ISMB 2008 » Comparative Transcriptomics

This data can be used as starting point

Ellie — Mon, 18 May 2009 08:08:00 +0000

We found sperm express many genes, and that the proteins encoded by these genes encompass many different categories. We identified numerous candidate genes whose involvement in sperm cell development and fertilization can be directly tested in Arabidopsis. USA. gov. Pacific Plant Gene Expression Center Albany_CA Title Comparative Transcriptomics of Arabidopsis thaliana Sperm Cells Authors Borges, Filipe GULBENKIAN INST PORTUGAL Submitted to Plant Physiology Publication Type Peer Reviewed Journal Publication Acceptance Date 27, Publication Date 30, Publishers URL httpwww. plantphysiol.

This data can be used as starting point to discover the roles of these spermexpressed proteins. Project Team McCormick, Sheila Publications Publications Related National Programs Plant Biological and Molecular Processes 302 Plant Genetic Resources, Genomics and Genetic Improvement 301 Related Projects ELUCIDATING THE MECHANISMS THAT CONNECT ACTIVATION OF ROP GTPASES, MEMBRANE DYNAMICS AND SIGNALING IN CELL GROWTH AND STRESS RESPONSES Last Modified ARS Home.

Technical Abstract In flowering plants the two sperm cells are embedded within the cytoplasm of the growing pollen tube and as such are passively transported to the embryo sac, wherein double fertilization occurs upon their release. Interpretive Summary We purified sperm cells from Arabidopsis plants. Studies of gene expression in male gametes of maize and Plumbago, and in lily generative cells already showed that the previously held view of transcriptionally inert male gametes was not true, but genomewide studies were lacking.

Comparative analysis of the sperm cell transcriptome with those of representative sporophytic tissues and of pollen showed that sperm has distinct and diverse transcriptional profile. Comparative Transcriptomics of Arabidopsis thaliana Sperm Cells Authors Borges, Filipe GULBENKIAN INST PORTUGAL Submitted to Plant Physiology Publication Type Peer Reviewed Journal Publication Acceptance Date 27, Publication Date 30, Publishers URL httpwww. plantphysiol. org Reprint URL Citation Borges, Gomes, Gardner, Moreno, Mccormick, Feijo, J., Becker, J. Comparative Transcriptomics of Arabidopsis thaliana Sperm Cells Authors Borges, Filipe GULBENKIAN INST PORTUGAL Submitted to Plant Physiology Publication Type Peer Reviewed Journal Publication Acceptance Date 27, Publication Date 30, Publishers URL httpwww. plantphysiol.

Functional classifications of genes with enriched expression in sperm cells showed that DNA repair, ubiquitinmediated proteolysis and cell cycle progression are overrepresented Gene Ontology categories

They might also have

Ellie — Sat, 16 May 2009 23:06:49 +0000

All rights reservedToute reproduction ou diffusion mme partielle, par quelque procd ou sur tout support que ce soit, ne pourra tre faite sans laccord pralable crit de lINISTCNRS. No part of these records be reproduced of distributed, in any form or by any means, without the prior written permission of INISTCNRS. The number of mouse cDNAs identified greatly exceeds the number of genes predicted from the sequenced human and mouse genomes. Custom Search. Notably, ncRNAs are major component of the transcriptomes of higher organisms, and many senseantisense pairs have been identified.

Custom Search. All rights reservedToute reproduction ou diffusion mme partielle, par quelque procd ou sur tout support que ce soit, ne pourra tre faite sans laccord pralable crit de lINISTCNRS. No part of these records be reproduced of distributed, in any form or by any means, without the prior written permission of INISTCNRS. This is largely because of extensive alternative splicing and the presence of many noncoding RNAs ncRNAs, which are difficult to predict from genomic sequences.

The ncRNAs function in range of regulatory mechanisms for gene expression and other biological processes. This is largely because of extensive alternative splicing and the presence of many noncoding RNAs ncRNAs, which are difficult to predict from genomic sequences. Custom Search. The number of mouse cDNAs identified greatly exceeds the number of genes predicted from the sequenced human and mouse genomes. All rights reservedToute reproduction ou diffusion mme partielle, par quelque procd ou sur tout support que ce soit, ne pourra tre faite sans laccord pralable crit de lINISTCNRS.

Center for Microbial Biotechnology Email Kontaktforfatter

Ellie — Sat, 16 May 2009 03:39:18 +0000

Center for Microbial Biotechnology Email Kontaktforfatter Nielsen, Jens Cwisno 1774 Technical University of Denmark, Department of Systems Biology, Center for Microbial Biotechnology Email Kontaktforfatter Nielsen, Jens Cwisno 1774 Technical University of Denmark, Department of Systems Biology, Center for Microbial Biotechnology Email Kontaktforfatter Nielsen, Jens Cwisno 1774 Technical University of Denmark, Department of Systems Biology, Center for Microbial Biotechnology Email Kontaktforfatter Nielsen, Jens Cwisno 1774 Technical University of Denmark, Department of Systems Biology, Center for Microbial Biotechnology Email Kontaktforfatter Nielsen, Jens Cwisno 1774 Technical University of Denmark, Department of Systems Biology, Center for Microbial Biotechnology Email Kontaktforfatter

Plant Biol The tissue was

Ellie — Fri, 01 May 2009 06:44:13 +0000

For rice, some sequences used to design the chip were complete, whereas others were partial cDNAs. Puhler, Nipponbare were surfacesterilized in sodium hypochlorite solution 2 active chlorine, washed repeatedly with sterile water, and planted in autoclaved sand. 95113. pmid15129719 CrossRefMedlineISI Manthey, Krajinski, Hohnjec, Firnhaber, Puhler, Perlick, & Kerp, & Allen, & Krajinski, & Smith, 2002 Science 92100. pmid11935018 AbstractFREE Full Text Harrison, 323328. pmid15134754 CrossRefMedlineISI Salzer, Corbiere, Development of the symbiosis requires significant physiological changes of both partners 14, 16, which must result from plantfungal communication and should, in part, be mirrored by changes in transcription of particular genes.

It has to be considered, however, that, for the majority of queries, only partial sequences had been available. small fraction of the dicot sequences were already described and characterized in the literature, and complete cDNAs were available. and and citations therein. The symbiosisspecific hits included phylogenetically related homologues of the mycorrhizainduced highaffinity phosphate transporter from Medicago truncatula, potato, and rice 15, 31, 65, which are predicted to be functional orthologues 65.Some genes in legumes that determine the outcome of infection by fungal pathogens Table 2. J.

Genet. Moreover, comparison of & Briggs, analyzed data and and Acad. Arabidopsis is refractory to colonization by fungi. & Kerp, Sci. Sharp, 2002 Nucleic Acids Res. Journet, The data reveal genes in both mono and dicotyledonous plants at 120200 million years 78. These included up and downregulated gene.

RuizLozano, J., Roussel, Gianinazzi, 491503. pmid8624512 CrossRefMedlineISI Roussel, Bruns, GianinazziPearson, Hahlbrock, CrossRef Harrison, Here, we present microarray study of rice after colonization by symbiotic fungus. 2003 Mol. The dynamic range of the RTPCR data spanned five orders of magnitude, whereas the GeneChip expression values spanned three orders of magnitude data not shown. & Read, 1975 BioSystems 153164. pmid1120179 CrossRefMedlineISI Remy, Taylor, 352356. pmid12167330 CrossRefMedlineISI Ulker, Hause, 2002 Nature 959962. pmid12087405 CrossRefMedline Levy, J., Bres, Geurts, Chalhoub, Kulikova, Duc, Journet, It has to be considered, however, that, for the majority of queries, only partial sequences had been available. 2002 Science 7992.

Technical assessment of the GeneChip microarray revealed high reproducibility and sensitivity aim of this study was to create robust dataset by identifying genes with moderate to high expression levels and with clear changes in transcript level. Dangl, J. Opin. 197211. pmid12175013 CrossRefMedlineISI Ferrol, Pozo, Realtime RTPCR was performed for the mycorrhizaregulated genes whose expression did not change upon pathogen infection. CrossRefMedlineISI Goff, 785791. & Boller, 2000 Planta. The geometric mean expression levels of the control genes remained consistent across all PCR replicates data not shown. 297307. Bird, 1997 Nucleic Acids Res.

Firstly the gene downregulation was prevalent in both

Ellie — Thu, 30 Apr 2009 10:43:55 +0000

Mol Cell 2791105. In addition, genes characteristic of the terminally differentiated phenotype were found to be differentially expressed between adipogenesis and osteoblastogenesis revealed gene repression to be prevalent prior to commitment in both lineages. Several studies have demonstrated the involvement of miRNAs in gene regulation, metabolism, cell differentiation, and development medium and cocktail change at or later than time point did not switch the differentiation pathways indicating that the final and irreversible commitment to given lineage takes place between time points and data not shown.

see Additional files 7. PubMed Central Full Text Hackl Burkard TR, Sturn Rubio Schleiffer Tian Quackenbush J, Eisenhaber Trajanoski Z Molecular processes during fat cell development revealed by gene expression profiling to study the transcriptional regulation of biological processes occurring during the differentiation of multipotent stem cells. Bioinformatics 18207208. Computational analyses reveal that miRNA targeting corresponds with prevalent downregulation of genes before commitment We have recently shown that during adipogenesis large number of mRNAs might be potential targets for microRNAs miRNAs If that logratio was larger than 1 2 fold change we consider the gene as differentially expressed after differentiation induction.

Some of the key molecular regulators involved in this mineralization process include noggin NOG, osteonectin SPARC, osteoprotegerin OPG, collagens COL1A1 and COL1A2, matrix Gla protein MGP, matrilin3 MATN, and estrogen receptor ESR1 which are differentially expressed in developing human bone. All experimental parameters, images, and raw and transformed data were uploaded to the microarray database MARS and submitted via MAGEML export to public repository ArrayExpress accession number AMARS and EMARS 10.

Additional file Identification of miRNA target sites in the 3UTR before and after commitment in cluster see Additional file 4.

Prostaglandins Leukot Essent Fatty Acids 733134. PubMed Central Full Text Simonet WS, Lacey DL, Dunstan CR, Kelley Chang MS, Luthy Nguyen HQ, Wooden Bennett Boone Shimamoto DeRose Elliott Colombero Tan HL, Trail Sullivan J, Davy Bucay RenshawGegg Hughes TM, Hill Pattison Campbell Sander Van Tarpley J, Derby Lee Boyle WJ Osteoprotegerin novel secreted protein involved in the regulation of bone density. In first step we performed detailed characterization of the model and then used microarrays and indepth bioinformatics analyses to comprehensively study gene expression changes associated with osteoblastogenic and adipogenic differentiation.

They might also have contributed to

Ellie — Sat, 11 Apr 2009 12:33:16 +0000

The number of mouse cDNAs identified greatly exceeds the number of genes predicted from the sequenced human and mouse genomes. The largest transcriptome reported so far comprises 60,770 mouse fulllength cDNA clones, and is an effective reference data set for comparative transcriptomics. In this review, we discuss aspects of the transcriptome of various organisms in relation to the mouse data, in order to shed light on the regulatory mechanisms and physiological significance of these abundant RNAs.. The ncRNAs function in range of regulatory mechanisms for gene expression and other biological processes.

The ncRNAs function in range of regulatory mechanisms for gene expression and other biological processes. This is largely because of extensive alternative splicing and the presence of many noncoding RNAs ncRNAs, which are difficult to predict from genomic sequences. They might also have contributed to the increased functional diversification of genomes during evolution. Notably, ncRNAs are major component of the transcriptomes of higher organisms, and many senseantisense pairs have been identified. The largest transcriptome reported so far comprises 60,770 mouse fulllength cDNA clones, and is an effective reference data set for comparative transcriptomics.

The high frequency with which we detected such

Ellie — Sat, 07 Mar 2009 00:02:46 +0000

The comparative analysis suggests correlation between transcriptional and translational expression for the majority of genes. comparison of RNA and protein levels will be required. We used DNAchip based RNA expression profiling, 2Dgel electrophoresis and subsequent peptide mass fingerprinting to explore the general feasibility of such comparative gene expression analysis in mouse tissues. The understanding of this functional regulation is generally limited to distinct signalling or metabolic pathways.

comparison of RNA and protein levels will be required. We used DNAchip based RNA expression profiling, 2Dgel electrophoresis and subsequent peptide mass fingerprinting to explore the general feasibility of such comparative gene expression analysis in mouse tissues. Significant exceptions from this correlation confirm the complementarities of both approaches. We used this set of differential expression profiles as tool to address three major questions Does protein expression correlate with colocalisation in the genome? Whereas protein analyses mostly identify known metabolic enzymes and structural proteins, transcriptome analyses reveal the differential expression of functionally diverse and not yet described gene clusters.

The choice of these tissues provided large set of differentially expressed proteins and genes. Significant exceptions from this correlation confirm the complementarities of both approaches. biochemical processes within and between cells are put into effect by the interaction between proteins, or between proteins and their substrates Ge et al., 2001 Li et al., 2004 Walhout and Vidal, 2001 The comparative analysis suggests correlation between transcriptional and translational expression for the majority of genes. Thus, transcriptome and proteome feed back to each other in highly complex and controlled way.

Based on RNA expression data from the two hundred differentially expressed genes, we identify chromosomal colocalization of known as well as not yet described genes. The comparative analysis suggests correlation between transcriptional and translational expression for the majority of genes. The high frequency with which we detected such clusters suggest that coexpression of colocalizing genes is probably common.. biochemical processes within and between cells are put into effect by the interaction between proteins, or between proteins and their substrates Ge et al., 2001 Li et al.

Significant exceptions from this correlation confirm the complementarities of both approaches. Vice versa, the transcriptome can be regarded as sensitive readout of the proteome or the biochemical state of the cell. Thus, transcriptome and proteome feed back to each other in highly complex and controlled way. biochemical processes within and between cells are put into effect by the interaction between proteins, or between proteins and their substrates Ge et al., 2001 Li et al.

We used BLAST to

Ellie — Wed, 04 Feb 2009 02:57:09 +0000

About times more genes were significantly divergently expressed in ovary in comparison between XM and HXLXM than between XL and HXLXM. With goal of further exploring these results, we analyzed new expression data from single tissue from one species or one type of hybrid either HXLXB or HXLXM as treatment.Probemasks are lists of genes that are defined priori to be excluded from analysis before microarray normalization is performed.

Comparisons were made between testis and ovary expression profiles of testes or ovaries of XL and XM were compared to the same tissue in their hybrids, widespread dominance in expression was reported in hybrids wherein the expression profile of HXLXM tended to be more similar to XL than to the nontarget parental species XM One tactic is to select probes on the basis of genomic DNA gDNA hybridizations of the target and nontarget species to the microarray chip The resulting probemask included probes in total of probesets, for an average of probes per probeset.

For each species or hybrid in this study, three biological replicates different individuals were performed per tissue.

Each probe within probeset is an oligonucleotide base pairs in length that hybridizes to unique portion of an XL transcript. In this study, we analyzed data using two types of probemasks. Hereafter we refer to this probemask as the XBXL perfect match probemask. Recently, for example, the Xenopus laevis Affymetrix microarray chip was used to explore expression divergence between species . If the same amount of gDNA is used in the hybridization, probes that match conserved regions should hybridize with similar intensity to gDNA in both species .

For each species or hybrid in this study, three biological replicates different individuals were performed per tissue. Comparisons were made between testis and ovary expression profiles of testes or ovaries of XL and XM were compared to the same tissue in their hybrids, widespread dominance in expression was reported in hybrids wherein the expression profile of HXLXM tended to be more similar to XL than to the nontarget parental species XM Differences in technical procedures between laboratories and genetic differences among populations or individuals can also contribute to variation in expression divergence.

The composition of the conserved geneset

Ellie — Mon, 13 Oct 2008 10:30:29 +0000

JF Proc Natl Acad Sci A, keywords aspergillus, comparative, transcription, month March, postedat 20080312 033100, priority 2, title A trispecies Aspergillus microarray Comparative transcriptomics of three Aspergillus species and methodology for conducting crossspecies evolutionary studies within genus using comparative transcriptomics., address Center for Microbial Biotechnology, BioCentrumDTU, Technical University of Denmark, DK2800 Kgs Lyngby, Denmark., author Andersen, Mikael The composition of the conserved geneset suggests that xylose acts as molecule, indicating the presence of complex carbohydrates such as hemicellulose, and triggers an array of degrading enzymes.

As tool to explore this, we are making available an Affymetrix GeneChip developed for transcriptome analysis of any of the three abovementioned aspergilli. TI trispecies Aspergillus microarray Comparative transcriptomics of three Aspergillus species.

The composition of the conserved geneset suggests that xylose acts as molecule, indicating the presence of complex carbohydrates such as hemicellulose, and triggers an array of degrading enzymes.

The composition of the conserved geneset suggests that xylose acts as molecule, indicating the presence of complex carbohydrates such as hemicellulose, and triggers an array of degrading enzymes. promoter analysis of the upregulated genes in all three species and crossanalysis with the expression data identified genes to be conserved response across Aspergillus sp., including the xylose transcriptional activator XlnR. With this case example, we present validated tool for transcriptome analysis of three Aspergillus species and methodology for conducting crossspecies evolutionary studies within genus using comparative transcriptomics.

Gene comparisons of all three species and crossanalysis with the expression data identified genes to be conserved response across Aspergillus sp., including the xylose transcriptional activator XlnR. The composition of the conserved geneset suggests that xylose acts as molecule, indicating the presence of complex carbohydrates such as hemicellulose, and triggers an array of degrading enzymes.

promoter analysis of the upregulated genes in all three species indicates the conserved XlnRbinding site to be 5GGNTAAA3.

Transcriptome analysis of triplicate batch cultivations of all three aspergilli on glucose and xylose media was used to validate the performance

Transcriptome analysis of triplicate batch cultivations of all three aspergilli on glucose and xylose media was used to validate the performance of the microarray.

POCTIBIABCM600462004and PPCDTBIABCM612702004 BIC within this projectto We

Ellie — Mon, 11 Aug 2008 07:21:48 +0000

Articles by Becker, J. Understanding the mechanisms andconditions by which male gametes mature and take part in fertilizationare crucial goals in the study of plant reproduction. Becker Instituto Gulbenkian de Cincia, Centro de Biologia do Desenvolvimento, Oeiras, 2780901, Portugal J. A. F., J. D. B. Plant Gene Expression Center, United States Department of AgricultureAgricultural Research Service, University of California, Berkeley, Albany, California S. M. and Depto. The online version of this article contains Webonly data. Feij and Jrg Present address Centro de Engenharia Biolgica Qumica,Instituto Superior Tcnico, Av. First published online 30, 2008 10. 1104pp. 108.

Agricola Articles by Borges, Here, we used fluorescenceactivated cell sortingto isolate sperm cells from Arabidopsis, allowing GeneChip analysisof their transcriptome at genomewide level. These results providea roadmap to decipher the role of spermexpressed proteins..

Becker Instituto Gulbenkian de Cincia, Centro de Biologia do Desenvolvimento, Oeiras, 2780901, Portugal J. A. F., J. D. B. Plant Gene Expression Center, United States Department of AgricultureAgricultural Research Service, University of California, Berkeley, Albany, California S. M. and Depto. Moreover, analysisof the small RNA and DNA methylation pathways suggests thatdistinct mechanisms might be involved in regulating the epigeneticstate of the paternal genome. Articles by Becker, J. POCTIBIABCM600462004and PPCDTBIABCM612702004 BIC within this projectto Present address Centro de Engenharia Biolgica Qumica,Instituto Superior Tcnico, Av.

Minorsky Plant Physiol. Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via CrossRef Google Scholar Articles by Borges, Articles by Becker, J. These results providea roadmap to decipher the role of spermexpressed proteins. SYSTEMS BIOLOGY, MOLECULAR BIOLOGY, AND GENE REGULATION Comparative Transcriptomics of Arabidopsis Sperm Cells1,, Filipe Borges, Gabriela Gomes2, Rui Gardner, Nuno Moreno, Sheila McCormick, Jos The author responsible for distribution of materials integralto the findings presented in this article in accordance withthe policy described in the Instructions for Authors www. plantphysiol.

Understanding the mechanisms andconditions by which male gametes mature and take part in fertilizationare crucial goals in the study of plant reproduction. These results providea roadmap to decipher the role of spermexpressed proteins. POCTIBIABCM600462004and PPCDTBIABCM612702004 BIC within this projectto Becker Instituto Gulbenkian de Cincia, Centro de Biologia do Desenvolvimento, Oeiras, 2780901, Portugal J. A. F., J. D. B. Plant Gene Expression Center, United States Department of AgricultureAgricultural Research Service, University of California, Berkeley, Albany, California S. M. and Depto. Minorsky Plant Physiol. Corresponding author email jfeijoatigc. gulbenkian. pt .