The Experts below are selected from a list of 273 Experts worldwide ranked by ideXlab platform
Jennifer Clarke - One of the best experts on this subject based on the ideXlab platform.
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Characteristics of Cross-Hybridization and Cross-alignment of expression in pseudo-xenograft samples by RNA-Seq and microarrays
Journal of clinical bioinformatics, 2013Co-Authors: Camilo Valdes, Pearl H. Seo, Nicholas F. Tsinoremas, Jennifer ClarkeAbstract:Background Exploring stromal changes associated with tumor growth and development is a growing area of oncologic research. In order to study molecular changes in the stroma it is recommended to separate tumor tissue from stromal tissue. This is relevant to xenograft models where tumors can be small and difficult to separate from host tissue. We introduce a novel definition of Cross-alignment/Cross-Hybridization to compare qualitatively the ability of high-throughput mRNA sequencing, RNA-Seq, and microarrays to detect tumor and stromal expression from mixed ‘pseudo-xenograft’ samples vis-a-vis genes and pathways in Cross-alignment (RNA-Seq) and Cross-Hybridization (microarrays). Samples consisted of normal mouse lung and human breast cancer cells; these were combined in fixed proportions to create a titration series of 25% steps. Our definition identifies genes in a given species (human or mouse) with undetectable expression in same-species RNA but detectable expression in Cross-species RNA. We demonstrate the comparative value of this method and discuss its potential contribution in cancer research.
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Abstract 2994: Characteristics of Cross-Hybridization/Cross-alignment of expression in xenograft samples by RNAseq and microarrays
Molecular and Cellular Biology, 2012Co-Authors: Camilo Valdes, Pearl H. Seo, Jennifer ClarkeAbstract:Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL Stromal changes have been the focus of numerous research publications and have led to insights in both tumor development and promising new avenues for treatment. In order to study molecular changes in stroma from tissue samples it is recommended to separate tumor tissue from stromal tissue. One such context is mouse tumor xenograft models where tumors, particularly metastatic tumors, can be small and difficult to separate from the host tissue. In our research we compared qualitatively the ability of RNA-seq and microarray data to detect tumor (human) and stromal (mouse) expression from mixed samples in terms of Cross-alignment and Cross-Hybridization. Samples were analyzed using HumanWG-6\_V3\_0\_R1 and MouseWG-6\_V2\_0\_R0 Expression BeadChips and the GenomeAnalyzer IIe (Illumina, Inc.). Samples consisted of total RNA from normal mouse lung from NOD/SCID gamma mice and total RNA from MDA-MB-231 breast cancer cells combined in fixed proportions in triplicate. We define a gene which Cross-hybridizes from mouse to human as one which exists in the set defined by (B U C U D) - A, where A, B, C, and D are defined as follows. A is the set of all genes detected when pure mouse RNA was hybridized onto mouse chips (or aligned to the mouse genome); B is the set of all genes detected when 25% human/75% mouse RNA was hybridized onto mouse chips (or aligned to the mouse genome); C is the set of all genes detected when 50% human/50% mouse RNA was hybridized onto mouse chips (or aligned to the mouse genome); D is the set of all genes detected when 75% human/25% mouse RNA was hybridized onto mouse chips (or aligned to the mouse genome). A gene that Cross-hybridizes from human to mouse is defined analogously. Our results show that observed levels of Cross-Hybridization are quite low (5.32% of human probes detected in mouse, 3.48% of mouse probes detected in human). The observed levels of Cross-alignment are practically comparable to the levels of Cross-Hybridization (6.50% of human genes detected in mouse, 2.27% of mouse genes detected in human). However, there are genes and pathways of considerable interest to oncology researchers which show significant Cross-Hybridization/Cross-alignment and, as such, their presence/absence or level of expression in tumor tissue versus stromal tissue cannot be determined using the platforms from this study. Cross-hybridizing/Cross-aligning genes in our studies include PDGF, b-Raf, Beta-catenin, erbB2, NF-kB, MDM2, Claudin, VEGF-R, Notch2, Cyclin B, HSP90 and Ubiquitin. Biological pathways significantly enriched for genes which show Cross-Hybridization/Cross-alignment include TGF-mediated regulation of cell proliferation, TGF/WNT and cytoskeletal remodeling, regulation of EMT, hedgehod signaling, and the FGFR signaling pathway. Which platform to use with mixed tissues from xenografts - microarrays or NGS - appears to be primarily a question of cost and specific genes of interest. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2994. doi:1538-7445.AM2012-2994
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abstract 2994 characteristics of Cross Hybridization Cross alignment of expression in xenograft samples by rnaseq and microarrays
Cancer Research, 2012Co-Authors: Camilo Valdes, Pearl Seo, Jennifer ClarkeAbstract:Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL Stromal changes have been the focus of numerous research publications and have led to insights in both tumor development and promising new avenues for treatment. In order to study molecular changes in stroma from tissue samples it is recommended to separate tumor tissue from stromal tissue. One such context is mouse tumor xenograft models where tumors, particularly metastatic tumors, can be small and difficult to separate from the host tissue. In our research we compared qualitatively the ability of RNA-seq and microarray data to detect tumor (human) and stromal (mouse) expression from mixed samples in terms of Cross-alignment and Cross-Hybridization. Samples were analyzed using HumanWG-6\_V3\_0\_R1 and MouseWG-6\_V2\_0\_R0 Expression BeadChips and the GenomeAnalyzer IIe (Illumina, Inc.). Samples consisted of total RNA from normal mouse lung from NOD/SCID gamma mice and total RNA from MDA-MB-231 breast cancer cells combined in fixed proportions in triplicate. We define a gene which Cross-hybridizes from mouse to human as one which exists in the set defined by (B U C U D) - A, where A, B, C, and D are defined as follows. A is the set of all genes detected when pure mouse RNA was hybridized onto mouse chips (or aligned to the mouse genome); B is the set of all genes detected when 25% human/75% mouse RNA was hybridized onto mouse chips (or aligned to the mouse genome); C is the set of all genes detected when 50% human/50% mouse RNA was hybridized onto mouse chips (or aligned to the mouse genome); D is the set of all genes detected when 75% human/25% mouse RNA was hybridized onto mouse chips (or aligned to the mouse genome). A gene that Cross-hybridizes from human to mouse is defined analogously. Our results show that observed levels of Cross-Hybridization are quite low (5.32% of human probes detected in mouse, 3.48% of mouse probes detected in human). The observed levels of Cross-alignment are practically comparable to the levels of Cross-Hybridization (6.50% of human genes detected in mouse, 2.27% of mouse genes detected in human). However, there are genes and pathways of considerable interest to oncology researchers which show significant Cross-Hybridization/Cross-alignment and, as such, their presence/absence or level of expression in tumor tissue versus stromal tissue cannot be determined using the platforms from this study. Cross-hybridizing/Cross-aligning genes in our studies include PDGF, b-Raf, Beta-catenin, erbB2, NF-kB, MDM2, Claudin, VEGF-R, Notch2, Cyclin B, HSP90 and Ubiquitin. Biological pathways significantly enriched for genes which show Cross-Hybridization/Cross-alignment include TGF-mediated regulation of cell proliferation, TGF/WNT and cytoskeletal remodeling, regulation of EMT, hedgehod signaling, and the FGFR signaling pathway. Which platform to use with mixed tissues from xenografts - microarrays or NGS - appears to be primarily a question of cost and specific genes of interest. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2994. doi:1538-7445.AM2012-2994
Camilo Valdes - One of the best experts on this subject based on the ideXlab platform.
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Characteristics of Cross-Hybridization and Cross-alignment of expression in pseudo-xenograft samples by RNA-Seq and microarrays
Journal of clinical bioinformatics, 2013Co-Authors: Camilo Valdes, Pearl H. Seo, Nicholas F. Tsinoremas, Jennifer ClarkeAbstract:Background Exploring stromal changes associated with tumor growth and development is a growing area of oncologic research. In order to study molecular changes in the stroma it is recommended to separate tumor tissue from stromal tissue. This is relevant to xenograft models where tumors can be small and difficult to separate from host tissue. We introduce a novel definition of Cross-alignment/Cross-Hybridization to compare qualitatively the ability of high-throughput mRNA sequencing, RNA-Seq, and microarrays to detect tumor and stromal expression from mixed ‘pseudo-xenograft’ samples vis-a-vis genes and pathways in Cross-alignment (RNA-Seq) and Cross-Hybridization (microarrays). Samples consisted of normal mouse lung and human breast cancer cells; these were combined in fixed proportions to create a titration series of 25% steps. Our definition identifies genes in a given species (human or mouse) with undetectable expression in same-species RNA but detectable expression in Cross-species RNA. We demonstrate the comparative value of this method and discuss its potential contribution in cancer research.
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Abstract 2994: Characteristics of Cross-Hybridization/Cross-alignment of expression in xenograft samples by RNAseq and microarrays
Molecular and Cellular Biology, 2012Co-Authors: Camilo Valdes, Pearl H. Seo, Jennifer ClarkeAbstract:Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL Stromal changes have been the focus of numerous research publications and have led to insights in both tumor development and promising new avenues for treatment. In order to study molecular changes in stroma from tissue samples it is recommended to separate tumor tissue from stromal tissue. One such context is mouse tumor xenograft models where tumors, particularly metastatic tumors, can be small and difficult to separate from the host tissue. In our research we compared qualitatively the ability of RNA-seq and microarray data to detect tumor (human) and stromal (mouse) expression from mixed samples in terms of Cross-alignment and Cross-Hybridization. Samples were analyzed using HumanWG-6\_V3\_0\_R1 and MouseWG-6\_V2\_0\_R0 Expression BeadChips and the GenomeAnalyzer IIe (Illumina, Inc.). Samples consisted of total RNA from normal mouse lung from NOD/SCID gamma mice and total RNA from MDA-MB-231 breast cancer cells combined in fixed proportions in triplicate. We define a gene which Cross-hybridizes from mouse to human as one which exists in the set defined by (B U C U D) - A, where A, B, C, and D are defined as follows. A is the set of all genes detected when pure mouse RNA was hybridized onto mouse chips (or aligned to the mouse genome); B is the set of all genes detected when 25% human/75% mouse RNA was hybridized onto mouse chips (or aligned to the mouse genome); C is the set of all genes detected when 50% human/50% mouse RNA was hybridized onto mouse chips (or aligned to the mouse genome); D is the set of all genes detected when 75% human/25% mouse RNA was hybridized onto mouse chips (or aligned to the mouse genome). A gene that Cross-hybridizes from human to mouse is defined analogously. Our results show that observed levels of Cross-Hybridization are quite low (5.32% of human probes detected in mouse, 3.48% of mouse probes detected in human). The observed levels of Cross-alignment are practically comparable to the levels of Cross-Hybridization (6.50% of human genes detected in mouse, 2.27% of mouse genes detected in human). However, there are genes and pathways of considerable interest to oncology researchers which show significant Cross-Hybridization/Cross-alignment and, as such, their presence/absence or level of expression in tumor tissue versus stromal tissue cannot be determined using the platforms from this study. Cross-hybridizing/Cross-aligning genes in our studies include PDGF, b-Raf, Beta-catenin, erbB2, NF-kB, MDM2, Claudin, VEGF-R, Notch2, Cyclin B, HSP90 and Ubiquitin. Biological pathways significantly enriched for genes which show Cross-Hybridization/Cross-alignment include TGF-mediated regulation of cell proliferation, TGF/WNT and cytoskeletal remodeling, regulation of EMT, hedgehod signaling, and the FGFR signaling pathway. Which platform to use with mixed tissues from xenografts - microarrays or NGS - appears to be primarily a question of cost and specific genes of interest. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2994. doi:1538-7445.AM2012-2994
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abstract 2994 characteristics of Cross Hybridization Cross alignment of expression in xenograft samples by rnaseq and microarrays
Cancer Research, 2012Co-Authors: Camilo Valdes, Pearl Seo, Jennifer ClarkeAbstract:Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL Stromal changes have been the focus of numerous research publications and have led to insights in both tumor development and promising new avenues for treatment. In order to study molecular changes in stroma from tissue samples it is recommended to separate tumor tissue from stromal tissue. One such context is mouse tumor xenograft models where tumors, particularly metastatic tumors, can be small and difficult to separate from the host tissue. In our research we compared qualitatively the ability of RNA-seq and microarray data to detect tumor (human) and stromal (mouse) expression from mixed samples in terms of Cross-alignment and Cross-Hybridization. Samples were analyzed using HumanWG-6\_V3\_0\_R1 and MouseWG-6\_V2\_0\_R0 Expression BeadChips and the GenomeAnalyzer IIe (Illumina, Inc.). Samples consisted of total RNA from normal mouse lung from NOD/SCID gamma mice and total RNA from MDA-MB-231 breast cancer cells combined in fixed proportions in triplicate. We define a gene which Cross-hybridizes from mouse to human as one which exists in the set defined by (B U C U D) - A, where A, B, C, and D are defined as follows. A is the set of all genes detected when pure mouse RNA was hybridized onto mouse chips (or aligned to the mouse genome); B is the set of all genes detected when 25% human/75% mouse RNA was hybridized onto mouse chips (or aligned to the mouse genome); C is the set of all genes detected when 50% human/50% mouse RNA was hybridized onto mouse chips (or aligned to the mouse genome); D is the set of all genes detected when 75% human/25% mouse RNA was hybridized onto mouse chips (or aligned to the mouse genome). A gene that Cross-hybridizes from human to mouse is defined analogously. Our results show that observed levels of Cross-Hybridization are quite low (5.32% of human probes detected in mouse, 3.48% of mouse probes detected in human). The observed levels of Cross-alignment are practically comparable to the levels of Cross-Hybridization (6.50% of human genes detected in mouse, 2.27% of mouse genes detected in human). However, there are genes and pathways of considerable interest to oncology researchers which show significant Cross-Hybridization/Cross-alignment and, as such, their presence/absence or level of expression in tumor tissue versus stromal tissue cannot be determined using the platforms from this study. Cross-hybridizing/Cross-aligning genes in our studies include PDGF, b-Raf, Beta-catenin, erbB2, NF-kB, MDM2, Claudin, VEGF-R, Notch2, Cyclin B, HSP90 and Ubiquitin. Biological pathways significantly enriched for genes which show Cross-Hybridization/Cross-alignment include TGF-mediated regulation of cell proliferation, TGF/WNT and cytoskeletal remodeling, regulation of EMT, hedgehod signaling, and the FGFR signaling pathway. Which platform to use with mixed tissues from xenografts - microarrays or NGS - appears to be primarily a question of cost and specific genes of interest. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2994. doi:1538-7445.AM2012-2994
Jonas S. Almeida - One of the best experts on this subject based on the ideXlab platform.
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A multivariate prediction model for microarray Cross-Hybridization
BMC bioinformatics, 2006Co-Authors: Yian Ann Chen, Cheng-chung Chou, Elizabeth H. Slate, Konan Peck, Eberhard O. Voit, Jonas S. AlmeidaAbstract:Background Expression microarray analysis is one of the most popular molecular diagnostic techniques in the post-genomic era. However, this technique faces the fundamental problem of potential Cross-Hybridization. This is a pervasive problem for both oligonucleotide and cDNA microarrays; it is considered particularly problematic for the latter. No comprehensive multivariate predictive modeling has been performed to understand how multiple variables contribute to (Cross-) Hybridization.
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Optimal cDNA microarray design using expressed sequence tags for organisms with limited genomic information
BMC bioinformatics, 2004Co-Authors: Yian Ann Chen, David J. Mckillen, Matthew J. Jenny, R. W. Chapman, Paul S. Gross, Gregory W. Warr, Jonas S. AlmeidaAbstract:Background Expression microarrays are increasingly used to characterize environmental responses and host-parasite interactions for many different organisms. Probe selection for cDNA microarrays using expressed sequence tags (ESTs) is challenging due to high sequence redundancy and potential Cross-Hybridization between paralogous genes. In organisms with limited genomic information, like marine organisms, this challenge is even greater due to annotation uncertainty. No general tool is available for cDNA microarray probe selection for these organisms. Therefore, the goal of the design procedure described here is to select a subset of ESTs that will minimize sequence redundancy and characterize potential Cross-Hybridization while providing functionally representative probes.
A M Lysenko - One of the best experts on this subject based on the ideXlab platform.
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DNA relatedness among some thermophilic members of the genus Methanobacterium: emendation of the species Methanobacterium thermoautotrophicum and rejection of Methanobacterium thermoformicicum as a synonym of Methanobacterium thermoautotrophicum.
International Journal of Systematic and Evolutionary Microbiology, 1992Co-Authors: J.p. Touzel, J. Noelling, T. Zhilina, E. Conway De Macario, A M LysenkoAbstract:DNA reassociation was used to determine levels of relatedness among four thermophilic Methanobacterium strains that are able to use formate and between these organisms and two representative strains of Methanobacterium thermoautotrophicum, strain ▵HT (= DSM 1053T = ATCC 29096T) (T = type strain) and strain Marburg (= DSM 2133). Three homology groups were delineated, and these groups coincided with the clusters identified by antigenic fingerprinting. The first group, which had levels of Cross Hybridization that ranged from 73 to 99%, included M. thermoautotrophicum ▵HT, Methanobacterium thermoformicicum Z-245, Methanobacterium sp. strain THF, and Methanobacterium sp. strain FTF. The second and third groups were each represented by only one strain, Methanobacterium sp. strain CB-12 and M. thermoautotrophicum Marburg, respectively (Cross-Hybridization levels, 13 to 30 and 29 to 33%, respectively). Our results indicate that the name M. thermoformicicum should be rejected as it is a synonym of M. thermoautotrophicum. The taxonomic positions of strains Marburg and CB-12 need further investigation.
I. N. Popov - One of the best experts on this subject based on the ideXlab platform.
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Taxonomic Analysis of Thermophilic Strains of the Genus Methanobacterium: Reclassification of Methanobacterium thermoalcaliphilum as a Synonym of Methanobacterium thermoautotrophicum
International Journal of Systematic and Evolutionary Microbiology, 1993Co-Authors: S. V. Kotelnikova, A.ya. Obraztsova, K.-h. Blotevogel, I. N. PopovAbstract:DNA reassociation, a comparative analysis of whole-cell protein patterns, and indirect immunofluorescence methods were used to determine the taxonomic relationships of thermophilic Methanobacterium strains. On the basis of the results dendrograms showing degrees of similarity among the organisms were constructed. The organisms studied are members of three different groups. One group, whose members exhibit 10 to 40% Cross-Hybridization, includes Methanobacterium wolfeii, “Methanobacterium defluvium” ADZ, and “Methanobacterium thermoflexum” IDZ. The second group contains Methanobacterium thermophilum MT (T = type strain) and Methanobacterium thermoaggregans (levels of DNA relatedness, 30 to 45%). The third group, whose members exhibit 65 to 99% Cross-Hybridization, includes Methanobacterium thermoautotrophicum ΔHT, F-1, and DV; Methanobacterium thermoformicicum Z-245T; and Methanobacterium thermoalcaliphilum AC60T. The combination of three independent taxonomic methods showed that the group of strains studied is phenotypically, genotypically, and antigenically diverse. The most distinct organisms are M. wolfeii, M. thermoaggregans, M. thermophilum, “M. defluvium,” “M. thermoflexum,” and M. thermoautotrophicum. These species names should be adopted. The results of a DNA-DNA Hybridization study (level of Hybridization, 99%), an immunological analysis (+3 reaction), and a protein similarity study (level of similarity, 75%) indicate that M. thermoalcaliphilum should be reclassified as a synonym of M. thermoautotrophicum.