FAM188B enhances cell survival via interaction with USP7.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29795372", "kind": "science-record", "revision": 7, "content_hash": "sha256:47070bda61b0149f4e7d6f16ef4820e286670c1eb42810a74e86a3abe7a85db0", "created_at": "2026-11-01T15:40:34Z", "updated_at": "2026-11-01T21:21:26Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "FAM188B enhances cell survival via interaction with USP7.", "doi": "10.1038/s41419-018-0650-6", "pmid": "29795372", "authors": ["Eun-Seok Choi", "Hanna Lee", "Jee Young Sung", "Chang-Hun Lee", "Hyonchol Jang", "Kyung Tae Kim", "Yong-Nyun Kim", "Hyoung-Pyo Kim", "Sung-Ho Goh"], "journal": "Cell death & disease", "year": 2018, "abstract": "We have previously reported that FAM188B showed significant differential exon usage in cancers (NCBI GEO GSE30727), but the expression and function of FAM188B is not well characterized. In the present study, we explored the functions of FAM188B by a knockdown strategy, using siRNAs specific for FAM188B in colon cancer cell lines. FAM188B is a novel gene that encodes a protein that is evolutionarily conserved among mammals. Its mRNA has been found to be highly expressed in most solid tumors, including colorectal cancer. FAM188B knockdown induced cell growth inhibition due to an increase in apoptosis in colon cancer cell lines. Interestingly, siFAM188B treatment induced the upregulation and activation of p53, and consequently increased p53-regulated pro-apoptotic proteins, PUMA and BAX. Proteomic analysis of FAM188B immunocomplexes revealed p53 and USP7 as putative FAM188B-interacting proteins. Deletion of the putative USP7-binding motif in FAM188B reduced complex formation of FAM188B with USP7. It is noteworthy that FAM188B knockdown resulted in a decrease in overall ubiquitination in the p53 immunocomplexes, as well as p53 ubiquitination, because USP7 is involved in p53 deubiquitination. FAM188B knockdown inhibited both colony formation and anchorage-independent growth in vitro. In addition, FAM188B knockdown by siRNA reduced tumor growth in xenografted mice, with an increase in p53 proteins. Taken together, our data suggest that FAM188B is a putative oncogene that functions via interaction with USP7. Therefore, control of FAM188B could be a possible target to inhibit tumor growth.", "claims": [{"id": "claim-method", "statement": "The statistical significance of differences between groups was determined using χ2-test and Student’s t-test. p-values <0.05 were considered statistically significant.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29795372", "locator": "sections[22] \"Statistical analysis\" paragraph 2", "quote": "The statistical significance of differences between groups was determined using χ2-test and Student’s t-test. p-values <0.05 were considered statistically significant."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Datasets were obtained from Cancer Cell Line Encyclopedia (CCLE) database (https://portals.broadinstitute.org/ccle)20 for cancer cell lines.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29795372", "locator": "sections[10] \"Datasets from the public databases\" paragraph 2", "quote": "Datasets were obtained from Cancer Cell Line Encyclopedia (CCLE) database (https://portals.broadinstitute.org/ccle)20 for cancer cell lines."}], "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:29795372"], "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:GSE20842"], "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:GSE20842"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:29795372", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41419-018-0650-6", "sha256": "sha256:b1722095dde52a4edafbd8738c4b615d9676d50d725aaaa3ce44c500fecaa162", "bytes": 45163, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41419-018-0650-6", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5967306", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE20842", "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=GSE20842", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE20842", "version": null, "note": "Datasets were obtained from Cancer Cell Line Encyclopedia (CCLE) database (https://portals.broadinstitute.org/ccle)20 for cancer cell lines.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Datasets were obtained from Cancer Cell Line Encyclopedia (CCLE) database (https://portals.broadinstitute.org/ccle)20 for cancer cell lines.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM521114", "GSM521115", "GSM521116", "GSM521117", "GSM521118", "GSM521119", "GSM521120", "GSM521121", "GSM521122", "GSM521123", "GSM521124", "GSM521125", "GSM521126", "GSM521127", "GSM521128", "GSM521129", "GSM521130", "GSM521131", "GSM521132", "GSM521133", "GSM521134", "GSM521135", "GSM521136", "GSM521137", "GSM521138", "GSM521139", "GSM521140", "GSM521141", "GSM521142", "GSM521143", "GSM521144", "GSM521145", "GSM521146", "GSM521147", "GSM521148", "GSM521149", "GSM521150", "GSM521151", "GSM521152", "GSM521153", "GSM521154", "GSM521155", "GSM521156", "GSM521157", "GSM521158", "GSM521159", "GSM521160", "GSM521161", "GSM521162", "GSM521163", "GSM521164", "GSM521165", "GSM521166", "GSM521167", "GSM521168", "GSM521169", "GSM521170", "GSM521171", "GSM521172", "GSM521173", "GSM521174", "GSM521175", "GSM521176", "GSM521177", "GSM521178", "GSM521179", "GSM521180", "GSM521181", "GSM521182", "GSM521183", "GSM521184", "GSM521185", "GSM521186", "GSM521187", "GSM521188", "GSM521189", "GSM521190", "GSM521191", "GSM521192", "GSM521193", "GSM521194", "GSM521195", "GSM521196", "GSM521197", "GSM521198", "GSM521199", "GSM521200", "GSM521201", "GSM521202", "GSM521203", "GSM521204", "GSM521205", "GSM521206", "GSM521207", "GSM521208", "GSM521209", "GSM521210", "GSM521211", "GSM521212", "GSM521213", "GSM521214", "GSM521215", "GSM521216", "GSM521217", "GSM521218", "GSM521219", "GSM521220", "GSM521221", "GSM521222", "GSM521223", "GSM521224", "GSM521225", "GSM521226", "GSM521227", "GSM521228", "GSM521229", "GSM521230", "GSM521231", "GSM521232", "GSM521233", "GSM521234", "GSM521235", "GSM521236", "GSM521237", "GSM521238", "GSM521239", "GSM521240", "GSM521241", "GSM521242", "GSM521243"], "sample_count": 130, "group_sizes": null, "group_sizes_basis": null, "platform": "4133", "taxon": "Homo sapiens", "title": "Mutated KRAS induces overexpression of DUSP4, a MAP-kinase phosphatase, and SMYD3, a histone methyltransferase, in rectal carcinomas", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE20916", "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=GSE20916", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE20916", "version": null, "note": "Datasets were obtained from Cancer Cell Line Encyclopedia (CCLE) database (https://portals.broadinstitute.org/ccle)20 for cancer cell lines.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Datasets were obtained from Cancer Cell Line Encyclopedia (CCLE) database (https://portals.broadinstitute.org/ccle)20 for cancer cell lines.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM523242", "GSM523243", "GSM523244", "GSM523245", "GSM523246", "GSM523247", "GSM523248", "GSM523249", "GSM523250", "GSM523251", "GSM523252", "GSM523253", "GSM523254", "GSM523255", "GSM523256", "GSM523257", "GSM523258", "GSM523259", "GSM523260", "GSM523261", "GSM523262", "GSM523263", "GSM523264", "GSM523265", "GSM523266", "GSM523267", "GSM523268", "GSM523269", "GSM523270", "GSM523271", "GSM523272", "GSM523273", "GSM523274", "GSM523275", "GSM523276", "GSM523277", "GSM523278", "GSM523279", "GSM523280", "GSM523281", "GSM523282", "GSM523283", "GSM523284", "GSM523285", "GSM523286", "GSM523287", "GSM523288", "GSM523289", "GSM523290", "GSM523291", "GSM523292", "GSM523293", "GSM523294", "GSM523295", "GSM523296", "GSM523297", "GSM523298", "GSM523299", "GSM523300", "GSM523301", "GSM523302", "GSM523303", "GSM523304", "GSM523305", "GSM523306", "GSM523307", "GSM523308", "GSM523309", "GSM523310", "GSM523311", "GSM523312", "GSM523313", "GSM523314", "GSM523315", "GSM523316", "GSM523317", "GSM523318", "GSM523319", "GSM523320", "GSM523321", "GSM523322", "GSM523323", "GSM523324", "GSM523325", "GSM523326", "GSM523327", "GSM523328", "GSM523329", "GSM523330", "GSM523331", "GSM523332", "GSM523333", "GSM523334", "GSM523335", "GSM523336", "GSM523337", "GSM523338", "GSM523339", "GSM523340", "GSM523341", "GSM523342", "GSM523343", "GSM523344", "GSM523345", "GSM523346", "GSM523347", "GSM523348", "GSM523349", "GSM523350", "GSM523351", "GSM523352", "GSM523353", "GSM523354", "GSM523355", "GSM523356", "GSM523357", "GSM523358", "GSM523359", "GSM523360", "GSM523361", "GSM523362", "GSM523363", "GSM523364", "GSM523365", "GSM523366", "GSM523367", "GSM523368", "GSM523369", "GSM523370", "GSM523371", "GSM523372", "GSM523373", "GSM523374", "GSM523375", "GSM523376", "GSM523377", "GSM523378", "GSM523379", "GSM523380", "GSM523381", "GSM523382", "GSM523383", "GSM523384", "GSM523385", "GSM523386"], "sample_count": 145, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Modeling oncogenic signaling in colon tumors by multidirectional analyses of microarray data", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE30727", "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=GSE30727", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE30727", "version": null, "note": "Datasets were obtained from Cancer Cell Line Encyclopedia (CCLE) database (https://portals.broadinstitute.org/ccle)20 for cancer cell lines.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Datasets were obtained from Cancer Cell Line Encyclopedia (CCLE) database (https://portals.broadinstitute.org/ccle)20 for cancer cell lines.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM762729", "GSM762730", "GSM762731", "GSM762732", "GSM762733", "GSM762734", "GSM762735", "GSM762736", "GSM762737", "GSM762738", "GSM762739", "GSM762740", "GSM762741", "GSM762742", "GSM762743", "GSM762744", "GSM762745", "GSM762746", "GSM762747", "GSM762748", "GSM762749", "GSM762750", "GSM762751", "GSM762752", "GSM762753", "GSM762754", "GSM762755", "GSM762756", "GSM762757", "GSM762758", "GSM762759", "GSM762760", "GSM762761", "GSM762762", "GSM762763", "GSM762764", "GSM762765", "GSM762766", "GSM762767", "GSM762768", "GSM762769", "GSM762770", "GSM762771", "GSM762772", "GSM762773", "GSM762774", "GSM762775", "GSM762776", "GSM762777", "GSM762778", "GSM762779", "GSM762780", "GSM762781", "GSM762782", "GSM762783", "GSM762784", "GSM762785", "GSM762786", "GSM762787", "GSM762788"], "sample_count": 60, "group_sizes": null, "group_sizes_basis": null, "platform": "5188", "taxon": "Homo sapiens", "title": "Comparison of exon-wise expression profiling between normal and cancer tissues of human stomach", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE20842 not downloaded", "asset:data:geo:GSE20842 licence not read", "asset:data:geo:GSE20916 not downloaded", "asset:data:geo:GSE20916 licence not read", "asset:data:geo:GSE30727 not downloaded", "asset:data:geo:GSE30727 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "contingency_analysis", "specific": "chi_square", "label": "Categorical (contingency table) analysis", "dsl_operations": ["chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The statistical significance of differences between groups was determined using χ2-test and Student’s t-test. p-values <0.05 were considered statistically significant."}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["chi_square_test"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: chi_square."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE20916", "GSE20842", "GSE30727"], "resolved_accessions": ["GSE20916", "GSE20842", "GSE30727"], "statements": ["Datasets were obtained from Cancer Cell Line Encyclopedia (CCLE) database (https://portals.broadinstitute.org/ccle)20 for cancer cell lines."], "basis": "The paper names GSE20916, GSE20842, GSE30727 in Oncomine and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["chi_square_test"], "assets": ["source:pmid:29795372", "data:geo:GSE20842"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE20842"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:11:39Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 36158, "completion_tokens": 2590, "cached_tokens": 792}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:29795372", "type": "paper", "label": "pmid:29795372"}, {"id": "source:pmid:29795372", "type": "manuscript", "label": "PMID 29795372 full text"}, {"id": "data:geo:GSE20842", "type": "dataset", "label": "GEO GSE20842"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:29795372", "type": "paper", "label": "pmid:29795372"}, {"id": "source:pmid:29795372", "type": "manuscript", "label": "PMID 29795372 full text"}, {"id": "data:geo:GSE20842", "type": "dataset", "label": "GEO GSE20842"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-29795372", "type": "extraction", "used": ["source:pmid:29795372"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE20842", "type": "accession_resolution", "used": ["data:geo:GSE20842"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:29795372", "parent_hash": "sha256:7c8acb15dada40fa2de9d3f47da32ceb7ae4eedab38e0968b5818284cc01eeec", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE20842 licence not read", "asset:data:geo:GSE20842 not downloaded", "asset:data:geo:GSE20916 licence not read", "asset:data:geo:GSE20916 not downloaded", "asset:data:geo:GSE30727 licence not read", "asset:data:geo:GSE30727 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["y, we explored the functions of FAM188B by a knockdown strategy, using siRNAs specific for FAM188B", "tumors, including colorectal cancer. FAM188B knockdown induced cell growth inhibition due to an inc", "88B with USP7. It is noteworthy that FAM188B knockdown resulted in a decrease in overall ubiquitina", "is involved in p53 deubiquitination. FAM188B knockdown inhibited both colony formation and anchorag"], "order_basis": "paper_text_order:263", "id": "assay:1"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["cell growth inhibition due to an increase in apoptosis in colon cancer cell lines. Interestingly, s"], "order_basis": "paper_text_order:609", "id": "assay:2"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["Materials and methods In vivo analysis of FAM188B silencing HCT-116 (2.0 ×"], "order_basis": "paper_text_order:1667", "id": "assay:3"}, {"role": "analysis", "definition_id": "contingency_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["chi_square_test"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The statistical significance of differences between groups was determined using χ2-test and Student’s t-test. p-values <0.05 were considered statistically significant."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}