BioExpress® System Publication References


Updated March 31st 2013
To know more about  BioExpress® System please see

http://www.ocimumbio.com/bioexpress-system/

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2014

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[PDF] Systematic evaluation of connectivity map for disease indications

J Cheng, L Yang, V Kumar, P Agarwal – Genome medicine, 2014 – biomedcentral.com
pairs. The disease signatures were generated using Gene Logic BioExpress? BioExpress?
system [20]. The BioExpress System provides gene expression data and associated
clin- ical and pathological information across a wide range of

A Framework for Comparative Analysis of Gene Expressions and Mutations Linked to Cancer

JA Theodore – 2014 – gradworks.umi.com
cancer types. In the course of analysis we also created HIVE Genecast, a mobile app for Android
devices which extends the BioMuta and BioExpress gene databases to Android devices. returns
data and analytics on gene expression findings from the BioExpress database

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2013

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Gene expression in the human brain: The current state of the study of specificity and spatiotemporal dynamics

OY Naumova, M Lee, SY Rychkov… – Child …, 2013 – Wiley Online Library
 ccr.cancer.gov), and the comparison of gene expression patterns in the brain in normal and
pathological development, such as Alzheimer’s and Parkinson’s diseases, major depression,
and schizophrenia (BioExpress ® Atlas Reference Data Suite, http://www.genelogic.com). 

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2012

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Organ-specific gene, method for identifying the same and use thereof

S Miyamoto, K Takami, A Horinouchi – EP Patent 2,465,932, 2012 – freepatentsonline.com
 kidney, left testis, liver, lung, stomach) from 2-month-old male Wistar rats were extracted from
BioExpress of Gene Logic on July 24, 2007. The parameters used in the extraction are shown
in Table 4. Fourteen tissues not covered in BioExpress of GeneLogic (spleen, duodenum 

[HTML] Targeting FGFR4 inhibits hepatocellular carcinoma in preclinical mouse models

DM French, BC Lin, M Wang, C Adams, T Shek… – PLoS One, 2012 – dx.plos.org
 FGFR4 Expression is Altered in Cancer. We evaluated FGFR4 expression in a variety of human
normal and cancerous tissues by analyzing the BioExpress database (Gene Logic, Inc.,
Gaithersburg, MD, USA). FGFR4 expression is highly variable in most types of cancer. 

Expression of G Protein-Coupled Receptor 19 in Human Lung Cancer Cells Is Triggered by Entry into S-Phase and Supports G2–M Cell-Cycle Progression

S Kastner, T Voss, S Keuerleber, C Glöckel… – Molecular Cancer …, 2012 – AACR
 Gene expression levels of Gpr19 (probe set 207183_at) in various human normal and
cancerous tissues were investigated by using the BioExpress database (Gene Logic; 12). 
Data were extracted from the BioExpress database (Gene Logic). 

Bioinformatics advances for clinical biomarker development

KPH Pritzker, LB Pritzker – Expert Opinion on Medical …, 2012 – informahealthcare.com
 The BioExpress System [68] is a comprehensive genome-wide gene expression database with
histopathology, clinical chemistry, hematology, treatment, follow-up and other clinical details
for > 22,000 clinically-defined tissue, blood and cell samples from human clinical studies 

Related articles All 2 versions Cite

Applications of Connectivity Map in drug discovery and development

XA Qu, DK Rajpal – Drug discovery today, 2012 – Elsevier
 of marketed drugs and compounds. BioExpress™, http://www.genelogic.com/
knowledge-suites/bioexpress-system, Commercial database for human
disease-centric gene expression data. Library of Integrated Network-based 

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2011

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Siglec-15, a member of the sialic acid-binding lectin, is a novel regulator for osteoclast differentiation

Y Hiruma, T Hirai, E Tsuda – Biochemical and biophysical research …, 2011 – Elsevier
 The human gene expression database, BioExpress System (Gene Logic Division, Ocimum
Biosolutions, Inc.), containing Affymetrix U133 GeneChip expression profiles of numerous human
samples from > 60 normal and diseased tissue types, was analyzed to identify genes 

Knowledge-Driven, Data-Assisted Integrative Pathway Analytics

PS Reddy, S Murray, W Liu – Handbook of Research on …, 2011 – books.google.com
 mechanisms. Examples include ICONIX’s Drug Matrix (Ganter, Snyder, Halbert,
& Lee, 2006) and Gene Logic’s BioExpress (http://www. genelogic. com/knowledge-
suites/bioexpress-system)(Katz, 231 Page 266. Knowledge 

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2010

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Upregulation of poly (ADP-ribose) polymerase-1 (PARP1) in triple-negative breast cancer and other primary human tumor types

V Ossovskaya, IC Koo, EP Kaldjian… – Genes & …, 2010 – gan.sagepub.com
 These results, as well as attendant pathology and clinical data, were annotated within sample
gene expression and analysis databases for both population-based and individual sample-based
studies (Ascenta, BioExpress Systems, Gene Logic; Cureline BioPathology

Mutated genes in pancreatic cancer

S He… – Chinese Journal of Cancer Research, 2010 – Springer
 Cao D et al utilized the Gene Logic Inc. BioExpress™ platform and Affymetrix U133 GeneChip®
set to determine the changes in gene expression associated with SMAD4 gene inactivation in
a series of well-characterized pancreatic cancer cell lines to define the downstream

TMPRSS13, a type II transmembrane serine protease, is inhibited by hepatocyte growth factor activator inhibitor type 1 and activates pro‐hepatocyte growth factor

T Hashimoto, M Kato, T Shimomura… – FEBS Journal, 2010 – Wiley Online Library
 members of the TTSP family. These proteases have been shown to be co-expressed
with HAI-1 in various tissues (database of BioExpress System, Gene Logic Inc.,
Gaithersburg, MD, USA). Then, the putative activation cleavage

[HTML] Molecular biomarker analyses using circulating tumor cells

EA Punnoose, SK Atwal, JM Spoerke, H Savage… – PLoS One, 2010 – dx.plos.org
 32], [33]. To examine the expression of marker genes in primary tumors, gene
expression profiles were extracted from the commercially available database
BioExpress (GeneLogic, Gaithersburg MD). Cell surface expression

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2009

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Similar compounds searching system by using the gene expression microarray database

H Toyoshiba, H Sawada, I Naeshiro… – Toxicology letters, 2009 – Elsevier
 Tong et al., 2003), ArrayExpress at the EBI (Parkinson et al., 2007), the Toxicogenomics Project
(TGP) (Takashima et al., 2006), Iconix DrugMatrix, the GeneLogic ToxExpress and BioExpress,
and the NCBI microarray data repository Gene Expression Omnibus (GEO) (www.ncbi

ORGAN-SPECIFIC GENE, METHOD FOR IDENTIFYING THE SAME AND USE THEREOF

S Miyamoto, K Takami… – EP Patent 2,077,327, 2009 – freepatentsonline.com
 1. Database used and method of data extraction. Gene expression data on male C57BL/6 mice
were extracted from BioExpress of Gene Logic on April 21, 2006.  The data used were extracted
from the gene expression database BioExpress, introduced from Gene Logic

[PDF] Using Gene Logic’s BioExpress® System to Reveal Disease Mechanism

P Kulkarni… – genelogic.com
 610 Professional Drive • Gaithersburg, Maryland 20879 • Phone: 1.800.GENELOGIC • Fax:
301.987.1701 Email: info@genelogic.com • Web: www.genelogic.com © 2005 Gene Logic Inc.
All Right Reserved. BioExpress, Genesis Enterprise System, and eNorthern are registered

ORGAN-SPECIFIC GENE, METHOD FOR IDENTIFYING THE SAME AND USE THEREOF

S Miyamoto, K Takami… – EP Patent 2,077,327, 2009 – freepatentsonline.com
 1. Database used and method of data extraction. Gene expression data on male C57BL/6 mice
were extracted from BioExpress of Gene Logic on April 21, 2006.  The data used were extracted
from the gene expression database BioExpress, introduced from Gene Logic

Similar compounds searching system by using the gene expression microarray database

H Toyoshiba, H Sawada, I Naeshiro… – Toxicology letters, 2009 – Elsevier
 Tong et al., 2003), ArrayExpress at the EBI (Parkinson et al., 2007), the Toxicogenomics Project
(TGP) (Takashima et al., 2006), Iconix DrugMatrix, the GeneLogic ToxExpress and BioExpress,
and the NCBI microarray data repository Gene Expression Omnibus (GEO) (www.ncbi

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2008

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From Pharmacogenomics to Translational Biomarkers

DL Mendrick – … IN MOLECULAR BIOLOGY-CLIFTON THEN TOTOWA-, 2008 – Springer
 renal cell carcinoma was recently described (21). Examination of Kim-1 in human
renal diseases was performed using the BioExpress® database at Gene Logic
(Gaithersburg, MD). The expression of Kim-1 mRNA was signif

A cancer-associated RING finger protein, RNF43, is a ubiquitin ligase that interacts with a nuclear protein, HAP95

T Sugiura, A Yamaguchi… – Experimental cell research, 2008 – Elsevier
 Materials and methods. Identification of RNF43 upregulated in colon cancers. Expression profiles
of RNF43 in various normal and diseased tissues were analyzed by virtue of the BioExpress
database (Gene Logic Inc., Gaithersburg, MA) as described previously [10] and [11]. 

Preventive and/or Therapeutic Agent for Cancer

T Yoshikawa, W Watanabe… – US Patent App. 11/547,334, 2005 – Google Patents
 23, 2008 2 profile database, BioExpress (GeneLogic Co., Ltd.) and an analysis software,
GeneExpress™ Explorer  database (Nucleic Acids Res., 31(1), 28-33 (2003)) of a gene
corresponding to  Set ID 229479_ at was searched by means of annotation in BioExpress data- 

[HTML] Molecular analysis of the vaginal response to estrogens in the ovariectomized rat and postmenopausal woman

S Jelinsky, S Choe, J Crabtree… – BMC medical …, 2008 – biomedcentral.com
 In order to do this, probe set annotations and ortholog assignments were obtained from BioExpress
2.0 (GeneLogic) and NCBI Homologene, respectively. When multiple probe sets on a chip query
the same gene, a per-gene score of differential expression was calculated by

Characterization of TRIM31, upregulated in gastric adenocarcinoma, as a novel RBCC protein

T Sugiura… – Journal of cellular biochemistry, 2008 – Wiley Online Library
 Data Mining of the BioExpress Database. We identified the genes upregulated in human
stomach adenocarcinoma by using the BioExpress database (Gene Logic Inc., Gaithersburg,
MA) as described previously [Sugiura et al., 2004, 2007b]. 

[HTML] Differential expression of multiple genes in association with MADH4/DPC4/SMAD4 inactivation in pancreatic cancer

D Cao, R Ashfaq, MG Goggins… – … journal of clinical and …, 2008 – ncbi.nlm.nih.gov
 in other tumor types [4, 5]. Considering the high rate of MADH4 inactivation in pancreatic cancers,
it is attractive to consider the genes differentially expressed in accord with MADH4 status in an
unbiased survey [6–9]. We utilized the Gene Logic Inc. BioExpress(tm) platform and

Evolution of closely linked gene pairs in vertebrate genomes

E Franck, T Hulsen, MA Huynen, WW De Jong… – Molecular biology and …, 2008 – SMBE
 Gene Expression. An expression data set consisting of a subset of normal human
and mouse tissue samples from the Gene Logic BioExpress Database product
(http://www.genelogic.com/genomics/bioexpress/) was used. The

[PDF] Protein phosphatase 1H, overexpressed in colon adenocarcinoma, is associated with CSE1L

T Sugiura, Y Noguchi, K Sakurai… – CANCER BIOLOGY AND …, 2008 – fly-bay.net
 Data mining of the BioExpress database. We identified the genes upregulated in human colon
adenocarcinomas using the BioExpress database (Gene Logic Inc., Gaithersburg, MA, USA)
comprising the Affymetrix U133 GeneChip expression profiles as described previously. 

[PDF] Determining the Tissue Distribution and Specificity of JM27/G antigen, family C, 1, a Prostate Cancer-associated Gene

…, G Logic – genelogic.com
 ACKNOWLEDGEMENTS e-Northern™ and BioExpress™ Human Atlas Suite are trademarks of
Gene Logic Inc. PHONE: 301-987-1700 •FAX: 301-987-1701 • www.genelogic.com • Corporate
Headquarters: 708 Quince Orchard Road•Gaithersburg, Maryland 20878

[HTML] TTLL7 Is a Mammalian-Tubulin Polyglutamylase Required for Growth of MAP2-positive Neurites

医学期刊, 医学会议, 医学教育, 医学书店… – journal.9med.net
 Analysis Using BioExpress Data Base-We performed a data base search and statistical analysis
on TTLL mRNA expression among various tissues in humans that were profiled by Affymetrix
GeneChip technology and stored in the commercial Gene Logic BioExpress data base

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2007

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A cardiac myosin light chain kinase regulates sarcomere assembly in the vertebrate heart

O Seguchi, S Takashima… – Journal of Clinical …, 2007 – Am Soc Clin Investig
 peptide (BNP) mRNA levels (194 probe sets). The tissue localization of each selected
probe set was then analyzed using the commercially available BioExpress database
(Gene Logic Inc.). We selected 10 probe sets, for which

PREVENTIVE AND/OR REMEDY FOR CANCER

T YOSHIKAWA, W WATANABE… – EP Patent …, 2007 – freepatentsonline.com
 4 were selected by the following procedures using an expression profile database, BioExpress
(GeneLogic Co., Ltd  database ( Nucleic Acids Res., 31(1), 28-33 (2003) ) of a gene corresponding
to  Set ID 229479_at was searched by means of annotation in BioExpress database. 

From the bench to the clinic and back again: translational biomarker discovery using in silico mining of pharmacogenomic data

DL Mendrick… – Biomarkers, 2007 – Future Medicine
 In silico mining of pharmacogenomic data within Gene Logic’s BioExpress ® and ToxExpress ®
databases quickly reveals that the expression of Kim-1 in normal human tissues resides primarily
in the kidney (Figure 1). A low level of expression was found in normal mouse

PARP1 gene over-expression in primary human cancers: A potential marker for PARP inhibition

V Ossovskaya, C Alvares… – Proceedings of the …, 2007 – aacrmeetingabstracts.org
 Experimental design: We used the Gene Logic BioExpress® System database to
analyze PARP1 expression in human ovarian, breast, uterine, lung and prostate
tumor samples in comparison to normal counterpart tissues. 

Bioinformatics approaches in the study of cancer

DA Hanauer, DR Rhodes… – Current molecular …, 2007 – ingentaconnect.com
 The BioExpress® Oncology Suite offers visualization and statistical analysis tools as well.  projects
ranging from management of clinical trials to tools for analysis of gene expression data.  [19]
http://www.genelogic.com/docs/pdfs/OncologyProductSheet.pdf Accessed on April 22

[PDF] DDX39, upregulated in lung squamous cell cancer, displays RNA helicase activities and promotes cancer cell growth

T Sugiura, Y Nagano… – CANCER BIOLOGY AND …, 2007 – orphanresearch.net
 to the gene expression profile database called BioExpress developed by GeneLogic Inc., which
74 LAC and 51 LSCC patient samples on the BioExpress (Gene Logic Inc.) database.  expressed
in NSCLC using the commercially available BioExpress gene expression database

Patterns of gene expression in the limbic system of suicides with and without major depression

A Sequeira, T Klempan, L Canetti – Molecular psychiatry, 2007 – nature.com
 (Gaithersburg, MD, USA, www.genelogic.com). All microarray data and clinical information were
embedded into Gene Logic’s Genesis 2.0 software as a component of its Bioexpress system.
RNA samples used in the current study had a minimum A260/A280 ratio of 1.9. 

Liver-specific activities of FGF19 require Klotho beta

BC Lin, M Wang, C Blackmore… – Journal of Biological …, 2007 – ASBMB
 KLB and FGFR4 Distribution Dictate FGF19 Tissue-specific Activity—We evaluated
KLB and FGFR4 expression in a variety of human tissues by analyzing the
BioExpress data base (Gene Logic, Inc.). In decreasing order of

METHOD FOR REDUCING OR ALLEVIATING INFLAMMATION IN THE DIGESTIVE TRACT

LA Tartaglia, TM Barnes… – US Patent App. 11/ …, 2007 – Google Patents
 LOUIS, MO 63105 (US) (73) Assignee: Gene Logic Inc., Gaithersburg, MD (US) (21) Appl.No.:
11/851,694 (22) Filed: Sep. 7, 2007 Related US Application Data (60) Provisional application
No. 60/825,075, filed on Sep. 8, 2006, provisional application No. 

Death-receptor O-glycosylation controls tumor-cell sensitivity to the proapoptotic ligand Apo2L/TRAIL

KW Wagner, EA Punnoose, T Januario… – Nature medicine, 2007 – nature.com
 Cutoffs were set as follows: GALNT3, 2,000 AU; FUT6, 200 AU; FUT3, 400 AU. To determine
the expression of GALNT14 in primary tumors, we extracted gene expression profiles from the
commercially available database BioExpress (GeneLogic) as described 36 . 

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2006

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Tissue and species distribution of the glutathione pathway transcriptome

WB Mattes, KK Daniels, M Summan, ZA Xu… – …, 2006 – informahealthcare.com
 arrays. Rat and canine gene expression data are resident in Gene Logic’s ToxExpress®
System Database, whereas mouse gene expression data are found within Gene Logic’s
BioExpress® System Database. Affymetrix probesets

Expression of stromal cell markers in distinct compartments of human skin cancers

MA Huber, N Kraut, N Schweifer… – Journal of …, 2006 – Wiley Online Library
 normal skin. For expression analysis, box- and whisker plots were generated via
the eNorthern tool of GeneExpress software based on normalized gene expression
data from the BioExpress ® database (GeneLogic). Box plots

TTLL7 is a mammalian β-tubulin polyglutamylase required for growth of MAP2-positive neurites

K Ikegami, M Mukai, J Tsuchida, RL Heier… – Journal of Biological …, 2006 – ASBMB
 Using BioExpress Data Base—We performed a data base search and statistical analysis on TTLL
mRNA expression among various tissues in humans that were profiled by Affymetrix GeneChip
technology and stored in the commercial Gene Logic BioExpress data base system. 

[HTML] A summarization approach for Affymetrix GeneChip data using a reference training set from a large, biologically diverse database

S Katz, R Irizarry, X Lin, M Tripputi… – BMC bioinformatics, 2006 – biomedcentral.com
 We have utilized an alternate RMA workflow that includes two distinct steps: (a) training of an
RMA model based on a large number of biologically distinct Affymetrix GeneChip samples from
Gene Logic’s BioExpress reference database and (b) application of the resulting RMA

HTML] Benchmarking ortholog identification methods using functional genomics data

T Hulsen, MA Huynen, J De Vlieg… – Genome …, 2006 – biomedcentral.com
 orthologous pair was calculated. The expression dataset used here [35] was a subset
of pathologically normal human and mouse tissue samples from the Gene Logic
BioExpress Database product [36]. Because of the small

Toxicogenomics and cross-species biomarker discovery: applications in drug discovery and safety assessment

MS Orr – Toxicology Mechanisms and Methods, 2006 – informahealthcare.com
 At Gene Logic Inc., Affymetrix GeneChips® microarrays were used to identify dysregulated
secreted genes in human or rat samples. Comparisons of the dysregulated genes identified in
either the human (BioExpress® database) or rat studies (ToxExpress® database) were

Detecting and profiling tissue-selective genes

S Liang, Y Li, X Be, S Howes… – Physiological genomics, 2006 – Am Physiological Soc
 present study is to take advantage of a very large set of gene expression data  tissue types were
used to generate expression data using Affymetrix’s U133 chip set by GeneLogic The expression
data used in the present study were derived from BioExpress database, which was

Amino acid transporter ATA2 is stored at the trans-Golgi network and released by insulin stimulus in adipocytes

T Hatanaka, Y Hatanaka, J Tsuchida… – Journal of Biological …, 2006 – ASBMB
 We performed a data base search and statistical analysis on ATA2 mRNA and GLUT4 mRNA
expression among various tissues in humans, mice, and rats that were profiled by Affymetrix
GeneChip technology and stored in the commercial Gene Logic BioExpress data base

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2005

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Clusters of adjacent and similarly expressed genes across normal human tissues complicate comparative transcriptomic discovery

C Liu, S Ghosh, DB Searls… – Omics: a journal of …, 2005 – online.liebertpub.com
 retrieved gene expression data profiled using human U133A&B chips (Affymetrix, Santa Clara,
CA; http://www.affymetrix.com) for 2695 normal human samples belonging to 101 tissue types from
BioExpress Sys- tem Database (Gene Logic Inc., Gaithersburg, MD; www.genelogic.com

[HTML] Characterization of cancer stroma markers: in silico analysis of an mRNA expression database for fibroblast activation protein and endosialin

H Dolznig, N Schweifer, C Puri, N Kraut… – Cancer …, 2005 – w.cancerimmunity.org
 mean gives the scaling factor, where one hundred is the standard value used by GeneLogic 4,
and 5) are given only if significant upregulation (P < 0.01) of the gene of interest  Although the
tissue samples used to construct the BioExpress™ database were not available for side

Revealing Transforming Growth Factor-β Signaling Transduction in Human Kidney by Gene Expression Data Mining

G Hu, K Jain… – Omics: a journal of integrative …, 2005 – online.liebertpub.com
 From the BioExpress® System, Gene Logic Inc.’s (Gaithersburg, MD http://www.genelogic.com/)
database of human U133 GeneChip® microarray data processed using MAS5.0, we chose 227
datasets derived from kid- ney samples that met three conditions: (i) scale factors

Immune response in silico (IRIS): immune-specific genes identified from a compendium of microarray expression data

AR Abbas, D Baldwin, Y Ma, W Ouyang… – Genes and …, 2005 – nature.com
 listed in Table 1 (immune level) and the following normal tissues (nonimmune level) in the
BioExpress™ System (Gene Logic Inc., Gaithersburg, MD, USA): breast, brain, spinal chord,
colorectal, heart, kidney, liver, lung, ovary, pancreas, prostate, small intestine and stomach. 

Molecular characterization of suicide by microarray analysis

FG Gwadry, A Sequeira, G Hoke… – American Journal of …, 2005 – Wiley Online Library
 Expression data were stored in the BioExpress™ CNS Suite (Gene Logic, Inc.,
Gaithersburg, MD) and analyzed using Avadis software (Strand Genomics Pvt. Ltd.,
http://www.strandgenomics.com). SELECTION OF ARRAYS. 

Loss of the forkhead transcription factor FoxM1 causes centrosome amplification and mitotic catastrophe

DR Wonsey… – Cancer research, 2005 – AACR
 Expression profiling data from primary human cancer samples was obtained from the GeneLogic
BioExpress Database (Gaithersburg, MD), a commercially  The entire data set has been deposited
in the National Center for Biotechnology Information’s Gene Expression Omnibus

Epithelial versus mesenchymal phenotype determines in vitro sensitivity and predicts clinical activity of erlotinib in lung cancer patients

RL Yauch, T Januario, DA Eberhard, G Cavet… – Clinical Cancer …, 2005 – AACR
 To examine the expression of marker genes in primary tumors, gene expression profiles
for 80 NSCLC tumors exhibiting ≥50% tumor content were extracted from the commercially
available database, BioExpress (GeneLogic, Gaithersburg MD). 

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2004

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Methods For Molecular Toxicology Modeling

JC Diggans… – US Patent App. 10/580,423, 2004 – Google Patents
 In a preferred embodiment, the database is a ToxExpress® or BioExpress® database marketed
by Gene Logic Inc., Gaithersburg, Md. [0061] The databases of the invention may be linked
to an outside or external database such as GenBank (www ncbi. 

[PDF] Research Paper Identification of Novel Highly Expressed Genes in Pancreatic Ductal Adenocarcinomas through a Bioinformatics Analysis of Expressed …

D Cao, SR Hustinx, G Sui, P Bala… – Cancer biology & …, 2004 – braintrusters.com
 completion of the human genome sequence provides a basis for characterizing these ESTs in
greater detail using computational and experimental methods.7 In this study we utilized the Gene
Logic Inc. BioExpress™ platform and the most current version of Affymetrix GeneChip

[BOOK] Analyzing microarray gene expression data

GJ McLachlan, KA Do… – 2004 – books.google.com
Page 1. Analyzing Microarray Gene Expression Data Page 2. This Page Intentionally
Left Blank Page 3. Analyzing Microarray Gene Expression Data Page 4. WILEY
SERIES IN PROBABILITY AND STATISTICS Established

A novel mitochondrial C1-tetrahydrofolate synthetase is upregulated in human colon adenocarcinoma

T Sugiura, Y Nagano, T Inoue… – Biochemical and biophysical …, 2004 – Elsevier
 We collected 117 normal and 77 adenocarcinoma colon samples on the BioExpress database
(Gene Logic Inc., Gaithersburg, MA) containing Affymetrix U133 GeneChip expression profiles
[3] and [4]. The Fold Change analysis tool equipped in the database was utilized to

Identification and validation of novel androgen-regulated genes in prostate cancer

AM Velasco, KA Gillis, Y Li, EL Brown… – Endocrinology, 2004 – Endocrine Soc
 search and statistical analysis on FKBP51 mRNA expression among various human prostate
tissue subtypes that were profiled by the Affymetrix GeneChip technology and stored in the
commercial Gene Logic BioExpress database system (http://www. genelogic.com/solutions

[PDF] Assessing the quality of clusters in microarray data–a comparison of functional and numerical measures

EVA BERGLUND – 2004 – ibg.uu.se
 This value is referred to as RNA QC. 2.4 The dataset The dataset used in this project
originates from BioExpress, a non-public database from Gene Logic (Gene Logic Inc,
Gaithersburg, MD, USA). The database stores post-mortem

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2003

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[CITATION] 12 Predictive Toxicogenomics

MW Porter, AL Castle, MS Orr… – An introduction to …, 2003 – Informa HealthCare

Disease-associated expression profiles in peripheral blood mononuclear cells from patients with advanced renal cell carcinoma

NC Twine, JA Stover, B Marshall, G Dukart… – Cancer research, 2003 – AACR
 CD4 T cells in culture (n = 3) were accessed from the GX2000 BioExpress database (GeneLogic
in Affymetrix Micro Array Suite 4 and then normalized using the GeneLogic normalization algorithm. 
mean to calculate average changes in the expression of a gene between groups

Highly expressed genes in pancreatic ductal adenocarcinomas

CA Iacobuzio-Donahue, R Ashfaq, A Maitra… – Cancer research, 2003 – AACR
 lethal cancer. We used the Gene Logic Inc. BioExpress platform and the most current
version of Affymetrix GeneChip arrays to perform a comprehensive study of gene
expression in pancreatic ductal adenocarcinomas. Gene

Expression profiling identifies a novel α-methylacyl-CoA racemase exon with fumarate hydratase homology

GL Shen-Ong, Y Feng… – Cancer research, 2003 – AACR
 BioExpress database containing Affymetrix U133 GeneChip expression profiles of 4400 human
samples from >60 tissue types was examined to  2 To whom requests for reprints should be
addressed, at Oncology Program, Gene Logic, Inc., 708  E-mail: gshen{at}genelogic.com. 

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2002

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Discovery of novel tumor markers of pancreatic cancer using global gene expression technology

CA Iacobuzio-Donahue, A Maitra… – The American journal of …, 2002 – Elsevier
 BioExpress platform and Affymetrix GeneChip arrays to identify genes differentially expressed
in pancreatic cancer.  Figure 3. Validation of gene expression by RT-PCR in 20 pancreatic cancer
cell lines  Rolfe Fund for Pancreatic Cancer Research, and a grant from GeneLogic Inc

Expression profiling of a human cell line model of prostatic cancer reveals a direct involvement of interferon signaling in prostate tumor progression

J Shou, R Soriano, SW Hayward… – Proceedings of the …, 2002 – National Acad Sciences
 Gene lists from both comparisons were then loaded into genespring software (Silicon
Genetics, Redwood City, CA) to look for common Affymetrix probe sets in both lists. 
GeneLogic (Gaithersburg, MD) BioExpress Database. 

[PDF] Relating GPCR Expression Patterns to Metabolic Syndrome Risk Factors

HHE Norseng – student.portal.chalmers.se
 Page 12. 6 2.4 BioExpress™ database The BioExpress database is the world’s most
comprehensive survey of gene expression in human disease related tissue. It is a part
of the GeneExpress data suite, produced by GeneLogic Inc. 
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2001
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Applying data warehouse concepts to gene expression data management

VM Markowitz… – … and Bioengineering Conference …, 2001 – ieeexplore.ieee.org
 GeneExpress products are available as DataSuites, such as BioExpress and ToxExpress,
which contain data on disease or tissue specific samples (see http://www.genelogic.com/gexpress
GeneExpress is notable for its size: it includes gene expression data on thousands of
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2000
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High-throughput gene expression analysis for drug discovery

GG Lennon – Drug discovery today, 2000 – Elsevier
 Gene Logic currently incorporates the Affymetrix GeneChip probe array in its closed gene  The
databases include quantitative information on gene expression for the relevant genes in the  One
GeneExpress database (BioExpress ™ ) is used primarily for target selection and

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