.2015.1067362","relatedIdentifierType":"DOI"},{"relationType":"IsPreviousVersionOf","relatedIdentifier":"10.6084/m9.figshare.1493050","relatedIdentifierType":"DOI"}],"relatedItems":[],"sizes":["404824 Bytes"],"formats":[],"version":null,"rightsList":[{"rights":"Creative Commons Attribution 4.0 International","rightsUri":"https://creativecommons.org/licenses/by/4.0/legalcode","schemeUri":"https://spdx.org/licenses/","rightsIdentifier":"cc-by-4.0","rightsIdentifierScheme":"SPDX"}],"descriptions":[{"description":"Aberrant activation or disruption of autophagy promotes tumorigenesis in various preclinical models of cancer, but whether the autophagy pathway is a target for recurrent molecular alteration in human cancer patient samples is unknown. To address this outstanding question, we surveyed 211 human autophagy-associated genes for tumor-related alterations to DNA sequence and RNA expression levels and examined their association with patient survival outcomes in multiple cancer types with sequence data from The Cancer Genome Atlas consortium. We found 3 (\u003ci\u003eRB1CC1/FIP200, ULK4, WDR45/WIPI4\u003c/i\u003e) and one (\u003ci\u003eATG7\u003c/i\u003e) core autophagy genes to be under positive selection for somatic mutations in endometrial carcinoma and clear cell renal carcinoma, respectively; while 29 autophagy regulators and pathway interactors, including previously identified \u003ci\u003eKEAP1, NFE2L2\u003c/i\u003e and \u003ci\u003eMTOR\u003c/i\u003e, were significantly mutated in 6 of the 11 cancer types examined. Gene expression analyses revealed that \u003ci\u003eGABARAPL1\u003c/i\u003e and \u003ci\u003eMAP1LC3C/LC3C\u003c/i\u003e transcripts were less abundant in breast cancer and non-small cell lung cancers than in matched normal tissue controls; \u003ci\u003eATG4D\u003c/i\u003e transcripts were increased in lung squamous cell carcinoma, as were \u003ci\u003eATG16L2\u003c/i\u003e transcripts in kidney cancer. Unsupervised clustering of autophagy-associated mRNA levels in tumors stratified patient overall survival in 3 of 9 cancer types (acute myeloid leukemia, clear cell renal carcinoma, and head and neck cancer). These analyses provide the first comprehensive resource of recurrently altered autophagy-associated genes in human tumors, and highlight cancer types and subtypes where perturbed autophagy may be relevant to patient overall survival.","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"xml":"PD94bWwgdmVyc2lvbj0iMS4wIiBlbmNvZGluZz0iVVRGLTgiPz4KPHJlc291cmNlIHhtbG5zPSJodHRwOi8vZGF0YWNpdGUub3JnL3NjaGVtYS9rZXJuZWwtNCIgeG1sbnM6eHNpPSJodHRwOi8vd3d3LnczLm9yZy8yMDAxL1hNTFNjaGVtYS1pbnN0YW5jZSIgeHNpOnNjaGVtYUxvY2F0aW9uPSJodHRwOi8vZGF0YWNpdGUub3JnL3NjaGVtYS9rZXJuZWwtNCBodHRwOi8vc2NoZW1hLmRhdGFjaXRlLm9yZy9tZXRhL2tlcm5lbC00LjEvbWV0YWRhdGEueHNkIj4KICA8aWRlbnRpZmllciBpZGVudGlmaWVyVHlwZT0iRE9JIj4xMC42MDg0L005LkZJR1NIQVJFLjE0OTMwNTAuVjE8L2lkZW50aWZpZXI+CiAgPGNyZWF0b3JzPgogICAgPGNyZWF0b3I+CiAgICAgIDxjcmVhdG9yTmFtZT5DaGFuZHJhIEIgTGVib3ZpdHo8L2NyZWF0b3JOYW1lPgogICAgPC9jcmVhdG9yPgogICAgPGNyZWF0b3I+CiAgICAgIDxjcmVhdG9yTmFtZT5BIEdvcmRvbiBSb2JlcnRzb248L2NyZWF0b3JOYW1lPgogICAgPC9jcmVhdG9yPgogICAgPGNyZWF0b3I+CiAgICAgIDxjcmVhdG9yTmFtZT5Sb2RyaWdvIEdveWE8L2NyZWF0b3JOYW1lPgogICAgPC9jcmVhdG9yPgogICAgPGNyZWF0b3I+CiAgICAgIDxjcmVhdG9yTmFtZT5TdGV2ZW4gSiBKb25lczwvY3JlYXRvck5hbWU+CiAgICA8L2NyZWF0b3I+CiAgICA8Y3JlYXRvcj4KICAgICAgPGNyZWF0b3JOYW1lPlJ5YW4gRCBNb3JpbjwvY3JlYXRvck5hbWU+CiAgICA8L2NyZWF0b3I+CiAgICA8Y3JlYXRvcj4KICAgICAgPGNyZWF0b3JOYW1lPk1hcmNvIEEgTWFycmE8L2NyZWF0b3JOYW1lPgogICAgPC9jcmVhdG9yPgogICAgPGNyZWF0b3I+CiAgICAgIDxjcmVhdG9yTmFtZT5TaGFyb24gTSBHb3Jza2k8L2NyZWF0b3JOYW1lPgogICAgPC9jcmVhdG9yPgogIDwvY3JlYXRvcnM+CiAgPHRpdGxlcz4KICAgIDx0aXRsZT5Dcm9zcy1jYW5jZXIgcHJvZmlsaW5nIG9mIG1vbGVjdWxhciBhbHRlcmF0aW9ucyB3aXRoaW4gdGhlIGh1bWFuIGF1dG9waGFneSBpbnRlcmFjdGlvbiBuZXR3b3JrPC90aXRsZT4KICA8L3RpdGxlcz4KICA8ZGVzY3JpcHRpb25zPgogICAgPGRlc2NyaXB0aW9uIGRlc2NyaXB0aW9uVHlwZT0iQWJzdHJhY3QiPiZsdDtkaXYmZ3Q7Jmx0O3AmZ3Q7Jmx0Oy9wJmd0OyZsdDtwJmd0O0FiZXJyYW50IGFjdGl2YXRpb24gb3IgZGlzcnVwdGlvbiBvZiBhdXRvcGhhZ3kgcHJvbW90ZXMgdHVtb3JpZ2VuZXNpcyBpbiB2YXJpb3VzIHByZWNsaW5pY2FsIG1vZGVscyBvZiBjYW5jZXIsIGJ1dCB3aGV0aGVyIHRoZSBhdXRvcGhhZ3kgcGF0aHdheSBpcyBhIHRhcmdldCBmb3IgcmVjdXJyZW50IG1vbGVjdWxhciBhbHRlcmF0aW9uIGluIGh1bWFuIGNhbmNlciBwYXRpZW50IHNhbXBsZXMgaXMgdW5rbm93bi4gVG8gYWRkcmVzcyB0aGlzIG91dHN0YW5kaW5nIHF1ZXN0aW9uLCB3ZSBzdXJ2ZXllZCAyMTEgaHVtYW4gYXV0b3BoYWd5LWFzc29jaWF0ZWQgZ2VuZXMgZm9yIHR1bW9yLXJlbGF0ZWQgYWx0ZXJhdGlvbnMgdG8gRE5BIHNlcXVlbmNlIGFuZCBSTkEgZXhwcmVzc2lvbiBsZXZlbHMgYW5kIGV4YW1pbmVkIHRoZWlyIGFzc29jaWF0aW9uIHdpdGggcGF0aWVudCBzdXJ2aXZhbCBvdXRjb21lcyBpbiBtdWx0aXBsZSBjYW5jZXIgdHlwZXMgd2l0aCBzZXF1ZW5jZSBkYXRhIGZyb20gVGhlIENhbmNlciBHZW5vbWUgQXRsYXMgY29uc29ydGl1bS4gV2UgZm91bmQgMyAoJmx0O2kmZ3Q7UkIxQ0MxL0ZJUDIwMCwgVUxLNCwgV0RSNDUvV0lQSTQmbHQ7L2kmZ3Q7KSBhbmQgb25lICgmbHQ7aSZndDtBVEc3Jmx0Oy9pJmd0OykgY29yZSBhdXRvcGhhZ3kgZ2VuZXMgdG8gYmUgdW5kZXIgcG9zaXRpdmUgc2VsZWN0aW9uIGZvciBzb21hdGljIG11dGF0aW9ucyBpbiBlbmRvbWV0cmlhbCBjYXJjaW5vbWEgYW5kIGNsZWFyIGNlbGwgcmVuYWwgY2FyY2lub21hLCByZXNwZWN0aXZlbHk7IHdoaWxlIDI5IGF1dG9waGFneSByZWd1bGF0b3JzIGFuZCBwYXRod2F5IGludGVyYWN0b3JzLCBpbmNsdWRpbmcgcHJldmlvdXNseSBpZGVudGlmaWVkICZsdDtpJmd0O0tFQVAxLCBORkUyTDImbHQ7L2kmZ3Q7IGFuZCAmbHQ7aSZndDtNVE9SJmx0Oy9pJmd0Oywgd2VyZSBzaWduaWZpY2FudGx5IG11dGF0ZWQgaW4gNiBvZiB0aGUgMTEgY2FuY2VyIHR5cGVzIGV4YW1pbmVkLiBHZW5lIGV4cHJlc3Npb24gYW5hbHlzZXMgcmV2ZWFsZWQgdGhhdCAmbHQ7aSZndDtHQUJBUkFQTDEmbHQ7L2kmZ3Q7IGFuZCAmbHQ7aSZndDtNQVAxTEMzQy9MQzNDJmx0Oy9pJmd0OyB0cmFuc2NyaXB0cyB3ZXJlIGxlc3MgYWJ1bmRhbnQgaW4gYnJlYXN0IGNhbmNlciBhbmQgbm9uLXNtYWxsIGNlbGwgbHVuZyBjYW5jZXJzIHRoYW4gaW4gbWF0Y2hlZCBub3JtYWwgdGlzc3VlIGNvbnRyb2xzOyAmbHQ7aSZndDtBVEc0RCZsdDsvaSZndDsgdHJhbnNjcmlwdHMgd2VyZSBpbmNyZWFzZWQgaW4gbHVuZyBzcXVhbW91cyBjZWxsIGNhcmNpbm9tYSwgYXMgd2VyZSAmbHQ7aSZndDtBVEcxNkwyJmx0Oy9pJmd0OyB0cmFuc2NyaXB0cyBpbiBraWRuZXkgY2FuY2VyLiBVbnN1cGVydmlzZWQgY2x1c3RlcmluZyBvZiBhdXRvcGhhZ3ktYXNzb2NpYXRlZCBtUk5BIGxldmVscyBpbiB0dW1vcnMgc3RyYXRpZmllZCBwYXRpZW50IG92ZXJhbGwgc3Vydml2YWwgaW4gMyBvZiA5IGNhbmNlciB0eXBlcyAoYWN1dGUgbXllbG9pZCBsZXVrZW1pYSwgY2xlYXIgY2VsbCByZW5hbCBjYXJjaW5vbWEsIGFuZCBoZWFkIGFuZCBuZWNrIGNhbmNlcikuIFRoZXNlIGFuYWx5c2VzIHByb3ZpZGUgdGhlIGZpcnN0IGNvbXByZWhlbnNpdmUgcmVzb3VyY2Ugb2YgcmVjdXJyZW50bHkgYWx0ZXJlZCBhdXRvcGhhZ3ktYXNzb2NpYXRlZCBnZW5lcyBpbiBodW1hbiB0dW1vcnMsIGFuZCBoaWdobGlnaHQgY2FuY2VyIHR5cGVzIGFuZCBzdWJ0eXBlcyB3aGVyZSBwZXJ0dXJiZWQgYXV0b3BoYWd5IG1heSBiZSByZWxldmFudCB0byBwYXRpZW50IG92ZXJhbGwgc3Vydml2YWwuJmx0Oy9wJmd0OyZsdDsvZGl2Jmd0OzwvZGVzY3JpcHRpb24+CiAgPC9kZXNjcmlwdGlvbnM+CiAgPHN1YmplY3RzPgogICAgPHN1YmplY3Q+UGxhbnQgQmlvbG9neTwvc3ViamVjdD4KICAgIDxzdWJqZWN0PkNhbmNlcjwvc3ViamVjdD4KICAgIDxzdWJqZWN0Pk1hcmluZSBCaW9sb2d5PC9zdWJqZWN0PgogICAgPHN1YmplY3Q+RGV2ZWxvcG1lbnRhbCBCaW9sb2d5PC9zdWJqZWN0PgogICAgPHN1YmplY3Q+TWF0aGVtYXRpY3M8L3N1YmplY3Q+CiAgICA8c3ViamVjdD5CaW9sb2dpY2FsIFNjaWVuY2VzPC9zdWJqZWN0PgogICAgPHN1YmplY3Q+SW1tdW5vbG9neTwvc3ViamVjdD4KICAgIDxzdWJqZWN0PkVhcnRoIGFuZCBFbnZpcm9ubWVudGFsIFNjaWVuY2VzPC9zdWJqZWN0PgogICAgPHN1YmplY3Q+TW9sZWN1bGFyIEJpb2xvZ3k8L3N1YmplY3Q+CiAgICA8c3ViamVjdD5HZW5ldGljczwvc3ViamVjdD4KICAgIDxzdWJqZWN0PkNlbGwgQmlvbG9neTwvc3ViamVjdD4KICA8L3N1YmplY3RzPgogIDxwdWJsaXNoZXI+VGF5bG9yICZhbXA7IEZyYW5jaXM8L3B1Ymxpc2hlcj4KICA8cHVibGljYXRpb25ZZWFyPjIwMTU8L3B1YmxpY2F0aW9uWWVhcj4KICA8ZGF0ZXM+CiAgICA8ZGF0ZSBkYXRlVHlwZT0iQ3JlYXRlZCI+MjAxNS0wOS0wMjwvZGF0ZT4KICAgIDxkYXRlIGRhdGVUeXBlPSJVcGRhdGVkIj4yMDIwLTA4LTI1PC9kYXRlPgogIDwvZGF0ZXM+CiAgPHJlc291cmNlVHlwZSByZXNvdXJjZVR5cGVHZW5lcmFsPSJEYXRhc2V0Ij5EYXRhc2V0PC9yZXNvdXJjZVR5cGU+CiAgPHNpemVzPgogICAgPHNpemU+NDA0ODI0IEJ5dGVzPC9zaXplPgogIDwvc2l6ZXM+CiAgPHJlbGF0ZWRJZGVudGlmaWVycz4KICAgIDxyZWxhdGVkSWRlbnRpZmllciByZWxhdGVkSWRlbnRpZmllclR5cGU9IkRPSSIgcmVsYXRpb25UeXBlPSJJc1N1cHBsZW1lbnRUbyI+MTAuMTA4MC8xNTU0ODYyNy4yMDE1LjEwNjczNjI8L3JlbGF0ZWRJZGVudGlmaWVyPgogICAgPHJlbGF0ZWRJZGVudGlmaWVyIHJlbGF0ZWRJZGVudGlmaWVyVHlwZT0iRE9JIiByZWxhdGlvblR5cGU9IklzUHJldmlvdXNWZXJzaW9uT2YiPjEwLjYwODQvbTkuZmlnc2hhcmUuMTQ5MzA1MDwvcmVsYXRlZElkZW50aWZpZXI+CiAgPC9yZWxhdGVkSWRlbnRpZmllcnM+CiAgPHJpZ2h0c0xpc3Q+CiAgICA8cmlnaHRzIHJpZ2h0c1VSST0iaHR0cHM6Ly9jcmVhdGl2ZWNvbW1vbnMub3JnL2xpY2Vuc2VzL2J5LzQuMC8iPkNDIEJZIDQuMDwvcmlnaHRzPgogIDwvcmlnaHRzTGlzdD4KPC9yZXNvdXJjZT4=","url":"https://tandf.figshare.com/articles/dataset/Cross_cancer_profiling_of_molecular_alterations_within_the_human_autophagy_interaction_network/1493050/1","contentUrl":null,"metadataVersion":3,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"viewCount":0,"viewsOverTime":[],"downloadCount":0,"downloadsOverTime":[],"referenceCount":0,"citationCount":0,"citationsOverTime":[],"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2016-01-20T01:19:13.000Z","registered":"2016-01-20T01:19:14.000Z","published":"2015","updated":"2020-09-04T16:25:49.000Z"},"relationships":{"client":{"data":{"id":"figshare.ars","type":"clients"}},"provider":{"data":{"id":"otjm","type":"providers"}},"media":{"data":{"id":"10.6084/m9.figshare.1493050.v1","type":"media"}},"references":{"data":[]},"citations":{"data":[]},"parts":{"data":[]},"partOf":{"data":[]},"versions":{"data":[]},"versionOf":{"data":[]}}}}