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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2020

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Overview of cancer genomics, organization, and variations in the human genome

M Yamin, HG Raza, I Fatima – ‘Essentials of Cancer Genomic …, 2020 – Springer

… However, microarray data analysis tools like “Gene Logic’s BioExpress ® System Oncology
Suite” and BioExpress ® Oncology Suite are specifically available for cancer research [4].

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2018

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[PDF] Identification of fat storage-inducing transmembrane proteins 1 and 2 as putative therapeutic targets for heart failure by integrated analysis of proteome and …

N Nishihama, Y Abe, K Kubota… – J Proteom …, 2018 – pdfs.semanticscholar.org

… The expression of all target genes in the heart was assessed by using the BioExpress database (GeneLogic, USA). Total RNA isolation and microarray analysis For the MI model, LV of three sham mice and four MI mice were used …

Cited by 1 Related articles

Klotho beta

L Desnoyers – US Patent App. 15/701,243, 2018 – Google Patents

… Whisker-box plots showing KLβ ( FIG. 4A ) and FGFR4 ( FIG. 4B ) expression in human tissues, as determined by mRNA analysis of the BioExpress database. The center line indicates the median; the box represents the inter-quartile range between the first and third quartiles … All 2 versions PDF] googleapis.com

Compositions and methods for treating and diagnosing cancer

AL Gurney, A Sato – US Patent App. 15/631,259, 2018 – Google Patents

The present invention relates to compositions and methods for characterizing, diagnosing and treating cancer. In particular, the present invention identifies LGR5 as a protein over-expressed in solid tumor stem cell. The present invention further identifies an interaction between … All 2 versions

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2017

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Compositions and methods for treating and diagnosing cancer

AL Gurney, AK Sato – US Patent 9,717,794, 2017 – Google Patents

US9717794B2 – Compositions and methods for treating and diagnosing cancer – Google Patents. Compositions and methods for treating and diagnosing cancer. Download PDF Info. Publication number US9717794B2. US9717794B2 … Related articles All 4 versions

Compositions and Methods for Treating and Diagnosing Cancer

AL Gurney – US Patent App. 15/441,700, 2017 – Google Patents

The present invention relates to compositions and methods for characterizing, diagnosing and treating cancer. In particular, the present invention identifies LGR5 as a protein over-expressed in solid tumor stem cells. The present invention further identifies an interaction between … All 2 versions

Rspo binding agents and uses thereof

AL Gurney, FT Axelrod, TC Hoey… – US Patent App. 15 …, 2017 – Google Patents

US20170298143A1 – Rspo binding agents and uses thereof – Google Patents. Rspo binding agents and uses thereof. Download PDF Info. Publication number US20170298143A1. US20170298143A1 US15/480,081 US201715480081A … All 2 versions

Anti-RSPO2 antibodies and uses thereof

AL Gurney, FT Axelrod, TC Hoey… – US Patent …, 2017 – Google Patents

US9644034B2 – Anti-RSPO2 antibodies and uses thereof – Google Patents. Anti-RSPO2 antibodies and uses thereof. Download PDF Info. Publication number US9644034B2. US9644034B2 US14/795,811 US201514795811A … Related articles All 2 versions

RSPO3 binding agents and uses thereof

AL Gurney, CJ Bond – US Patent 9,598,497, 2017 – Google Patents

US9598497B2 – RSPO3 binding agents and uses thereof – Google Patents. RSPO3 binding agents and uses thereof. Download PDF Info. Publication number US9598497B2. US9598497B2 US14/870,145 US201514870145A … Cited by 2 Related articles All 4 versions

RSPO3 Binding Agents and Uses Thereof

AL Gurney, CJ Bond – US Patent App. 15/439,288, 2017 – Google Patents

The present invention relates to RSPO-binding agents, particularly RSPO3-binding agents and methods of using the agents for treating diseases such as cancer. The present invention provides antibodies that specifically bind human RSPO3 proteins and modulate β-catenin activity … All 2 versions

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2016

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Bruton tyrosine kinase–dependent immune cell cross-talk drives pancreas cancer

AJ Gunderson, MM Kaneda, T Tsujikawa, AV Nguyen… – Cancer discovery, 2016 – AACR

[HTML] sciencedirect.com

[HTML] Bone health nutraceuticals alter microarray mRNA gene expression: A randomized, parallel, open-label clinical study

Y Lin, V Kazlova, S Ramakrishnan, MA Murray, D Fast… – Phytomedicine, 2016 – Elsevier

… using Feature Extraction software, version 9.5.3. Functionally annotated genes (those linked to any metabolic processes) were further analyzed for their relationship to bone health by comparison with the Gene Logic BioExpress ® gene expression database (Markowitz and … Cited by 11 Related articles All 9 versions

Method to improve expression and other biological analysis

R Lehrer – US Patent App. 14/776,621, 2016 – Google Patents

… on a large number of biological samples. For example, Gene Logic’s BioExpress system is a database of 22,000 human tissue samples with data generated on the Aggy HU133 2+platform. The data may be selected as those …

[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 …

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…

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[HTML] from plos.org

[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…

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…

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

[HTML] from sagepub.com

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…

Cited by 10 – Related articles – All 6 versions

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

[HTML] from plos.org

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…

Cited by 30 – Related articles – Cached – All 9 versions

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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

[PDF] from genelogic.com

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

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]. …

Cited by 12 – Related articles – All 5 versions

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- …

All 2 versions

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

[HTML] from biomedcentral.com

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…

Cited by 3 – Related articles – Cached – All 12 versions

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

[HTML] from nih.gov

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

[HTML] from oxfordjournals.org

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

[PDF] from fly-bay.net

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. …

Cited by 10 – Related articles – View as HTML – BL Direct – All 16 versions

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

[PDF] from genelogic.com

…, 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

[HTML] from 9med.net

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…

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

[HTML] from nih.gov

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…

Cited by 38 – Related articles – BL Direct – All 9 versions

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. …

Cached

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

[PDF] from future-science-group.com

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. …

Cited by 1 – Related articles

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…

Cited by 24 – Related articles – BL Direct – All 8 versions

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

[PDF] from orphanresearch.net

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…

Cited by 13 – Related articles – View as HTML – BL Direct – All 16 versions

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

[PDF] from genelogic.com

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. …

Cited by 48 – Related articles – BL Direct – All 9 versions

Liver-specific activities of FGF19 require Klotho beta

[HTML] from jbc.org

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…

Cited by 63 – Related articles – All 7 versions

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. …

All 2 versions

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

[PDF] from ncku.edu.tw

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 . …

Cited by 181 – Related articles – BL Direct – All 12 versions

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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…

Cited by 27 – Related articles – BL Direct – All 5 versions

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

[HTML] from jbc.org

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. …

Cited by 55 – Related articles – All 10 versions

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

[HTML] from biomedcentral.com

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…

Cited by 43 – Related articles – Cached – All 16 versions

HTML] Benchmarking ortholog identification methods using functional genomics data

[HTML] from biomedcentral.com

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…

Cited by 96 – Related articles – Cached – All 29 versions

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

[HTML] from physiology.org

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…

Cited by 24 – Related articles – BL Direct – All 6 versions

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

[HTML] from jbc.org

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…

Cited by 21 – Related articles – All 8 versions

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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

[HTML] from cancerimmunity.org

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…

Cited by 47 – Related articles – Cached – All 9 versions

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

[PDF] from gene.com

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. …

Cited by 71 – Related articles – All 9 versions

Molecular characterization of suicide by microarray analysis

[PDF] from genelogic.com

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. …

Cited by 14 – Related articles – All 6 versions

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

[HTML] from aacrjournals.org

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…

Cited by 136 – Related articles – All 6 versions

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

[HTML] from aacrjournals.org

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). …

Cited by 222 – Related articles – All 7 versions

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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. …

All 2 versions

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

[PDF] from braintrusters.com

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…

Cited by 25 – Related articles – View as HTML – All 20 versions

[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…

Cited by 228 – Related articles – All 14 versions

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…

Cited by 20 – Related articles – All 5 versions

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

[HTML] from endojournals.org

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…

Cited by 76 – Related articles – BL Direct – All 7 versions

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

[PDF] from uu.se

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…

[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

[PDF] from aacrjournals.org

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…

Cited by 76 – Related articles – BL Direct – All 4 versions

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…

Cited by 269 – Related articles – BL Direct – All 6 versions

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

[HTML] from aacrjournals.org

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. …

Cited by 34 – Related articles – BL Direct – All 5 versions

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2002

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

[HTML] from nih.gov

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…

Cited by 242 – Related articles – BL Direct – All 13 versions

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

[HTML] from pnas.org

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. …

Cited by 76 – Related articles – BL Direct – All 11 versions

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

[PDF] from chalmers.se

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. …

Applying data warehouse concepts to gene expression data management

[PDF] from utoronto.ca

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…

Cited by 14 – Related articles – All 7 versions

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2000

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High-throughput gene expression analysis for drug discovery

[PDF] from bu.edu

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…

Cited by 55 – Related articles – All 9 versions

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BioExpress® System Publication References

[PDF] Systematic evaluation of connectivity map for disease indications

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

[HTML] Molecular biomarker analyses using circulating tumor cells

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

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

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

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

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

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

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

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

HTML] Benchmarking ortholog identification methods using functional genomics data

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

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

[BOOK] Analyzing microarray gene expression data

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

[CITATION] 12 Predictive Toxicogenomics

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

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