ArticleBMC genomics2005
In vitro identification and in silico utilization of interspecies sequence similarities using GeneChip technology.
Article in BMC genomics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
21 citing papers in PubMed.
- Expression Comparison of Oil Biosynthesis Genes in Oil Palm Mesocarp Tissue Using Custom Array.Microarrays (Basel, Switzerland) · 2014Article
- Understanding mechanism of in vitro maturation, fertilization and culture of sheep embryoes through in silico analysis.Bioinformation · 2012Article
- Gene expression profiles in a rabbit model of systemic lupus erythematosus autoantibody production.Journal of immunology (Baltimore, Md. : 1950) · 2010Article
- A Method to Detect Differential Gene expression in Cross-Species Hybridization Experiments at Gene and Probe Level.Biomedical informatics insights · 2010Article
- Vaccinia virus-specific molecular signature in atopic dermatitis skin.The Journal of allergy and clinical immunology · 2010Article
- Kidney ischemia-reperfusion injury induces caspase-dependent pulmonary apoptosis.American journal of physiology. Renal physiology · 2009Article
- Nuclear reprogramming in heterokaryons is rapid, extensive, and bidirectional.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2009Article
- Epidermal growth factor receptor (EGFR) regulates mechanical ventilation-induced lung injury in mice.Translational research : the journal of laboratory and clinical medicine · 2008Article
- Single-species microarrays and comparative transcriptomics.PloS one · 2008Article
- Identification of candidate genes in scleroderma-related pulmonary arterial hypertension.Translational research : the journal of laboratory and clinical medicine · 2008Article
- The local and systemic inflammatory transcriptome after acute kidney injury.Journal of the American Society of Nephrology : JASN · 2008Article
- Genetic and pharmacologic evidence links oxidative stress to ventilator-induced lung injury in mice.American journal of respiratory and critical care medicine · 2007Article
- Optimising the analysis of transcript data using high density oligonucleotide arrays and genomic DNA-based probe selection.BMC genomics · 2007Article
- Biomarker discovery in animal health and disease: the application of post-genomic technologies.Biomarker insights · 2007Article
- Cross-species analysis of gene expression in non-model mammals: reproducibility of hybridization on high density oligonucleotide microarrays.BMC genomics · 2007Article
- EGFR-activated signaling and actin remodeling regulate cyclic stretch-induced NRF2-ARE activation.American journal of respiratory cell and molecular biology · 2007Article
- Toward a universal microarray: prediction of gene expression through nearest-neighbor probe sequence identification.Nucleic acids research · 2007Article
- Detection of transcriptional difference of porcine imprinted genes using different microarray platforms.BMC genomics · 2006Article
- Cross-species hybridizations on a multi-species cDNA microarray to identify evolutionarily conserved genes expressed in oocytes.BMC genomics · 2006Article
- Derivation of species-specific hybridization-like knowledge out of cross-species hybridization results.BMC genomics · 2006Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
backgroundGenomic approaches in large animal models (canine, ovine etc) are challenging due to insufficient genomic information for these species and the lack of availability of corresponding microarray platforms. To address this problem, we speculated that conserved interspecies genetic sequences can be experimentally detected by cross-species hybridization. The Affymetrix platform probe redundancy offers flexibility in selecting individual probes with high sequence similarities between related species for gene expression analysis.
resultsGene expression profiles of 40 canine samples were generated using the human HG-U133A GeneChip (U133A). Due to interspecies genetic differences, only 14 +/- 2% of canine transcripts were detected by U133A probe sets whereas profiling of 40 human samples detected 49 +/- 6% of human transcripts. However, when these probe sets were deconstructed into individual probes and examined performance of each probe, we found that 47% of human probes were able to find their targets in canine tissues and generate a detectable hybridization signal. Therefore, we restricted gene expression analysis to these probes and observed the 60% increase in the number of identified canine transcripts. These results were validated by comparison of transcripts identified by our restricted analysis of cross-species hybridization with transcripts identified by hybridization of total lung canine mRNA to new Affymetrix Canine GeneChip.
conclusionThe experimental identification and restriction of gene expression analysis to probes with detectable hybridization signal drastically increases transcript detection of canine-human hybridization suggesting the possibility of broad utilization of cross-hybridizations of related species using GeneChip technology.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.