Updated: May 2022
This is a list of publications that reference some of the bioinformatics tools that we developed at Ocimum Biosolutions
Genchek was the earliest. iRNAchek is the latest one.
Genowiz™ is one of our earliest software packages that was developed right after Genchek ( Sequence analysis). It was designed to ensure that scientists can find it really easy to navigate and manage their data in one single place.
After the acquisition of gene Logic, we also added Genesis to our gene expression packages but Genowiz is still widely used both internally and externally by our partners worldwide.
A big thank you to the team that developed it and continues to develop it.
For more information please email info@ocimumbio.com
As with my other posts on publications, this is chronological and starts with 2022…. As you can see several publications this year already.
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2022
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Ethanol Extract of Elaeagnus glabra f. oxyphylla Branches Alleviates the Inflammatory Response Through Suppression of Cyclin D3/Cyclin-Dependent Kinase 11p58 …
HS Lim, E Sohn, YJ Kim, BY Kim… – Natural Product …, 2022 – journals.sagepub.com
… Normalized data were analyzed using Genowiz 4.0 (Ocimum Biosolutions). The
normalization decides the average intensity of all samples numerically equivalent to the average …
[HTML] Comparison of transcriptome between high-and low-marbling fineness in longissimus thoracis muscle of Korean cattle
SH Beak, M Baik – Animal Bioscience, 2022 – ncbi.nlm.nih.gov
… The read count data were processed based on the quantile normalization method using
Genowiz ver. 4.0.5.6 (Ocimum Biosolutions, Hyderabad, India). For functional annotation, we
Anti-obesity effect of sulforaphane in broccoli leaf extract on 3T3-L1 adipocytes and ob/ob mice
SS Ranaweera, P Natraj, P Rajan… – The Journal of …, 2022 – Elsevier
… The read count data were processed based on Quantile normalization method using the
Genowiz version 4.0.5.6 (Ocimum Biosolutions, India). The PPI network was analyzed using …
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2021
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Blue laser-induced selective vasorelaxation by the activation of NOSs
SW Park, S Park, HK Choi, HJ Park, W Yu, HS Kim… – Microvascular …, 2021 – Elsevier
… The RC (Read Count) data were processed based on Global normalization method using
the Genowiz ™ version 4.0.5.6 (Ocimum Biosolutions, India). Gene classification was based
[HTML] Association of protein Z with prediabetes and type 2 diabetes
YU Bae, JH You, NH Cho, LE Kim… – Endocrinology and …, 2021 – ncbi.nlm.nih.gov
… The numerical data were analyzed using the Genowiz 4.0 software (Ocimum Biosolutions,
Indianapolis, IN, USA). After analysis, the data on protein information were annotated using …
[HTML] Restoration of the adipogenic gene expression by naringenin and naringin in 3T3-L1 adipocytes
LA Dayarathne, SS Ranaweera, P Natraj… – Journal of Veterinary …, 2021 – ncbi.nlm.nih.gov
… The RT (read count) data were processed based on the quantile normalization method
using the Genowiz version 4.0.5.6 (Ocimum Biosolutions, India). Gene classification was …
Functional study of acetaldehyde dehydrogenase 1 (ALDH1) in keratinocytes: microarray integrating bioinformatics approaches
SJ Yin, MW Park, BN Lee, JM Yang… – Journal of …, 2021 – Taylor & Francis
… The numeric data were analyzed using Genowiz 4.0 TM (Ocimum Biosolutions, India). After
… Data were normalized with Genowiz 4.0 TM (Ocimum Biosolutions, India) software. Scatter …
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2020
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Functional study of 14-3-3 protein epsilon (YWHAE) in keratinocytes: microarray integrating bioinformatics approaches
SJ Yin, JR Lee, H Kwak, BN Lee, JW Han… – Journal of …, 2020 – Taylor & Francis
… The numeric data were analyzed using Genowiz 4.0™ (Ocimum Biosolutions, India). After …
Data were normalized with Genowiz 4.0™ (Ocimum Biosolutions, India) software. Scatter plot …
Effects of enzymatically modified chestnut starch on the gut microbiome, microbial metabolome, and transcriptome of diet-induced obese mice
ES Lee, EJ Song, YD Nam, TG Nam, HJ Kim… – International Journal of …, 2020 – Elsevier
… The read count data were processed based on the global normalization method using
Genowiz version 4.0.5.6 (Ocimum Biosolutions, Hyderabad, India). Gene classification was based …
HTML] Anti-inflammatory effect of sulforaphane on LPS-stimulated RAW 264.7 cells and ob/ob mice
SS Ranaweera, CY Dissanayake, P Natraj… – Journal of veterinary …, 2020 – ncbi.nlm.nih.gov
… The Read count (RT) data were analyzed based on the Quantile normalization method
using the Genowiz™ version 4.0.5.6 (Ocimum Biosolutions, India). The PPI network was …
[HTML] Comparison of transcriptome between high-and low-marbling fineness in longissimus thoracis muscle of Korean cattle
SH Beak, M Baik – Animal Bioscience, 2022 – ncbi.nlm.nih.gov
… The read count data were processed based on the quantile normalization method using
Genowiz ver. 4.0.5.6 (Ocimum Biosolutions, Hyderabad, India). For functional annotation, we …
Protein profiling and angiogenic effect of hypoxia-cultured human umbilical cord blood-derived mesenchymal stem cells in hindlimb ischemia
KH Han, AK Kim, MH Kim, DH Kim, HN Go, D Kang… – Tissue and Cell, 2017 – Elsevier
… The numeric data were analyzed with Genowiz 4.0TM (Ocimum Biosolutions, India) and
protein information was annotated by means of the UniProt DB. The phosphorylation ratio was
Dynein-mediated nuclear translocation of yes-associated protein through microtubule acetylation controls fibroblast activation
E You, P Ko, J Jeong, S Keum, JW Kim, YJ Seo… – Cellular and Molecular …, 2020 – Springer
… The Read Count data were processed based on the Global normalization method using
the Genowiz™ version 4.0.5.6 (Ocimum Biosolutions, India). Hierarchical clustering analysis
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2019
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[HTML] Enhanced Anti-Cancer Effects of Conditioned Medium from Hypoxic Human Umbilical Cord–Derived Mesenchymal Stem Cells
KH Han, AK Kim, GJ Jeong, HR Jeon… – … journal of stem cells, 2019 – ncbi.nlm.nih.gov
… The data were analyzed using Genowiz 4.0TM (Ocimum Biosolutions, India) and proteins
that were upregulated or downregulated in H-CM compared with N-CM (>1.5 fold) were …
Histone demethylase KDM3B regulates the transcriptional network of cell-cycle genes in hepatocarcinoma HepG2 cells
MJ An, DH Kim, CH Kim, M Kim, S Rhee, SB Seo… – Biochemical and …, 2019 – Elsevier
… The RC (Read Count) data were processed based on Quantile normalization method using
the Genowiz™ version 4.0.5.6 (Ocimum Biosolutions, India). Gene classification and gene …
Annona atemoya leaf extract ameliorates cognitive impairment in amyloid-β injected Alzheimer’s disease-like mouse model
HS Lim, YJ Kim, E Sohn, J Yoon… – Experimental …, 2019 – journals.sagepub.com
… Data normalization was conducted using the Genowiz 4.0 (Ocimum Biosolutions, Gaithersburg,
- MD) and determined the average intensity of samples comparable to that of all genes. …
Dexamethasone induces a specific form of ramified dysfunctional microglia
MJ Park, HS Park, MJ You, J Yoo, SH Kim… – Molecular …, 2019 – Springer
… The RT (Read Count) data were processed based on global normalization method using
the Genowiz™ version 4.0.5.6 (Ocimum Biosolutions, India). Gene classification was based on …
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2018
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Histone demethylase KDM7A controls androgen receptor activity and tumor growth in prostate cancer
KH Lee, S Hong, M Kang, CW Jeong… – … Journal of Cancer, 2018 – Wiley Online Library
… The RT (Read Count) data were processed based on Global normalization method using
the Genowiz ™ version 4.0.5.6 (Ocimum Biosolutions, India). We performed gene clustering …
[HTML] The LuxS/AI-2 quorum-sensing system of Streptococcus pneumoniae is required to cause disease, and to regulate virulence-and metabolism-related genes in …
MK Yadav, JE Vidal, YY Go, SH Kim… – Frontiers in cellular …, 2018 – frontiersin.org
… The microarray data were analyzed using Genowiz 4.0™ (Ocimum Biosolutions,
Hyderabad, India), and normalized with Global LOWESS. The cutoffs for upregulated and …
Phytochemical allylguaiacol exerts a neuroprotective effect on hippocampal cells and ameliorates scopolamine-induced memory impairment in mice
HS Lim, BY Kim, YJ Kim, SJ Jeong – Behavioural Brain Research, 2018 – Elsevier
… Normalized data were analyzed using Genowiz 4.0 (Ocimum Biosolutions, India). The
normalization makes the average intensity of all samples numerically equivalent to the average …
Licochalcone A attenuates acne symptoms mediated by suppression of NLRP3 inflammasome
G Yang, HE Lee, SH Yeon, HC Kang… – Phytotherapy …, 2018 – Wiley Online Library
… The RT (Read Count) data were processed based on Quantile normalization method
using the Genowiz ™ version 4.0.5.6 (Ocimum Biosolutions, Hyderabad, India). …
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2017
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[HTML] Enhanced Anti-Cancer Effects of Conditioned Medium from Hypoxic Human Umbilical Cord–Derived Mesenchymal Stem Cells
KH Han, AK Kim, GJ Jeong, HR Jeon… – … journal of stem cells, 2019 – ncbi.nlm.nih.gov
… The data were analyzed using Genowiz 4.0TM (Ocimum Biosolutions, India) and proteins
that were upregulated or downregulated in H-CM compared with N-CM (>1.5 fold) were
S Singh, D Singh, S Kumar – Process Biochemistry, 2017 – Elsevier
… 288 bp of CsPPO. In addition, codons were optimized for the expression of CsPPO synin E. coli using OptGene™ (Ocimum Biosolutions, USA) as mentioned in supplementary data (Supplementary Fig. 1). CsPPO syn was synthesized …
Estimation of low-dose radiation-responsive proteins in the absence of genomic instability in normal human fibroblast cells
JH Yim, JM Yun, JY Kim, SY Nam… – International Journal of …, 2017 – Taylor & Francis
… , the normalization data were analyzed using Genewiz 4.0™ (Ocimum Biosolution, India). All
… The numerical data were analyzed using Genexiz 4.0™ (Ocimum Biosolutions, India). After …
Save Cite Cited by 9 Related articles All 3 versions
Control of cancer stem cell like population by intracellular target identification followed by the treatment with peptide-siRNA complex
JS Suh, HJ Lee, H Nam, BS Jo, DW Lee, JH Kim… – Biochemical and …, 2017 – Elsevier
… The numeric data were analyzed using Genowiz 4.0TM (Ocimum Biosolutions, Hyderabad,
India). Phosphorylation ratio was calculated as below. phosphorylation ratio = phospho …
[HTML] Characteristics of a regulator of G-protein signaling (RGS) rgsC in Aspergillus fumigatus
Y Kim, IB Heo, JH Yu, KS Shin – Frontiers in microbiology, 2017 – frontiersin.org
… Loess normalization and selection of fold-changed genes were performed using GenoWiz
4.0 (Ocimum biosolutions, India). The data is available in the Gene Expression Omnibus (GEO…
An ultra-effective method of generating extramultipotent cells from human fibroblasts by ultrasound
YS Lee, H Heo, J Lee, SU Moon, WY Jung, YK Park… – Biomaterials, 2017 – Elsevier
… The RC (Read Count) data were processed based on the quantile normalization method
using Genowiz ™ version 4.0.5.6 (Ocimum Biosolutions, India). Gene classification was based
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2016
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[HTML] Identification of novel therapeutic targets in the secretome of ionizing radiation‑induced senescent tumor cells
HJ Hwang, SH Jung, HC Lee, NK Han… – Oncology …, 2016 – spandidos-publications.com
… The obtained numerical data were analyzed using Genowiz 4.0™ (Ocimum Biosolutions,
Indianapolis, IN, USA). Following analysis, the protein data were annotated using UniProt DB (…
Latent Kaposi’s sarcoma-associated herpesvirus infection in bladder cancer cells promotes drug resistance by reducing reactive oxygen species
S Lee, J Jang, H Jeon, J Lee, SM Yoo, J Park… – Journal of …, 2016 – Springer
… The numeric data were analyzed using Genowiz 4.0TM (Ocimum Biosolutions). The array
data were deposited in NCBI’s Gene Expression Omnibus (GEO) and can be accessed by
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2015
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Process for designing diverged, codon-optimized large repeated dna sequences
DJ Merlo, I Larrinua, S Bevan – US Patent App. 14/415,115, 2015 – Google Patents
… sequence according to predetermined parameters. In particular embodiments, the computer-implemented software program may be OPTGENE™ (available from Ocimum Biosolutions). A sample amino acid repeat sequence.
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2013
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HS Heo, E Kim, SM Jeon, EY Kwon, SK Shin, H Paik… – Molecules and …, 2013 – Springer
… 1. Clustering of hepatic gene transcripts For clustering of hepatic gene transcripts, the Self-Organizing Map (SOM) algorithm (Quackenbush, 2001) was applied. We used Genowiz (Ocimum Biosolutions, India) with the SOM tool to arrange all data samples …Cited by 8 Related articles
WA Laviña, M Sugiyama, Y Kaneko… – Journal of bioscience and …, 2013 – Elsevier
… All strains were cultivated in YPDA media and calcium treatment was done by supplementing the YPDA medium with 0.3 M CaCl 2 . Four independent DNA microarray data were analyzed using Genowiz (Ocimum Biosolutions) …
P Sharma, H Lata, DK Arya, AK Kashyap… – Journal of Biological …, 2013 – ASBMB
… Hybridized chips were scanned using an Affymetrix 428TMArray scanner at three different PMT gains, and the images were analyzed using Genowiz software (Ocimum Biosolutions). Analysis was performed to detect differentially expressed genes among the groups …Cited by 27 Related articles
P Nair, A Misra, A Singh, AK Shukla, MM Gupta… – PLoS …, 2013 – journals.plos.org
… chip. Hybridized chips were scanned using Affymetrix 428TM Array Scanner at three different PMT gains (40, 50 and 60) and the data was analyzed using Genowiz software (Ocimum Biosolutions, Hyderabad). Image analysis …
WA Laviña, H Shahsavarani, A Saidi, M Sugiyama… – 2013 – researchgate.net
… was performed in triplicates. Gene enrichment analysis using Genowiz The microarray data were analyzed for distinctive expression using Genowiz 4.0 (Ocimum Biosolutions, India). Replicated gene values were combined …
Decreased defense gene expression in tolerance versus resistance to Verticillium dahliae in potato
HH Tai, C Goyer, D De Koeyer, A Murphy… – Functional & integrative …, 2013 – Springer
… Analysis of microarray data. Microarray data were analyzed using the Genowiz 4.0 software (Ocimum Biosolutions, Gaithersburg, MD, USA). Double channel analysis of 07506-01 and 12120-03 data was done using print-tip loess normalization with a smoothing factor of 0.1 … Cited by 11
P Shyamsunder, P Vidyasekar, AR Shukla, S Mohan… – Gene, 2013 – Elsevier
… The statistical analysis was carried out using R package and the biological analysis was carried out using Genowiz software (Ocimum Biosolutions, USA) and Gene Spring GX 10 (Agilent Technologies, USA). 2.5. Gene ontology analysis … Cited by 14 Related articles
BR Oh, WK Hong, SY Heo, M Joe, JW Seo… – Journal of industrial …, 2013 – Springer
… expression ratios (reference vs. test) were obtained. Microarray data analysis was performed using Genowiz 4.0 (Ocimum Biosolutions, Hyderabad, India). Global lowess was used for data analysis with normalization. The cut-offs for …Cited by 6 Related articles
[HTML] Escherichia coli YmdB regulates biofilm formation independently of its role as an RNase II modulator
T Kim, J Lee, K Kim – BMC microbiology, 2013 – bmcmicrobiol.biomedcentral.com
… ratios (reference vs. test sample). Microarray data analysis was performed using Genowiz 4.0™ (Ocimum Biosolutions). Global lowess (Locally weighted scatter plot smoothing) method was used for data normalization. The cut-off … Cited by 7 Related articles All 11 versions
Identification of novel target genes involved in Indian Fanconi anemia patients using microarray
P Shyamsunder, KS Ganesh, P Vidyasekar, S Mohan… – Gene, 2013 – Elsevier
… obtained. The statistical analysis was carried out using the R package and the biological analysis was carried out using Genowiz TM software (Ocimum Biosolutions, USA). 2.4. Functional clustering and gene ontology analysis … Cited by 8 Related articles All 6 versions
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2012
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[PDF] Functional annotation of expressed sequence tags of Papaver somniferum
A Priya, H Tripathi, DK Yadav, F Khan, V Gupta… – Plant Omics, 2012 – pomics.com
… sequences retrieved from dbEST were cleaned, clustered and assembled through PHRED (Ewing and Green, 1998), RepeatMasker, Cross-Match, PHRAP and CAP3 (Huang and Madan, 1999) softwares with the help of Gencheck software (Ocimum Biosolutions, USA; www …
Gene expression profile of early in vitro biofilms of Streptococcus pneumoniae
MK Yadav, SK Kwon, CG Cho, SW Park… – Microbiology and …, 2012 – Wiley Online Library
… ratios (planktonic vs biofilm samples). Microarray data analysis was carried out by Genowiz 4.0 (Ocimum Biosolutions, Hyderabad, India). Global Lowess was used for data analysis with normalization. The benchmarks for up …Cited by 19 Related articles All 11 versions
HJ Sung, J Kim, Y Kim, SW Jang, J Ko – Molecular biology reports, 2012 – Springer
… Data were analyzed by Genowiz 4.0 TM (Ocimum Biosolutions, Hyderabad, India) and normalized using intensity-dependent global normalization (LOWESS). To categorize the functional annotation of genes, the database of Gene Ontology TM Consortium was applied …Cited by 15 Related articles All 11 versions
The effect of secretory factors of adipose-derived stem cells on human keratinocytes
KM Moon, YH Park, JS Lee, YB Chae, MM Kim… – International journal of …, 2012 – mdpi.com
The beneficial effects of adipose-derived stem cell conditioned medium (ADSC-CM) on skin regeneration have been reported. Although the mechanism of how ADSC-CM promotes skin regeneration is unclear, ADSC-CM contained various growth factors and it is an excellent raw …Cited by 90 Related articles All 16 versions
[PDF] Differential Gene Expression Profile in Essential Hypertension
P Yang – Genetics and Pathophysiology of Essential …, 2012 – intechopen.com
… rats treated with FPTIII kidney Codelink Uniset Rat 1Bioarrays Affymetrix Scanner 428, Imagene and Genowiz softwares by Ocimum Biosolutions (India) and subjected to arsinh transformation 2398 genes were upregulated and …Related articles All 3 versions
KA Schat, J Bingham, JM Butler, LM Chen, S Lowther… – PloS one, 2012 – journals.plos.org
Highly pathogenic H5N1 avian influenza viruses have caused major disease outbreaks in domestic and free-living birds with transmission to humans resulting in 59% mortality amongst 564 cases. The mutation of the amino acid at position 627 of the viral polymerase basic-2 protein …Cited by 39 Related articles All 21 versions
D Frank – 2012 – qspace.library.queensu.ca
… Page 30. ` 19 Microarray analysis Microarray data were analyzed using the Genowiz 4.1 software (Ocimum Biosolutions, Madhapur, Hyderabad). For double channel analysis, data was normalized using print-tip lowess normalization with a smoothing factor of 0.1 …Related articles All 2 versions
S Mukherjee, S Majumdar, VC Vipat… – Virology …, 2012 – virologyj.biomedcentral.com
The Non-Structural (NS1) protein of Influenza A viruses is an extensively studied multifunctional protein which is commonly considered as key viral component to fight against host immune responses. Even though there has been a lot of studies on the involvement of NS1 protein …Cited by 14 Related articles All 19 versions
김승민 – 2012 – s-space.snu.ac.kr
Page 1. 저작자표시-비영리-변경금지 2.0 대한민국 이용자는 아래의 조건을 따르는 경우에 한하여 자유롭게 ● 이 저작물을 복제, 배포, 전송, 전시, 공연 및 방송할 수 있습니다. 다음과 같은 조건을 따라야 합니다: ● 귀하는, 이 저작물의 …
[PDF] Yersiniosis and Food Safety
K Isshiki, RC Ray, D Montet – downloads.hindawi.com
Page 1. Journal of Pathogens Guest Editors: Latiful Bari, Dike O. Ukuku, Kenji Isshiki, Ramesh C. Ray, and Didier Montet Yersiniosis and Food Safety Page 2. Yersiniosis and Food Safety Page 3. Journal of Pathogens Yersiniosis and Food Safety …Related articles
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2011
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HTML] A review on worldwide essential software resources in pharmacy
PY Mali, SJ Panchal – Chronicles of Young Scientists, 2011 – cysonline.org
… history recording, etc. http://www.applied-maths.com/gelcompar/gelcompar.htm GenchekIt is an integral database system that can used to access, store, organize and retrieve DNA, protein and vector sequences. http://www.ocimumbio …Related articles All 2 versions Cite
Differentially expressed genes in sensitive and tolerant rice varieties in response to salt-stress
A Pandit, V Rai, TR Sharma, PC Sharma… – Journal of plant …, 2011 – Springer
… genes. The array data were analyzed using GeneChip Operating Software (GCOS 1.2) and Genowiz software (Ocimum Biosolutions, India). Robust multichip average (RMA) algorithm method was used for normalization. Two
Cited by 24 Related articles All 7 versions
DK Kim, SJ Hong, JH Bae, N Yim, ES Jin… – Biotechnology and …, 2011 – Springer
… sample). Microarray data analysis was carried out by Genowiz 4.0TM (Ocimum Biosolutions,India). Global LOWESS was used for data analysis with normalization. The benchmarks for up-regulated and down-regulated genes in hybridization were 2.0 and 0.5-fold, respectively …Cited by 30 Related articles All 7 versions
MS GEIER, TM CROWLEY – 22 nd ANNUAL AUSTRALIAN POULTRY … – researchgate.net
… Statistical tests were carried out using Genowiz Version 4.0. 5.3 (Ocimum Biosolutions) to determine all genes that were differentially expressed (p= 0.01) between the groups under consideration, either high and low AME groups or good and poor FCR groups …Related articles All 3 versions
S Mukherjee, VC Vipat, AC Mishra… – Virology …, 2011 – virologyj.biomedcentral.com
… Data Analysis. Microarray data analysis was carried out with GENOWIZ Microarray data and pathway analysis tool (Ocimum Biosolutions, Hyderabad, India). Replicated values for genes were merged and median values of the expression ratios were considered for the dataset …Cited by 27 Related articles All 19 versions
R Wenne, L Handschuh, A Pocwierz-Kotus… – Marine Biology …, 2011 – Taylor & Francis
… After normalization (double-channel normalization between arrays based on subtraction of control probe mean, followed by log2-transformation) using Genowiz 4.0 software (Ocimum Biosolutions), the probe intensity data was analysed using R (http:// http://www.R-project.org; R …Cited by 3 Related articles All 5 versions
CS Vasamsetty, SR Peri, AA Rao, K Srinivas… – International Journal of …, 2011 – ijetch.org
… expressed genes. ACKNOWLEDGMENT The authors acknowledge Ocimum Biosolutions, Hyderabad, India for analysis of the microarray data using their proprietary microarray analysis tool Genowiz. REFERENCES [1] John …
Related articles All 3 versions
S Johanningsmeier – 2011 – repository.lib.ncsu.edu
Page 1. ABSTRACT JOHANNINGSMEIER, SUZANNE DUNN. Biochemical Characterization of Fermented Cucumber Spoilage using Non-targeted, Comprehensive, Two-dimensional Gas Chromatography-Time-of-Flight Mass …
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2010
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Retrotransposon expression in ethanol-stressed Saccharomyces cerevisiae
D Stanley, S Fraser, GA Stanley… – Applied microbiology and …, 2010 – Springer
… reference pool (Gasch et al. 2000). Following hybridisation, the glass slides were scanned using a GenePix-Pro 4000B scanner and analysed using Genowiz™ 4.0.2.1 software (Ocimum Biosolutions). The original data from this
Cited by 16 Related articles All 19 versions
Transcriptional changes associated with ethanol tolerance in Saccharomyces cerevisiae
D Stanley, PJ Chambers, GA Stanley… – Applied microbiology …, 2010 – Springer
… Following hybridisation, the glass slides were scanned using a GenePix 4000B scanner and analysed using Genowiz™ 4.0.2.1 software (Ocimum Biosolutions). Microarray data were normalised prior to statistical analysis using a print tip Lowess (Yang et al …
Cited by 41 Related articles All 19 versions
AK Chakrabarti, VC Vipat, S Mukherjee… – Virology …, 2010 – virologyj.biomedcentral.com
… Grid alignment was done using gene annotation files and raw data were extracted into MS EXCEL. Data Analysis. Data was analyzed using GENOWIZ Microarray and Pathway analysis tool (Ocimum Biosolutions, Hyderabad, India)
Cited by 58 Related articles All 20 versions
Immunomodulatory cytokines determine the outcome of Japanese encephalitis virus infection in mice
SM Biswas, S Kar, R Singh… – Journal of medical …, 2010 – Wiley Online Library
… Data Analysis Data were analyzed using Genowiz Microarray and Pathway analysis tool (OcimumBiosolutions, Hyperabad, India). Replicated genes were merged and median values of the expression ratios of these repli- cated genes were further considered for the dataset … Cited by 35 Related articles All 8 versions
VC Sekhar, AA Rao, PS Rao… – 2010 3rd International …, 2010 – ieeexplore.ieee.org
… is under progress. ACKNOWLEDGMENT The Authors Acknowledges Ocimum Biosolutions, Hyderabad, India. For analysis of the microarray data using their proprietary microarray analysis tool Genowiz. REFERENCES [I] M …Related articles All 2 versions
D Verma, A Kanagaraj, S Jin, ND Singh… – Plant biotechnology …, 2010 – Wiley Online Library
Skip to Main Content … Cited by 114 Related articles All 12 versions
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2009
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D Biswas, SK Gupta, G Sindhwani… – BMC research …, 2009 – biomedcentral.com
… of Biochemistry, University of Delhi, India. To sense the SNPs in the selected DNA sequences, multiple sequence alignment was performed using built in interface for ClustalW[8] in Genchek software version 2.4.1.5 from Ocimum Biosolutions. …Cited by 10 Related articles All 12 versions Cite
[HTML] BMC research notes Volume: 2 ISSN: 1756-0500 ISO Abbreviation: BMC Res Notes Publication Date: 2009
D Biswas, SK Gupta, G Sindhwani, A Patras – Detail: – biomedsearch.com
… of Biochemistry, University of Delhi, India. To sense the SNPs in the selected DNA sequences, multiple sequence alignment was performed using built in interface for ClustalW [8 ] in Genchek software version 2.4.1.5 from Ocimum Biosolutions. …Related articles
IF Benter, H Canatan, M Benboubetra, MHM Yousif… – Vascular …, 2009 – Elsevier
..supplier (GE Healthcare). Data analysis was performed using Imagene and Genowiz softwares by Ocimum Biosolutions (India) and subjected to arsinh transformationas described by Huber et al. (2002). The Benjamini and Cited by 24 Related articles
A systematic approach to understanding bacterial responses to oxygen using Taverna and Webservices
S Maleki-Dizaji, M Rolfe, P Fisher… – … Conference on Biomedical …, 2009 – Springer
… (ie GeneSpring, GenoWiz) that can provide links to data- bases that define pathways, functional …Hybridisation took place to Ocimum OciChip K-12 V2 microarrays (Ocimum; Hydera- bad, India) at 42 °C overnight and washed according to the manufacturers instructions …Cited by 7 Related articles
[PDF] Transcriptional Activation of p53 gene and stabilization of p53 by its Amino-Terminus Domain
AK Sharma – 2009 – ir.inflibnet.ac.in
… information management system. Genowiz ™ incorporates an entire army of analysis tools for the efficient analysis of microarray data. Ocimum also provides analyses that are not required as a part of this study. A list of services provided in the microarray realm can be found at …Related articles
[PDF] Generation and characterisation of ethanol-tolerant saccharomyces cerevisiae mutants
D Stanley – 2009 – vuir.vu.edu.au
Page 1. \ v;l \.TIOM AMD CHARACISRISA. jmm wBS Page 2. GENERATION AND CHARACTERISATION OF ETHANOL-TOLERANT Saccharomyces cerevisiae MUTANTS A thesis submitted for the degree of DOCTOR OF PHILOSOPHY By DRAGANA STANLEY …Related articles All 3 versions
STATISTICAL ANALYSIS IDENTIFIES GENES IN PROSTATE CANCER
M Vidhya – International Journal of Medical Engineering and …, 2009 – Inderscience
… microarray data obtained for the normal and malignant samples for 8,900 genes was taken and it was analysed to identify the genes that are differently expressed in tumour samples in comparison to the normal samples from tissues and cell lines using the tool Genowiz™ 3.1. …Related articles – All 7 versions
Application of Data Mining Algorithms in Pharmaceutical Research and Development
KV Balakin… – Pharmaceutical Data Mining, 2009 – Wiley Online Library
… ac.uk/microarray/maxd/ A data warehouse and visualization environment for genomic expression data Genowiz ™ http://www.ocimumbio.com/ web/default.asp A comprehensive multiplatform package for tracking and analyzing Gene Expressions data …Related articles – All 3 versions
S Mukherjee, VC Vipat, AC Mishra, SD Pawar… – Virol J, 2011 – biomedcentral.com
… Grid align- ment was done by gene annotation files and raw data were extracted into MS EXCEL[15]. Data Analysis Microarray data analysis was carried out with GENO– WIZ Microarray dataand pathway analysis tool (Oci- mum Biosolutions, Hyderabad, India). … Cited by 6 – Related articles – View as HTML – All 9 versions
A Systematic Approach to Understanding Bacterial Responses to Oxygen Using Taverna and Webservices
S Maleki-Dizaji, M Rolfe, P Fisher… – … Conference on Biomedical …, 2009 – Springer
… 23 _____ (ie GeneSpring, GenoWiz) that can provide links to data- bases that define pathways, functional categories and gene ontologies. Many …Cited by 1 – Related articles – All 3 versions
New approach to Genomics Experients Taking Advantage of Virtual Laboratory System
L Handschuh, M Lawenda, P Stępniak… – … Methods In Science …, 2009 – man.poznan.pl
… Raw data in a text file (csv, gpr or similar) are then submitted to normaliza- tion, filtration and high-level analysis, using sophisticated software (eg R Bioconductor, Multi Experiment Viewer, Gene Spring, Genowiz). Result reports are saved as text or graphic files (eg pdf, jpg). …Cited by 3 – Related articles – View as HTML – All 2 versions
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2008
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[PDF] Subtype selectivity in phosphodiesterase 4 (PDE4): a bottleneck in rational drug design
RD Design – Current Pharmaceutical Design, 2008 – 203.199.182.73
Page 1. 3854 Current Pharmaceutical Design, 2008,14, 3854-3872 Subtype Selectivity in Phosphodiesterase 4 (PDE4): A Bottleneck in Rational Drug Design P. Srivani1, D. Usharani2’3, Eluvathingal D. Jemmis2′” and G. Narahari …Cited by 22 Related articles All 9 versions Cite
Design of microarray probes for detection of mutations
P Almeida, L Carreto, JL Oliveira – … , 2008. BIOTECHNO’08. …, 2008 – ieeexplore.ieee.org
… efficiency and robustness, ie finding the best set of probes for specific hybridization conditions [4]. Several software packages already exist to assist on the design of microarray probes: AlleleID [5], Oligowiz [6], Gencheck [7], Oligo … [7] OcimumBiosolutions, “GenChek,” GenChek. …Cited by 1 Related articles All 4 versions Cite
Visual software tools for bioinformatics
T Arndt – Journal of Visual Languages & Computing, 2008 – Elsevier
… View Within Article. Genchek [7] (available for Linux, Mac, Windows and Unix) is a comprehensive software suit. It has support for several operations on DNA and proteins. … Gencheck is shown in Fig. 10. …Cited by 4 Related articles All 2 versions Cite
Y Takahara, M Takahashi, QW Zhang… – World journal of …, 2008 – ncbi.nlm.nih.gov
… The gene expression data were subjected to hierarchical clustering analysis using Genowiz™ software (Ocimum Biosolutions). … All genes in Figure Figure11 were subjected to hierarchical clustering analysis using Genowiz™. …
Cited by 11 – Related articles – BL Direct – All 8 versions
P Priyadarsiny, SK Khattar, R Malik… – The Journal of …, 2008 – J-STAGE
… Hierarchi- cal analysis and self-organizing maps were used to cluster the genes in different groups. Furthermore, gene annota- tion and pathway analysis was carried out using Genowiz software. RESULTS AND DISCUSSION …Cited by 3 – Related articles – BL Direct – All 7 versions
NKF Chen, J San Wong, IHC Kee, SH Lai… – PloS one, 2008 – dx.plos.org
… All statistical tests and the area under the curve (AUC) were calculated with GraphPad Prism (GraphPad Software Inc., USA). Cluster analysis of GeneChip® data was performed using algorithms in Genowiz (Ocimum Biosolutions Ltd., India). P<0.05 was considered significant. … Cited by 10 – Related articles – Cached – All 9 versions
NKF Chen, J San Wong, IHC Kee, SH Lai, CH Thng… – PLoS …, 2008 – journals.plos.org
BackgroundCurrent gene- and cell-based therapies have significant limitations which impede widespread clinical application. Taking diabetes mellitus as a paradigm, we have sought to overcome these limitations by ex vivo electrotransfer of a nonviral insulin expression vector into … Cited by 25 Related articles All 14 versions
Y Takahara, M Takahashi, QW Zhang… – World journal of …, 2008 – ncbi.nlm.nih.gov
… This calculation was performed using SPSS (SPSS Inc., IL, USA). The gene expression data were subjected to hierarchical clustering analysis using Genowiz™ software (Ocimum Biosolutions). Pathway analysis of PCR data …Cited by 31 Related articles All 9 versions
Gene expression microarray data analysis demystified
PC Roberts – Biotechnology annual review, 2008 – Elsevier
Skip to main content Skip to article Elsevier logo: Journals & Books. Create accountSign in. Sign inCreate account. Journals & Books. Help. Download PDFDownload. Share. Cited by 36 Related articles All 4 versions
Microarray Data Analysis Tool (MAT)
S Selvaraja – 2008 – rave.ohiolink.edu
Page 1. MICROARRAY DATA ANALYSIS TOOL (MAT) A Thesis Presented to The Graduate Faculty of The University of Akron In Partial Fulfillment of the Requirements for the Degree Master of Science Sudarshan Selvaraja December, 2008 Page 2. ii … Related articles All 3 versions
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2007
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R Lapointe, K Tanaka, WE Barney, JB Whitfield… – Journal of …, 2007 – Am Soc Microbiol
… University of Kentucky. The DNA sequences were first edited to remove vector sequences and then assembled using either SeqMan II (Lasergene DNAStar) or Genchek v. 2061 (Ocimum Biosolutions). Contigs were built using …
Cited by 40 Related articles BL Direct All 8 versions Cite
< i> Pisum sativum contains a factor with strong homology to eIF5B
S Rasheedi, S Ghosh, M Suragani, N Tuteja… – Gene, 2007 – Elsevier
… Multiple sequence alignments and phylogenetic tree analysis were performed by CLUSTALW version1.74 (Thompson et al., 1994) and Genchek™ sequence analysis software package (Ocimum Biosolutions, India). Hydrophilicity …Cited by 2 Related articles All 6 versions Cite
Shared and species-specific features among ichnovirus genomes
K Tanaka, R Lapointe, WE Barney, AM Makkay… – Virology, 2007 – Elsevier
… The DNA sequences were first edited to remove vector sequences and then assembled using either SeqMan II (Lasergene DNAStar) or Genchek v. 2061 (OcimumBiosolutions). Contigs were built with a minimum of 50 nt overlap …Cited by 36 Related articles All 4 versions Cite
Automatic design of microarray probes for mutations detection
PRSG Almeida – 2007 – ria.ua.pt… 26 3.3. Genchek ….. 26 3.4. … 27 Figure 3.2- OligoWiz software. …. 28 Figure 3.3 –
Genchek software….. 28 Figure 3.4 – OligoDesign software. …Related articles All 2 versions
Analysis of expression data: an overview
A Grewal, P Lambert, J Stockton – Current protocols in human …, 2007 – Wiley Online Library
… X. DecisionSite for Microarray Analysis (Spotfire). X. X. Expressionist (GeneData). X. X. X.
GeneSpring (Agilent Technologies). X. X. Genowiz (Ocimum Biosolutions). X. X. RMAExpress 0.4.1 (Bolstad, 2006). X. S+ArrayAnalyzer (Insightful). X. X. X. X. TeraGenomics (IMC). X. X … Cited by 24 Related articles All 7 versions
J Kirby, PR Heath, PJ Shaw, FC Hamdy – Advances in clinical chemistry, 2007 – Elsevier
Skip to main content …
[PDF] Data Integration and Analysis: P. falciparum Microarray Data as a Case Study
R Rao, A Sivakumar, G Rao – bioinformatics.cs.vt.edu
… 6.ACKNOWLEDGMENTS We would like to thank Dr. Sandhya Kiran, Mr. JP Mehta and Ms. Madhuri for critical comments. We would also like to thank Ocimum Biosolutions Ltd. for their technical support and the Genowiz team for their encouragement. Page 5 … Related articles All 3 versions
23 Visualization of Protein Microarray Data
K Clancy – Functional Protein Microarrays in Drug Discovery, 2007 – books.google.com
… s Page 442. # GeneX Genowiz Longhorn Array Database LIMaS (Laboratory Information … net Ocimum Biosolutions Section of Molecular Genetics and Microbiology, Institute for Cellular and Molecular Biology, University of Texas at Austin Mammalian Genetics Unit, Harwell UK …Related articles
CJ Martyniuk, ER Gerrie, JT Popesku, M Ekker… – Aquatic toxicology, 2007 – Elsevier
… 2.4. Microarray analysis and gene categorization. Raw intensity data were analyzed using GenoWiz™. To normalize the microarray data, we log 2 transformed raw expression data and used the double channel normalization function in Genowiz. …Cited by 40 – Related articles – All 9 versions
[HTML] Software-MIAME-FGED
N Abeygunawardena – 2007 – mged.org
… included! If you’d like to be informed of new developments as they occur, please join the maxd_announce mailing list.”; Genowiz™ – A comprehensive multi platform package for tracking and analyzing Gene Expressions data. …Cached
[CITATION] 23 Visualization of Protein Microarray Data
K Clancy – Functional protein microarrays in drug discovery, 2007 – CRC
J Kirby, PR Heath, PJ Shaw… – Advances in clinical chemistry, 2007 – Elsevier
… Gene Sight, BioDiscovery. Expressionist, Gene Data. Chip Inspector, Genomatix. Teragenomic,IMC. JMP microarray, SAS. Genowiz, Ocimum Biosolutions. Genomics Suite, Partek. Resolver,Rosetta. Decision Site, Spotfire. Avadis, Strand Genomics. Freeware. …Cited by 15 – Related articles – BL Direct – All 5 versions
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Analysis of expression data: an overview
A Grewal, P Lambert, J Stockton – Current protocols in human …, 2007 – Wiley Online Library
… X. DecisionSite for Microarray Analysis (Spotfire). X. X. Expressionist (GeneData). X. X. X. GeneSpring (Agilent Technologies). X. X. Genowiz (Ocimum Biosolutions). X. X. RMAExpress 0.4.1 (Bolstad, 2006). X. S+ArrayAnalyzer (Insightful). X. X. X. X. TeraGenomics (IMC). X. X … Cited by 24 Related articles All 7 versions
Genomic and morphological features of a banchine polydnavirus: comparison with bracoviruses and ichnoviruses
R Lapointe, K Tanaka, WE Barney, JB Whitfield… – Journal of …, 2007 – Am Soc Microbiol
… The DNA sequences were first edited to remove vector sequences and then assembled
using either SeqMan II (Lasergene DNAStar) or Genchek v. 2061 (Ocimum Biosolutions). …
J Kirby, PR Heath, PJ Shaw, FC Hamdy – Advances in clinical chemistry, 2007 – Elsevier
Skip to main content …Cited by 31 Related articles All 6 versions
[PDF] Data Integration and Analysis: P. falciparum Microarray Data as a Case Study
R Rao, A Sivakumar, G Rao – bioinformatics.cs.vt.edu
… 6.ACKNOWLEDGMENTS We would like to thank Dr. Sandhya Kiran, Mr. JP Mehta and Ms. Madhuri for critical comments. We would also like to thank Ocimum Biosolutions Ltd. for their technical support and the Genowiz team for their encouragement. Page 5 … Related articles All 3 versions
23 Visualization of Protein Microarray Data
K Clancy – Functional Protein Microarrays in Drug Discovery, 2007 – books.google.com
… s Page 442. # GeneX Genowiz Longhorn Array Database LIMaS (Laboratory Information … Ocimum Biosolutions Section of Molecular Genetics and Microbiology, Institute for Cellular andMolecular Biology, University of Texas at Austin Mammalian Genetics Unit, Harwell UK …
[PDF] DATA INTEGRATION AND ANALYSIS: P. FALCIPARUM MICROARRAY DATA AS A CASE STUDY
R Rao, A Sivakumar… – bioinformatics.cs.vt.edu
… In this paper, we explore further insights into published P. falciparum microarray data using the application Genowiz™. … The genes involved in various steps of the pathway have been traced to their various clusters generated by using Genowiz™ SOM. …Related articles – View as HTML – All 3 versions
E McLucas, H Gallagher, Y Rochev… – … Research Part A, 2006 – Wiley Online Library
… analysis. Genowiz software and MAVI software (Ocimum Biosolutions) were then used to generate fold increases or decreases induced by the two different drug concentrations relative to the values generated for the polymer alone. …Cited by 3 – Related articles – BL Direct – All 6 versions
Data Mining in Gene Expression Data Analysis: A Survey
J Han… – Processing and managing complex data for …, 2006 – books.google.com
Page 392. Data Mining in Gene Expression Data Analysis: A Survey 375 Chapter XII Data Mining in Gene Expression Data Analysis: A Survey Jilin Han, University of Oklahoma, USA Le Gruenwald, University of Oklahoma, USA …Related articles
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2005
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Growth of Indian biotech companies, in the context of the international biotechnology industry
U Palnitkar – Journal of commercial biotechnology, 2005 – ingentaconnect.com
… Ocimum Biosolutions Labronica Inc., USA Global marketing of Biotracker-LIMS United Bioinformatics Inc., Canada Marketing rights for Gencheck and Biotracker Hospital for JointDiseases Orthopaedic Institute (HJD), New York Research into musculoskeletal disease using …Cited by 5 Related articles All 7 versions Cite
SE Ouakfaoui, B Miki – The Plant Journal, 2005 – Wiley Online Library Skip to Main Content …
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[PDF] Suppression mechanism of the calcium sensitivity in Saccharomyces cerevisiae ptp2Dmsg5D double disruptant involves a novel HOG-independent function of …
The microarray data were analyzed for distinctive expression using Genowiz 4.0
(Ocimum Biosolutions, India). Replicated gene values were …
Decreased defense gene expression in tolerance versus resistance to Verticillium dahliae in potato
(Ocimum Biosolutions, Gaithersburg, MD, USA). … Gene ontology (GO) annotations for the two
groups of filtered genes were analyzed by the Genowiz software package. …
Suppression mechanism of the calcium sensitivity in< i> Saccharomyces cerevisiae ptp2Δmsg5Δ</i> double disruptant involves a novel HOG-independent function of …
The microarray data were analyzed for distinctive expression using Genowiz 4.0
(Ocimum Biosolutions, India). Replicated gene values were …
[CITATION] Multi-level functional redundancy mechanisms of Saccharomyces cerevisiae in response to high extracellular calcium stress
analysis 50 3.2.4 Gene enrichment analysis using Genowiz 50 3.2.5 Determination of mRNA
level using quantitative PCR 51 3.3 Results 55 Page 6. 6 Subject Page …
Lowered expression levels of a tumor suppressor gene—Caveolin-1 within dysregulated gene networks of Fanconi anemia
carried out using Genowiz software (Ocimum Biosolutions, USA) and Gene Spring GX
10 (Agilent Technologies, USA). 2.5. Gene ontology analysis. …
The role of aldehyde/alcohol dehydrogenase (AdhE) in ethanol production from glycerol by Klebsiella pneumoniae
performed using Genowiz 4.0 (Ocimum Biosolutions, Hyderabad, India). Global lowess
was used for data analysis with normalization. The cut-offs …
Transcriptome analysis of salt-stressed< i> Deinococcus radiodurans</i> and characterization of salt-sensitive mutants
Pro 6.0 software (Molecular Devices). All of the calculations and normalizations were
performed using the Genowiz 4.0 software. The intensity …
Identification of novel target genes involved in Indian Fanconi anemia patients using microarray
analysis was carried out using Genowiz TM software (Ocimum Biosolutions, USA).
2.4. Functional clustering and gene ontology analysis. The …
A nutrigenomic framework to identify time-resolving responses of hepatic genes in diet-induced obese mice
Self-Organizing Map (SOM) algorithm (Quackenbush, 2001) was applied. We used Genowiz
(Ocimum Biosolutions, India) with the SOM tool to arrange all data samples. …
Escherichia coli YmdB regulates biofilm formation independently of its role as an RNase III modulator
Genowiz 4.0 TM (Ocimum Biosolutions). Global lowess (Locally weighted scatter
plot smoothing) method was used for data normalization. The cut …
Comparative analysis of Papaver somniferum genotypes having contrasting latex and alkaloid profiles
different photomultiplier (PMT) gains (40, 50, 60) and the data was analyzed using
Genowiz software (Ocimum Biosolutions, Hyderabad, India). …
Role of Pilus Proteins in Adherence and Invasion of Streptococcus agalactiae to the Lung and Cervical Epithelial Cells
gains, and the images were analyzed using Genowiz software (Ocimum Biosolutions). Analysis
was performed to detect differentially expressed genes among the groups. …
[HTML] Differentially Expressed Genes during Contrasting Growth Stages of Artemisia annua for Artemisinin Content
at three different PMT gains (40, 50 and 60) and the data was analyzed using Genowiz
software (Ocimum Biosolutions, Hyderabad). Image analysis …
PLANTS HAVING STRESS RELATED TRAITS AND METHODS FOR MAKING THE SAME
(OminiGird, GeneMachine). Genes that were differentially expressed under drought condition
with confidence of P<0.05 were selected using Genowiz program. …
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2012
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N-acetyl cysteine suppresses the foam cell formation that is induced by oxidized low density lipoprotein via regulation of gene expression
using intensity-dependent global normalization (LOW- ESS). To categorize the functional
annotation of genes, the database of Gene OntologyTM Consortium was applied. …
Gene expression profile of early in vitro biofilms of Streptococcus pneumoniae
Genowiz 4.0 (Ocimum Biosolutions, Hyderabad, India). Global Lowess was used
for data analysis with normalization. The benchmarks for up …
Functionally redundant protein phosphatase genes< i> PTP2</i> and< i> MSG5</i> co-regulate the calcium signaling pathway in< i> Saccharomyces cerevisiae</i> …
supplementing the YPDA medium with 0.3 M CaCl 2 . Four independent DNA
microarray data were analyzed using Genowiz (Ocimum Biosolutions). …
[PDF] Differential Gene Expression Profile in Essential Hypertension
428, Imagene and Genowiz softwares by Ocimum Biosolutions (India) and subjected
to arsinh transformation 2398 genes were upregulated and …
Gene expression profiling through microarray analysis in Arabidopsis thaliana colonized by Pseudomonas putida MTCC5279, a plant growth promoting …
a gene expression analysis and tracking tool that enables to determine biological significance
of differentially expressed genes and facilitates expression pattern analysis and …
[PDF] The effect of secretory factors of adipose-derived stem cells on human keratinocytes
analyzed by Genowiz 4.0 TM as described in Materials and Methods. The median
streptavidin–Cy3 fluorescence from all microsphere subsets was exported. …
[PDF] Non structural protein of avian influenza A (H11N1) virus is a weaker suppressor of immune responses but capable of inducing apoptosis in host cells
Biosolutions, Hydera- bad, India). Data analysis was performed as described earlier [23].
In order to detect highly expressed genes, fold change analysis was done. …
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2011
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METHODS AND SYSTEMS FOR ANALYSIS OF DYNAMIC BIOLOGICAL PATHWAYS
http://www.genotypictech.com/genowizard.html as available via the internet and printed on Nov.
2, 2003. Glover, D., “DNA Cloning: A Practical Approach,” vol. I, 1985. …
TRANSCRIPTOMIC ANALYSIS OF HAEMATOCOCCUS LACUSTRIS DURING ASTAXANTHIN ACCUMULATION UNDER HIGH IRRADIANCE AND NUTRIENT STARVATION
India). Global LOWESS was used for data analysis with normalization. The benchmarks for up-
regulated and down-regulated genes in hybridization were 2.0 and 0.5-fold, respectively. …
Software and Tools for Microarray Data Analysis
compatible to different data formats and have large number of features for various analysis. …
4.1. Genespring 4.2. Partek 4.3. Genowiz 4.4. GenomatixSuite Fig. …
The application of microarray technology to the identification of Tc1-like element sequences in fish genomes
probe mean, followed by log 2 -transformation) using Genowiz 4.0 software (Ocimum Biosolutions),
the probe intensity data was analysed using R (http://www.R-project.org; R …
Differentially expressed genes in sensitive and tolerant rice varieties in response to salt-stress
of TIGR predicted genes. The array data were analyzed using GeneChip Operating Software
(GCOS 1.2) and Genowiz software (Ocimum Biosolutions, India). …
[PDF] Differential Gene Expression Profile in Essential Hypertension
428, Imagene and Genowiz softwares by Ocimum Biosolutions (India) and subjected
to arsinh transformation 2398 genes were upregulated and …
[PDF] Gene Expression Analysis for Type-2 Diabetes Mellitus–A Case Study on Healthy vs Diabetes with Parental History
Ocimum Biosolutions, Hyderabad, India for analysis of the microarray data using their
proprietary microarray analysis tool Genowiz. REFERENCES [1 …
[HTML] A review on worldwide essential software resources in pharmacy
It is a powerful gene expression analysis program that has been designed to store,
process and visualize gene expression data efficiently. …
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TRANSCRIPTIONAL CHANGES ASSOCIATED WITH ETHANOL TOLERANCE IN SACCHAROMYCES CEREVISIAE
analysed using Genowiz™ 4.0.2.1 software (Ocimum Biosolutions). … 2001) smoothing parameter
of 0.1 and a polynomial degree of 1 and 2 robust interactions (Genowiz™). …
Differential Gene Expression Analysis for Diabetes with and without parental history
ACKNOWLEDGMENT The Authors Acknowledges Ocimum Biosolutions, Hyderabad, India. For
analysis of the microarray data using their proprietary microarray analysis tool Genowiz. …
Immunomodulatory cytokines determine the outcome of Japanese encephalitis virus infection in mice
into MS EXCEL. Data Analysis Data were analyzed using Genowiz Microarray and
Pathway analysis tool (Ocimum Biosolutions, Hyperabad, India). …
RETROTRANSPOSON EXPRESSION IN ETHANOL-STRESSED SACCHAROMYCES CEREVISIAE
scanner and analysed using Genowiz™ 4.0.2.1 software (Ocimum Biosolutions). … 2002) until the
analysis was repeated using Genowiz™ or MAPPFinder (designed by Doniger et al. …
[PDF] HOST GENE EXPRESSION PROFILING IN INFLUENZA A VIRUS-INFECTED LUNG EPITHELIAL (A549) CELLS: A COMPARATIVE ANALYSIS BETWEEN HIGHLY PATHOGENIC AND MODIFIED H5N1 …
tool (Ocimum Biosolutions, Hyderabad, India). … Cluster analysis of the differentially
expressed genes was carried out using GENOWIZ software. …
Array platforms and bioinformatics tools for the analysis of plant transcriptome in response to abiotic stress
Integrated gene expression tool Genowiz (C) http://www .ocimumbio.com/ Integrated gene
expression tool Genespring GX (C) http://www .chem.agilent.com/en-US/products/software/ …
Virtual Laboratory and Its Application in Genomics
high-level analysis, using sophisticated software (eg, R Bioconductor, Multi, Experiment Viewer,
Gene Spring, Genowiz). Result reports are saved as text or graphic files (eg, pdf, jpg). …
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STATISTICAL ANALYSIS IDENTIFIES GENES IN PROSTATE CANCER
it was analysed to identify the genes that are differently expressed in tumour samples in
comparison to the normal samples from tissues and cell lines using the tool Genowiz™ 3.1. …
Application of Data Mining Algorithms in Pharmaceutical Research and Development
expression data Genowiz ™ http://www.ocimumbio.com/ web/default.asp A comprehensive
multiplatform package for tracking and analyzing Gene Expressions data …
[PDF] PANDEMIC (H1N1) 2009 INFLUENZA VIRUS INDUCES WEAKER HOST IMMUNE RESPONSES IN VITRO: A POSSIBLE MECHANISM OF HIGH TRANSMISSIBILITY
[15]. Data Analysis Microarray data analysis was carried out with GENO– WIZ Microarray data
and pathway analysis tool (Oci- mum Biosolutions, Hyderabad, India). …
A Systematic Approach to Understanding Bacterial Responses to Oxygen Using Taverna and Webservices
pathways, functional categories and gene ontologies. Many …
Global upregulation of gene expression associated with renal dysfunction in DOCA–salt-induced hypertensive rats occurs via signaling cascades involving epidermal …
softwares by Ocimum Biosolutions (India) and subjected to arsinh transformation
as described by Huber et al. (2002). The Benjamini and …
[PDF] New approach to Genomics Experiments Taking Advantage of Virtual Laboratory System
high-level analysis, using sophisticated software (eg R Bioconductor, Multi Experiment Viewer,
Gene Spring, Genowiz). Result reports are saved as text or graphic files (eg pdf, jpg). …
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2008
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[HTML] SERIAL CHANGES IN EXPRESSION OF FUNCTIONALLY CLUSTERED GENES IN PROGRESSION OF LIVER FIBROSIS IN HEPATITIS C PATIENTS
Genowiz™ software (Ocimum Biosolutions). … All genes in Figure Figure11 were
subjected to hierarchical clustering analysis using Genowiz™. …
Differential gene expression analysis of a known hepatotoxin, N-acetyl-p-amino-phenol (APAP) as compared to its non-toxic analog, N-acetyl-m-amino-phenol (AMAP …
in different groups. Furthermore, gene annota- tion and pathway analysis was carried
out using Genowiz software. RESULTS AND DISCUSSION …
[HTML] Nonvirally modified autologous primary hepatocytes correct diabetes and prevent target organ injury in a large preclinical model
(GraphPad Software Inc., USA). Cluster analysis of GeneChip® data was performed using
algorithms in Genowiz (Ocimum Biosolutions Ltd., India). P<0.05 was considered significant. …
[PDF] Microarray Data Analysis Tool (MAT)
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2007
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MICROARRAY ANALYSIS IN THE ZEBRAFISH (DANIO RERIO) LIVER AND TELENCEPHALON AFTER EXPOSURE TO LOW CONCENTRATION OF 17ALPHA-ETHINYLESTRADIOL
GenoWiz™. To normalize the microarray data, we log 2 transformed raw expression data
and used the double channel normalization function in Genowiz. …
Analysis of expression data: an overview
Biosolutions) X X RMAExpress 0.4.1 (Bolstad, 2006) X … X X X X GeneSpring (Agilent Technologies)
X X X X Genowiz (Ocimum Biosolutions) X X X X J-Express Pro (Molmine) X X X X …
[HTML] Software-MIAME-FGED
join the maxd_announce mailing list.”; Genowiz™ – A comprehensive multi platform
package for tracking and analyzing Gene Expressions data. …
[CITATION] 23 Visualization of Protein Microarray Data
Gene expression assays
IMC. JMP microarray, SAS. Genowiz, Ocimum Biosolutions. Genomics Suite, Partek. Resolver,
Rosetta. Decision Site, Spotfire. Avadis, Strand Genomics. Freeware. …
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2006
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[PDF] DATA INTEGRATION AND ANALYSIS: P. FALCIPARUM MICROARRAY DATA AS A CASE STUDY
the application Genowiz™. … The genes involved in various steps of the pathway have been
traced to their various clusters generated by using Genowiz™ SOM. …
Global gene expression analysis of the effects of vinblastine on endothelial cells, when eluted from a thermo‐responsive polymer
to generate fold increases or decreases induced by the two different drug concentrations
relative to the values generated for the polymer alone. …
Data Mining in Gene Expression Data Analysis: A Survey
XII Data Mining in Gene Expression Data Analysis: A Survey Jilin Han, University
of Oklahoma, USA Le Gruenwald, University of Oklahoma, USA …
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2005
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[CITATION] Abstract| Full Text (PDF, 2,027 KB) Title: Industry Watch
collaboration of this type with a leading Australian drug development company such as
Cytopia. Our company was founded with the vision to aid in the further development of the …
The stability of the Arabidopsis transcriptome in transgenic plants expressing the marker genes nptII and uidA
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2002
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[PDF] CORRELATIONS BETWEEN VARIABLE BROILER PERFORMANCE AND GENE EXPRESSION AND MICROFLORA IN THE GUT RJ MOORE, D. STANLEY, …2002
4.0. 5.3 (Ocimum Biosolutions … and poor FCR groups. Gene ontology and pathway
analysis was also performed in Genowiz. c) Microbial profiling …
Janampatri to Genomepatri - Anu Acharya 
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