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n3:pmcid: PMC0
bibo:doi: 10.1371%2Fjournal.pone.0009983
n5:contains: _:vb7476295 _:vb7476258 _:vb7476255 _:vb7476250

Subject Item: _:vb7476250
rdf:type: n5:Section
dc:title: introduction
n5:contains: _:vb7476252 _:vb7476253 _:vb7476254 _:vb7476251

Subject Item: _:vb7476251
rdf:type: n3:Context
rdf:value: Numerous gene expression studies have identified lists of genes with significantly altered expression, but disappointingly there is little consensus between studies [>>1<<]. While gene expression studies are useful in identifying broad categories of pathways altered in cancer and clinically important subtypes [2], on their own they may not be able to distinguish the genetically altered key driver genes. An
n3:mentions: n2:18217975

Subject Item: _:vb7476252
rdf:type: n3:Context
rdf:value: While gene expression studies are useful in identifying broad categories of pathways altered in cancer and clinically important subtypes [>>2<<], on their own they may not be able to distinguish the genetically altered key driver genes.
n3:mentions: n2:18698038

Subject Item: _:vb7476253
rdf:type: n3:Context
rdf:value: Early studies were hampered because the technologies for genome-wide genomic analysis lacked the resolution to adequately refine cancer associated loci [>>3<<]. The problem of resolution has been overcome with the development of ultra-high resolution aCGH and SNP arrays. Recently, our group has used these latest-generation SNP arrays to annotate even small regions (as small as 25 kb) of genomic
n3:mentions: n2:19383377

Subject Item: _:vb7476254
rdf:type: n3:Context
rdf:value: Recently, our group has used these latest-generation SNP arrays to annotate even small regions (as small as 25 kb) of genomic alteration [>>4<<]. This data also demonstrated that the genetic events occurring in ovarian cancers are more numerous and complex than previously suspected. While some potential driver genes could be rapidly identified from this data due to their location
n3:mentions: n2:17699850

Subject Item: _:vb7476255
rdf:type: n5:Section
dc:title: materials and methods
n5:contains: _:vb7476256 _:vb7476257

Subject Item: _:vb7476256
rdf:type: n3:Context
rdf:value: Louis, Missouri) and Bioconductor packages in the R-open source software framework [34], [>>35<<]. SNP 6.0 CEL files were imported into Partek using default settings for background correction and summarisation. Human Genome Build 36.1 (hg18, March 2006) was used for base pair locations. Probeset copy number ratios were calculated by
n3:mentions: n2:15461798

Subject Item: _:vb7476257
rdf:type: n3:Context
rdf:value: Circular binary segmentation [>>36<<] was performed using the R-based package “DNAcopy” to segment the data into distinct regions of change using default package settings.
n3:mentions: n2:15475419

Subject Item: _:vb7476258
rdf:type: n5:Section
dc:title: results
n5:contains: _:vb7476292 _:vb7476293 _:vb7476294 _:vb7476288 _:vb7476289 _:vb7476290 _:vb7476291 _:vb7476268 _:vb7476269 _:vb7476270 _:vb7476271 _:vb7476264 _:vb7476265 _:vb7476266 _:vb7476267 _:vb7476260 _:vb7476261 _:vb7476262 _:vb7476263 _:vb7476259 _:vb7476284 _:vb7476285 _:vb7476286 _:vb7476287 _:vb7476280 _:vb7476281 _:vb7476282 _:vb7476283 _:vb7476276 _:vb7476277 _:vb7476278 _:vb7476279 _:vb7476272 _:vb7476273 _:vb7476274 _:vb7476275

Subject Item: _:vb7476259
rdf:type: n3:Context
rdf:value: We have previously conducted an integrated expression analysis of candidate tumour suppressor genes within regions of loss of heterozygosity on an overlapping tumour cohort [>>6<<], thus for this study we chose to focus on the identification of candidate genes located within amplicons.
n3:mentions: n2:19603523

Subject Item: _:vb7476260
rdf:type: n3:Context
rdf:value: Our main approach to identify cancer-related genes was to filter for the most frequent aberrations but we noted that well characterised cancer driver genes, such as CCNE1 and ERBB2 [>>7<<], were not identified since they were amplified in less than 40% of tumours.
n3:mentions: n2:20029424

Subject Item: _:vb7476261
rdf:type: n3:Context
rdf:value: Genes in italics are known oncogenes (based on Cancer Gene Census [>>38<<]), *Genes that show a strong (r>0.6) positive correlation of copy number with expression, †Not on expression microarray.
n3:mentions: n2:14993899

Subject Item: _:vb7476262
rdf:type: n3:Context
rdf:value: GeneChrStartEndTotal gain (%)CommentsOther genes in regionPDCD103168.884168.93543Angiogenesis disorder [>>39<<], ERK pathway [40] PRKCI3171.423171.50651Oncogene in ovarian and other cancers [41], [42] SKIL, PHC3, MYNNECT23173.955174.02250Cytokinesis [43].
n3:mentions: n2:15543491

Subject Item: _:vb7476263
rdf:type: n3:Context
rdf:value: GeneChrStartEndTotal gain (%)CommentsOther genes in regionPDCD103168.884168.93543Angiogenesis disorder [39], ERK pathway [>>40<<] PRKCI3171.423171.50651Oncogene in ovarian and other cancers [41], [42] SKIL, PHC3, MYNNECT23173.955174.02250Cytokinesis [43].
n3:mentions: n2:17360971

Subject Item: _:vb7476264
rdf:type: n3:Context
rdf:value: GeneChrStartEndTotal gain (%)CommentsOther genes in regionPDCD103168.884168.93543Angiogenesis disorder [39], ERK pathway [40] PRKCI3171.423171.50651Oncogene in ovarian and other cancers [>>41<<], [42] SKIL, PHC3, MYNNECT23173.955174.02250Cytokinesis [43].
n3:mentions: n2:17570678

Subject Item: _:vb7476265
rdf:type: n3:Context
rdf:value: GeneChrStartEndTotal gain (%)CommentsOther genes in regionPDCD103168.884168.93543Angiogenesis disorder [39], ERK pathway [40] PRKCI3171.423171.50651Oncogene in ovarian and other cancers [41], [>>42<<] SKIL, PHC3, MYNNECT23173.955174.02250Cytokinesis [43].
n3:mentions: n2:16651413

Subject Item: _:vb7476266
rdf:type: n3:Context
rdf:value: gain (%)CommentsOther genes in regionPDCD103168.884168.93543Angiogenesis disorder [39], ERK pathway [40] PRKCI3171.423171.50651Oncogene in ovarian and other cancers [41], [42] SKIL, PHC3, MYNNECT23173.955174.02250Cytokinesis [>>43<<]. Transforming protein [44].
n3:mentions: n2:10579713

Subject Item: _:vb7476267
rdf:type: n3:Context
rdf:value: Transforming protein [>>44<<]. Interacts with PRKCI [45] TBL1XR1*3178.221178.39850Oncogene in breast cancer [46], transcriptional repressor [47] PIK3CA*3180.349180.43550Known oncogeneMRPL47, NDUFB5SENP23186.787186.83251SUMO1 deconjugating peptidase.
n3:mentions: n2:8464478

Subject Item: _:vb7476268
rdf:type: n3:Context
rdf:value: Interacts with PRKCI [>>45<<] TBL1XR1*3178.221178.39850Oncogene in breast cancer [46], transcriptional repressor [47] PIK3CA*3180.349180.43550Known oncogeneMRPL47, NDUFB5SENP23186.787186.83251SUMO1 deconjugating peptidase.
n3:mentions: n2:19617897

Subject Item: _:vb7476269
rdf:type: n3:Context
rdf:value: Interacts with PRKCI [45] TBL1XR1*3178.221178.39850Oncogene in breast cancer [>>46<<], transcriptional repressor [47] PIK3CA*3180.349180.43550Known oncogeneMRPL47, NDUFB5SENP23186.787186.83251SUMO1 deconjugating peptidase.
n3:mentions: n2:19706770

Subject Item: _:vb7476270
rdf:type: n3:Context
rdf:value: Interacts with PRKCI [45] TBL1XR1*3178.221178.39850Oncogene in breast cancer [46], transcriptional repressor [>>47<<] PIK3CA*3180.349180.43550Known oncogeneMRPL47, NDUFB5SENP23186.787186.83251SUMO1 deconjugating peptidase.
n3:mentions: n2:12628926

Subject Item: _:vb7476271
rdf:type: n3:Context
rdf:value: Possible role in degradation of beta-catenin [>>48<<].TMEM41AMRPL15*855.21055.22442Mitochondrial ribosomal protein [49] RLBP1L1*862.36362.57746Clavesin 1 (CLVS1), regulates endosome morphology [50], upregulated in liver cancer [51] YWHAZ*8102.000102.0355314-3-3 isoform zeta, oncogenic
n3:mentions: n2:11489887

Subject Item: _:vb7476272
rdf:type: n3:Context
rdf:value: Possible role in degradation of beta-catenin [48].TMEM41AMRPL15*855.21055.22442Mitochondrial ribosomal protein [>>49<<] RLBP1L1*862.36362.57746Clavesin 1 (CLVS1), regulates endosome morphology [50], upregulated in liver cancer [51] YWHAZ*8102.000102.0355314-3-3 isoform zeta, oncogenic functions in inhibiting apoptosis and adhesion [52]
n3:mentions: n2:10593885

Subject Item: _:vb7476273
rdf:type: n3:Context
rdf:value: TMEM41AMRPL15*855.21055.22442Mitochondrial ribosomal protein [49] RLBP1L1*862.36362.57746Clavesin 1 (CLVS1), regulates endosome morphology [>>50<<], upregulated in liver cancer [51] YWHAZ*8102.000102.0355314-3-3 isoform zeta, oncogenic functions in inhibiting apoptosis and adhesion [52] DERL1*8124.095124.12460Endoplasmic reticulum protein [53] with role in stress response.
n3:mentions: n2:19651769

Subject Item: _:vb7476274
rdf:type: n3:Context
rdf:value: TMEM41AMRPL15*855.21055.22442Mitochondrial ribosomal protein [49] RLBP1L1*862.36362.57746Clavesin 1 (CLVS1), regulates endosome morphology [50], upregulated in liver cancer [>>51<<] YWHAZ*8102.000102.0355314-3-3 isoform zeta, oncogenic functions in inhibiting apoptosis and adhesion [52] DERL1*8124.095124.12460Endoplasmic reticulum protein [53] with role in stress response.
n3:mentions: n2:18271718

Subject Item: _:vb7476275
rdf:type: n3:Context
rdf:value: protein [49] RLBP1L1*862.36362.57746Clavesin 1 (CLVS1), regulates endosome morphology [50], upregulated in liver cancer [51] YWHAZ*8102.000102.0355314-3-3 isoform zeta, oncogenic functions in inhibiting apoptosis and adhesion [>>52<<] DERL1*8124.095124.12460Endoplasmic reticulum protein [53] with role in stress response.
n3:mentions: n2:17704798

Subject Item: _:vb7476276
rdf:type: n3:Context
rdf:value: regulates endosome morphology [50], upregulated in liver cancer [51] YWHAZ*8102.000102.0355314-3-3 isoform zeta, oncogenic functions in inhibiting apoptosis and adhesion [52] DERL1*8124.095124.12460Endoplasmic reticulum protein [>>53<<] with role in stress response. Elevated expression in cancer [54], [55] WDR67*, C8orf76*ATAD2*8124.401124.47860ATPase.
n3:mentions: n2:15215855

Subject Item: _:vb7476277
rdf:type: n3:Context
rdf:value: Elevated expression in cancer [>>54<<], [55] WDR67*, C8orf76*ATAD2*8124.401124.47860ATPase.
n3:mentions: n2:18927294

Subject Item: _:vb7476278
rdf:type: n3:Context
rdf:value: Elevated expression in cancer [54], [>>55<<] WDR67*, C8orf76*ATAD2*8124.401124.47860ATPase.
n3:mentions: n2:18205950

Subject Item: _:vb7476279
rdf:type: n3:Context
rdf:value: E2F target, binds MYC, expression correlates with poor outcome in breast cancer [>>56<<]. Interacts with ER and AR and is required for target gene expression [57] WDYHV1/C8ORF32*, FBXO32*, FAM91A1*RNF139*8125.556125.57060Translocation causes hereditary renal cancer. Interacts with VHL [58] NDUFB9*, TRMT12*, TMEM65*,
n3:mentions: n2:19843847

Subject Item: _:vb7476280
rdf:type: n3:Context
rdf:value: Interacts with ER and AR and is required for target gene expression [>>57<<] WDYHV1/C8ORF32*, FBXO32*, FAM91A1*RNF139*8125.556125.57060Translocation causes hereditary renal cancer.
n3:mentions: n2:19318566

Subject Item: _:vb7476281
rdf:type: n3:Context
rdf:value: Interacts with VHL [>>58<<] NDUFB9*, TRMT12*, TMEM65*, SQLE*FAM84B*8127.634127.64061–FAM49B*8130.923131.02161–NDRG1*8134.319134.37960Diverse role in stress response including hypoxia [59].
n3:mentions: n2:12032852

Subject Item: _:vb7476282
rdf:type: n3:Context
rdf:value: Interacts with VHL [58] NDUFB9*, TRMT12*, TMEM65*, SQLE*FAM84B*8127.634127.64061–FAM49B*8130.923131.02161–NDRG1*8134.319134.37960Diverse role in stress response including hypoxia [>>59<<]. Fusions with ERG in prostate cancer [60].ZFAT*8135.559135.79460Zinc finger and AT hook protein, anti-apoptotic role [61] PTK2*8141.738142.08160Focal adhesion kinase. Involved in signal transduction for proliferation[62] CHRAC1*,
n3:mentions: n2:17916902

Subject Item: _:vb7476283
rdf:type: n3:Context
rdf:value: Fusions with ERG in prostate cancer [>>60<<].ZFAT*8135.559135.79460Zinc finger and AT hook protein, anti-apoptotic role [61] PTK2*8141.738142.08160Focal adhesion kinase.
n3:mentions: n2:19649210

Subject Item: _:vb7476284
rdf:type: n3:Context
rdf:value: ZFAT*8135.559135.79460Zinc finger and AT hook protein, anti-apoptotic role [>>61<<] PTK2*8141.738142.08160Focal adhesion kinase.
n3:mentions: n2:19162026

Subject Item: _:vb7476285
rdf:type: n3:Context
rdf:value: Involved in signal transduction for proliferation[>>62<<] CHRAC1*, NIBP/TRAPPC9*, SLC45A4*PTP4A3*8142.501142.51160Protein tyrosine phosphatase.
n3:mentions: n2:16069815

Subject Item: _:vb7476286
rdf:type: n3:Context
rdf:value: Increases proliferation and metastasis [>>63<<] JRK*, TSTA3, ZC3H3, LY6EPUF608144.971144.98460mRNA splicing factor [25] CYC1, ZNF623, ZNF7, CYHR1ERBB2*1735.09835.138Known oncogene in breast cancerTPX2*2029.79129.85342Activator of Aurora-A and involved in spindle assembly [30].
n3:mentions: n2:18224294

Subject Item: _:vb7476287
rdf:type: n3:Context
rdf:value: Increases proliferation and metastasis [63] JRK*, TSTA3, ZC3H3, LY6EPUF608144.971144.98460mRNA splicing factor [>>25<<] CYC1, ZNF623, ZNF7, CYHR1ERBB2*1735.09835.138Known oncogene in breast cancerTPX2*2029.79129.85342Activator of Aurora-A and involved in spindle assembly [30].
n3:mentions: n2:17579712

Subject Item: _:vb7476288
rdf:type: n3:Context
rdf:value: [63] JRK*, TSTA3, ZC3H3, LY6EPUF608144.971144.98460mRNA splicing factor [25] CYC1, ZNF623, ZNF7, CYHR1ERBB2*1735.09835.138Known oncogene in breast cancerTPX2*2029.79129.85342Activator of Aurora-A and involved in spindle assembly [>>30<<]. Interacts with BRCA1/BARD1 [64] UBE2C2043.87543.87942Ubiquitin-conjugating enzyme E2C, degradation of mitotic cyclins and cell cycle progression [65] PIGTZFP642050.13450.24243Zinc finger protein, Notch signalling [66]
n3:mentions: n2:12177045

Subject Item: _:vb7476289
rdf:type: n3:Context
rdf:value: Interacts with BRCA1/BARD1 [>>64<<] UBE2C2043.87543.87942Ubiquitin-conjugating enzyme E2C, degradation of mitotic cyclins and cell cycle progression [65] PIGTZFP642050.13450.24243Zinc finger protein, Notch signalling [66] AURKA2054.37854.40143Aurora kinase, cell cycle
n3:mentions: n2:17081976

Subject Item: _:vb7476290
rdf:type: n3:Context
rdf:value: Interacts with BRCA1/BARD1 [64] UBE2C2043.87543.87942Ubiquitin-conjugating enzyme E2C, degradation of mitotic cyclins and cell cycle progression [>>65<<] PIGTZFP642050.13450.24243Zinc finger protein, Notch signalling [66] AURKA2054.37854.40143Aurora kinase, cell cycle regulation, chromosome segregation, microtubule/spindle function [67] CSTF1, RAE1, C20orf43SS18L12060.15260.19146Synovial
n3:mentions: n2:9122200

Subject Item: _:vb7476291
rdf:type: n3:Context
rdf:value: Interacts with BRCA1/BARD1 [64] UBE2C2043.87543.87942Ubiquitin-conjugating enzyme E2C, degradation of mitotic cyclins and cell cycle progression [65] PIGTZFP642050.13450.24243Zinc finger protein, Notch signalling [>>66<<] AURKA2054.37854.40143Aurora kinase, cell cycle regulation, chromosome segregation, microtubule/spindle function [67] CSTF1, RAE1, C20orf43SS18L12060.15260.19146Synovial sarcoma translocation fusion gene [68]); calcium-responsive
n3:mentions: n2:18430783

Subject Item: _:vb7476292
rdf:type: n3:Context
rdf:value: of mitotic cyclins and cell cycle progression [65] PIGTZFP642050.13450.24243Zinc finger protein, Notch signalling [66] AURKA2054.37854.40143Aurora kinase, cell cycle regulation, chromosome segregation, microtubule/spindle function [>>67<<] CSTF1, RAE1, C20orf43SS18L12060.15260.19146Synovial sarcoma translocation fusion gene [68]); calcium-responsive transactivator [67] GTPBP5, LSM14B,
n3:mentions: n2:19774610

Subject Item: _:vb7476293
rdf:type: n3:Context
rdf:value: protein, Notch signalling [66] AURKA2054.37854.40143Aurora kinase, cell cycle regulation, chromosome segregation, microtubule/spindle function [67] CSTF1, RAE1, C20orf43SS18L12060.15260.19146Synovial sarcoma translocation fusion gene [>>68<<]); calcium-responsive transactivator [67] GTPBP5, LSM14B,
n3:mentions: n2:12696068

Subject Item: _:vb7476294
rdf:type: n3:Context
rdf:value: kinase, cell cycle regulation, chromosome segregation, microtubule/spindle function [67] CSTF1, RAE1, C20orf43SS18L12060.15260.19146Synovial sarcoma translocation fusion gene [68]); calcium-responsive transactivator [>>67<<] GTPBP5, LSM14B,
n3:mentions: n2:19774610

Subject Item: _:vb7476295
rdf:type: n5:Section
dc:title: discussion
n5:contains: _:vb7476320 _:vb7476321 _:vb7476322 _:vb7476323 _:vb7476324 _:vb7476312 _:vb7476313 _:vb7476314 _:vb7476315 _:vb7476316 _:vb7476317 _:vb7476318 _:vb7476319 _:vb7476304 _:vb7476305 _:vb7476306 _:vb7476307 _:vb7476308 _:vb7476309 _:vb7476310 _:vb7476311 _:vb7476296 _:vb7476297 _:vb7476298 _:vb7476299 _:vb7476300 _:vb7476301 _:vb7476302 _:vb7476303

Subject Item: _:vb7476296
rdf:type: n3:Context
rdf:value: in ovarian cancer but identification of specific driver genes using this methodology alone has been hampered by the fact that expression is rather plastic and there has been little consensus in the genes identified between such studies [>>1<<], [8]. One reason for this lack of consistency is that most studies have analysed RNA from whole tumour samples without verification of the percentage cancer epithelium and/or have used diverse control tissues such as whole ground ovary
n3:mentions: n2:18217975

Subject Item: _:vb7476297
rdf:type: n3:Context
rdf:value: cancer but identification of specific driver genes using this methodology alone has been hampered by the fact that expression is rather plastic and there has been little consensus in the genes identified between such studies [1], [>>8<<]. One reason for this lack of consistency is that most studies have analysed RNA from whole tumour samples without verification of the percentage cancer epithelium and/or have used diverse control tissues such as whole ground ovary [9].
n3:mentions: n2:15949568

Subject Item: _:vb7476298
rdf:type: n3:Context
rdf:value: One reason for this lack of consistency is that most studies have analysed RNA from whole tumour samples without verification of the percentage cancer epithelium and/or have used diverse control tissues such as whole ground ovary [>>9<<]. In contrast to gene expression, genomic alterations may be a more stable and reliable predictor of the location of driver genes. Ovarian cancer has long been suspected to be cytogenetically complex [10] and recent advances in genomics
n3:mentions: n2:14581352

Subject Item: _:vb7476299
rdf:type: n3:Context
rdf:value: Ovarian cancer has long been suspected to be cytogenetically complex [>>10<<] and recent advances in genomics technology has confirmed the profound genomic aberrations that characterise most ovarian cancers [4], [11], [12], [13].
n3:mentions: n2:10379876

Subject Item: _:vb7476300
rdf:type: n3:Context
rdf:value: Ovarian cancer has long been suspected to be cytogenetically complex [10] and recent advances in genomics technology has confirmed the profound genomic aberrations that characterise most ovarian cancers [>>4<<], [11], [12], [13].
n3:mentions: n2:17699850

Subject Item: _:vb7476301
rdf:type: n3:Context
rdf:value: Ovarian cancer has long been suspected to be cytogenetically complex [10] and recent advances in genomics technology has confirmed the profound genomic aberrations that characterise most ovarian cancers [4], [>>11<<], [12], [13].
n3:mentions: n2:12586079

Subject Item: _:vb7476302
rdf:type: n3:Context
rdf:value: Ovarian cancer has long been suspected to be cytogenetically complex [10] and recent advances in genomics technology has confirmed the profound genomic aberrations that characterise most ovarian cancers [4], [11], [>>12<<], [13]. Despite this complexity, published copy number profiles of ovarian cancers are highly comparable at a global level [3] and many studies have identified very similar regions of frequent copy number alteration. However, progress at
n3:mentions: n2:19419571

Subject Item: _:vb7476303
rdf:type: n3:Context
rdf:value: Ovarian cancer has long been suspected to be cytogenetically complex [10] and recent advances in genomics technology has confirmed the profound genomic aberrations that characterise most ovarian cancers [4], [11], [12], [>>13<<]. Despite this complexity, published copy number profiles of ovarian cancers are highly comparable at a global level [3] and many studies have identified very similar regions of frequent copy number alteration. However, progress at
n3:mentions: n2:17538174

Subject Item: _:vb7476304
rdf:type: n3:Context
rdf:value: Despite this complexity, published copy number profiles of ovarian cancers are highly comparable at a global level [>>3<<] and many studies have identified very similar regions of frequent copy number alteration.
n3:mentions: n2:19383377

Subject Item: _:vb7476305
rdf:type: n3:Context
rdf:value: For example, the chromosome 20 amplicon driver has variously been suggested to be ADRM1 [>>14<<], EYA2 [15], AURKA and ZNF217 [16], among several others.
n3:mentions: n2:18615678

Subject Item: _:vb7476306
rdf:type: n3:Context
rdf:value: For example, the chromosome 20 amplicon driver has variously been suggested to be ADRM1 [14], EYA2 [>>15<<], AURKA and ZNF217 [16], among several others.
n3:mentions: n2:15705892

Subject Item: _:vb7476307
rdf:type: n3:Context
rdf:value: For example, the chromosome 20 amplicon driver has variously been suggested to be ADRM1 [14], EYA2 [15], AURKA and ZNF217 [>>16<<], among several others.
n3:mentions: n2:12417041

Subject Item: _:vb7476308
rdf:type: n3:Context
rdf:value: Early studies integrating expression and copy number data have either used cancer cell lines to identify over expressed genes [>>17<<], [18] and/or microarray platforms with limited resolution and genome coverage [19], [20].
n3:mentions: n2:15688027

Subject Item: _:vb7476309
rdf:type: n3:Context
rdf:value: Early studies integrating expression and copy number data have either used cancer cell lines to identify over expressed genes [17], [>>18<<] and/or microarray platforms with limited resolution and genome coverage [19], [20].
n3:mentions: n2:12414653

Subject Item: _:vb7476310
rdf:type: n3:Context
rdf:value: Early studies integrating expression and copy number data have either used cancer cell lines to identify over expressed genes [17], [18] and/or microarray platforms with limited resolution and genome coverage [>>19<<], [20]. To date few studies have exploited a truly genome-wide integrated copy number and expression analysis on matched samples for the unbiased identification of candidate genes [21], [22], [23] and there has only been one previous study
n3:mentions: n2:15611932

Subject Item: _:vb7476311
rdf:type: n3:Context
rdf:value: Early studies integrating expression and copy number data have either used cancer cell lines to identify over expressed genes [17], [18] and/or microarray platforms with limited resolution and genome coverage [19], [>>20<<]. To date few studies have exploited a truly genome-wide integrated copy number and expression analysis on matched samples for the unbiased identification of candidate genes [21], [22], [23] and there has only been one previous study of a
n3:mentions: n2:16489013

Subject Item: _:vb7476312
rdf:type: n3:Context
rdf:value: To date few studies have exploited a truly genome-wide integrated copy number and expression analysis on matched samples for the unbiased identification of candidate genes [>>21<<], [22], [23] and there has only been one previous study of a smaller cohort of ovarian tumours [12].
n3:mentions: n2:18772890

Subject Item: _:vb7476313
rdf:type: n3:Context
rdf:value: To date few studies have exploited a truly genome-wide integrated copy number and expression analysis on matched samples for the unbiased identification of candidate genes [21], [>>22<<], [23] and there has only been one previous study of a smaller cohort of ovarian tumours [12].
n3:mentions: n2:18089785

Subject Item: _:vb7476314
rdf:type: n3:Context
rdf:value: To date few studies have exploited a truly genome-wide integrated copy number and expression analysis on matched samples for the unbiased identification of candidate genes [21], [22], [>>23<<] and there has only been one previous study of a smaller cohort of ovarian tumours [12].
n3:mentions: n2:18335499

Subject Item: _:vb7476315
rdf:type: n3:Context
rdf:value: truly genome-wide integrated copy number and expression analysis on matched samples for the unbiased identification of candidate genes [21], [22], [23] and there has only been one previous study of a smaller cohort of ovarian tumours [>>12<<]. In this study we have therefore attempted to circumvent some of the issues of examining expression or copy number in isolation by integrating two data sets obtained from microdissected tumour epithelial cells.
n3:mentions: n2:19419571

Subject Item: _:vb7476316
rdf:type: n3:Context
rdf:value: The proportion of differentially expressed genes in our study is consistent with previous studies of other cancer types [>>24<<] supporting the concept that copy number can have a strong influence on gene expression.
n3:mentions: n2:12297621

Subject Item: _:vb7476317
rdf:type: n3:Context
rdf:value: This gene encodes for a pre-mRNA splicing factor thought to be involved in the recognition of 3′ splice sites [>>25<<]. It may also inhibit transcription by interacting with the TFIIH helicase, the key factor mutated in the cancer-prone syndrome xeroderma pigmentosum, and this interaction is implicated in the correct regulation of MYC transcription [26],
n3:mentions: n2:17579712

Subject Item: _:vb7476318
rdf:type: n3:Context
rdf:value: It may also inhibit transcription by interacting with the TFIIH helicase, the key factor mutated in the cancer-prone syndrome xeroderma pigmentosum, and this interaction is implicated in the correct regulation of MYC transcription [>>26<<], [27].
n3:mentions: n2:11239393

Subject Item: _:vb7476319
rdf:type: n3:Context
rdf:value: may also inhibit transcription by interacting with the TFIIH helicase, the key factor mutated in the cancer-prone syndrome xeroderma pigmentosum, and this interaction is implicated in the correct regulation of MYC transcription [26], [>>27<<].
n3:mentions: n2:10882074

Subject Item: _:vb7476320
rdf:type: n3:Context
rdf:value: e BTB/POZ-ZF family of transcription factors [>>28<<]. First discovered in Drosophila, this family consists of about 60 human proteins including several cancer related proteins such as leukaemia related factor (LRF/ZBTB7) and B-cell lymphoma 6 (BCL6).
n3:mentions: n2:10873615

Subject Item: _:vb7476321
rdf:type: n3:Context
rdf:value: While the role of MYNN in cancer is yet to be characterised, other members of this family are similarly overexpressed in tumors [>>29<<].
n3:mentions: n2:16996269

Subject Item: _:vb7476322
rdf:type: n3:Context
rdf:value: The protein encoded by this gene functions as an activator of Aurora-A with a role in spindle assembly [>>30<<]. Interestingly for ovarian cancer, it has been shown to interact with the BRCA1/BARD1 complex (15). Recently, it has been identified as a potential oncogene in pancreatic cancer [31].
n3:mentions: n2:12177045

Subject Item: _:vb7476323
rdf:type: n3:Context
rdf:value: Recently, it has been identified as a potential oncogene in pancreatic cancer [>>31<<].
n3:mentions: n2:19861455

Subject Item: _:vb7476324
rdf:type: n3:Context
rdf:value: The example of MYC, not strongly expressed in our data but previously shown to have a functional effect in ovarian cancer cell lines [>>32<<], clearly indicates that our approach should be considered complementary to others such as functional screens and deep sequencing of primary cancer samples.
n3:mentions: n2:17908964

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