Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

AtMYB60

ABSTRACT: Stomatal guard-cells modulate gas exchange between the plant and the atmosphere.

Regulation of transcription is emerging as an important mechanism in

controlling guard cells activity. The Arabidopsis transcription factor

AtMYB60, is specifically expressed in guard cells and controls stomatal

movements. Opening of stomatal pores is constitutively reduced in the

atmyb60-1 null allele, and water loss during drought is diminished in

the mutant compared to wild type. To address the effect of the AtMYB60

disruption on global gene expression, total mRNAs, derived from

atmyb60-1 and WT rosette leaves, grown in standard conditions, were hybridized to a cDNA microarray.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Paul Van Hummelen

PROVIDER: E-MEXP-225 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcription profiling of ovarium cancer samples from patients with tumors of different stages and sensitivity to platinum chemotherapy treatment

Project description:We investigated whether prognostic information is reflected in the expression patterns of ovarian carcinoma samples. RNA obtained from seven FIGO stage I without recurrence, seven platin-sensitive advanced-stage (III or IV), and six platin-resistant advanced-stage ovarian tumors was hybridized on a complementary DNA microarray with 21,372 spotted clones. The results revealed that a considerable number of genes exhibit nonaccidental differential expression between the different tumor classes. Principal component analysis reflected the differences between the three tumor classes and their order of transition. Using a leave-one-out approach together with least squares support vector machines, we obtained an estimated classification test accuracy of 100% for the distinction between stage I and advanced-stage disease and 76.92% for the distinction between platin-resistant versus platin-sensitive disease in FIGO stage III/IV. These results indicate that gene expression patterns could be useful in clinical management of ovarian cancer.<br> KEYWORDS: clinical, FIGO stage, microarrays, ovarian cancer, platin resistance.

2007-02-10 | E-MEXP-979 | biostudies-arrayexpress

Transcription profiling of CD4+ T lymphocytes in response to an irradiation dose of 1 Gy.radiation

Project description:Differences in radiosensitivity existing among cells which constitute the lymphocyte population have been known for a long time, although the molecular basis of this differential radiation sensitivity remains unclear. In an attempt to get more insight into the molecular mechanisms leading to radiation effects, we used microarray analysis to study transcriptional changes in CD4+ T lymphocytes to an irradiation dose of 1 Gy. The contribution of the cell type to the radiation response of CD4+ lymphocytes was deduced by comparing our results with a gene expression profile observed in Peripheral Blood Lymphocytes published by other groups (Amundson, 2000; Kang, 2003, Jen, 2003).

2005-12-31 | E-MEXP-320 | biostudies-arrayexpress

Transcription profiling of primary hippocampal neurons isolated from mouse E17 embryos and undergoing differentiation in the culture for 7h, 18h, 33h, 72h, 8 days, 12 days (at which time points the RNA was extracted) vs RNA isolated from a newborn brain

Project description:A time-course experiment, in which the gene expression in the primary hippocampal neurons isolated from E17 embryos and undergoing differentiation in the culture for 7h, 18h, 33h, 72h, 8 days, 12 days (at which time points the RNA was extracted) was compared by competitive hybridization with a common reference sample which was RNA isolated from a newborn brain.

2003-06-01 | E-MEXP-11 | biostudies-arrayexpress

Transcription profiling of human NF1 heterozygous (NF1+/-) melanocytes from a Neurofibromatosis type 1 patient and NF1 wild type (NF1+/+) melanocytes of a healthy control patient

Project description:One of the major primary features of the neurocutaneous genetic disorder Neurofibromatosis type 1 are the hyperpigmentary café-au-lait macules where dysregulation of melanocyte development, proliferation and differentiation is considered to play a key etiopathogenic role. To gain better insight in the possible role of the tumor suppressor gene NF1, a transcriptomic microarray analysis was performed on human NF1 heterozygous (NF1+/-) melanocytes of a Neurofibromatosis type 1 patient and NF1 wild type (NF1+/+) melanocytes of a healthy control patient, both cultured from normally pigmented and hyperpigmented lesional café-au-lait skin. Out of 13,850 unique genes, a total of 137 had a significant twofold or more up- (72) or down-regulated (65) expression in NF1+/- melanocytes compared to NF1+/+ melanocytes (genotype effect). Considering possible intrinsic genetic variation in lesional skin, melanocytes showed a total of 51 genes having a significant twofold or more up- (37) or down-regulated (14) expression when they were cultured from hyperpigmentary café-au-lait skin compared to normally pigmented skin (lesional skin type effect). NF1+/- café-au-lait skin melanocytes showed 468 genes with a significant two-fold or more up- (183) or down-regulated (285) expression going beyond the sum of the separate main effects (interaction). Detailed analysis enabled the identification of several modulated genes in NF1+/- (café-au-lait skin) melanocytes, mainly involved in controlling cell proliferation and cell maintenance, in cell adhesion and, surprisingly, in the immune response. An interesting finding was that a high number of transcription factor genes were differentially modulated, among which a specific subset - important in melanocyte-lineage development - showed downregulation in a transcriptional cis-regulatory network governing the activation of the melanocyte-specific dopachrome tautomerase (DCT) gene.

2005-02-05 | E-MEXP-258 | biostudies-arrayexpress

Transcription profiling of Arabidopsis leaf blades sampled throughout development from meristematic to expanding to mature state at 10 different timepoints

Project description:Arabidopsis leaf blades were sampled throughout development from meristematic through expanding to mature state at 10 different timepoints. The transcript data can be compared to a kinematic and flowcytometric characterisation of the system.

2004-09-20 | E-MEXP-144 | biostudies-arrayexpress

Transcription profiling of multiple mouse myeloma (MM) cells during intra-medullary progression in the 5T2MM mouse model

Project description:Insights into mechanisms involved during intra-medullary myeloma progression could be helpful in the better understanding of this disease and in the development of new therapeutical strategies. Herein gene expression profile of multiple myeloma (MM) cells during intra-medullary progression was investigated using the 5T2MM murine model. MM-cells from 3 subsequent disease stages, quiescent, intermediate and end stage were analyzed using microarrays containing 21,492 Unigene cDNA sequences. ~ 3000 calls of differentially expressed genes were obtained. Most of these genes were silenced during tumor progression. In the early stage the MM-cells had up-regulated genes involved in bone marrow (BM) homing (CCR2, CCR5), motility (tetraspanins, 67kD laminin receptor, paxillin, zyxin, prolactin receptor), invasion (annexin II, cathepsins), adhesion (integrins, ALCAM) and cell adhesion mediated drug resistance (fibronectin). Genes involved in apoptosis (Mcl-1), plasma cell differentiation (XBP-1), angiogenesis (neuropilin-2, angiopoietin-like 4), hypoxia (HIF-1a, carbonic anhydrase 9) and in retention (CXCR4/CXCL12) and anchoring of MM-cells (laminin, collgens) in the BM were up-regulated during progressive stages. Quantative RT-PCR confirmed the trend of expression. These data provide a framework of mechanisms involved in intra-medullary myeloma progression; several genes known to be important in MM-biology are highlighted and novel candidate genes are illuminated as potentially more effective therapeutical targets.

2008-03-27 | E-MEXP-186 | biostudies-arrayexpress

Genotyping of Arabidopsis ecotypes

Project description:Large-scale screening studies carried out to date to elucidate the causal mechanism of an allelic imbalance are generally limited to descriptions of allele-specific differences in expression detected in vivo and to linking them to differences in cis- and trans-regulatory changes. Although such gene surveys for regulatory variation leave the underlying mechanisms unexplored, they are a first step in identifying the specific nucleotide changes that govern gene expression differences. We describe a quantitative genetics approach to distinguish between cis- and trans-regulatory changes at a genome-wide scale and, hence, to detect cis-regulatory variation. For this purpose, we took advantage of diallel designs that are often used in plant breeding programs in which the goal is the estimation of general combining abilities (GCAs) of specific inbred lines and the identification of high yielding hybrid combinations of parents based on their specific combining abilities (SCAs). We show that in a context of gene expression, empirical estimates of GCA and SCA are valid parameters to distinguish between cis- and trans-regulatory changes and, hence, to detect cis-regulatory variation. By using this approach, we identified a considerable number of genes that showed evidence of cis-regulated allele-specific expression in a total of 10 diploid Arabidopsis hybrids. The method can also be used to explore naturally occurring cis-regulatory variation among inbred lines for laboratory animals, such as mouse and rat. This experiment covers data from 10 pairs of reciprocal hybrid samples, referred to as Hx.y where x=1...10 and y=1,2; The related data from 20 Recombinant Inline Line samples is submitted as experiment : - VIB Plant Systems Biology "RIL")

2006-12-02 | E-TABM-67 | biostudies-arrayexpress

Transcription profiling of mouse primary capillary PlGF-/- endothelial cells treated with 100 ng/ml PlGF for 6 hours

Project description:PlGF expression profile in primary capillary PlGF-/- endothelial cells treated with 100 ng/ml PlGF during 6 hours.

2003-05-28 | E-MEXP-6 | biostudies-arrayexpress

Transcription profiling of ovarium cancer samples from patients with tumors of different stages, sensitivity to platinum chemotherapy and with no disease recurrence, recurrence or progression to evaluate models of clinical behaviour

Project description:Ovarian cancer is the leading cause of death in gynaecological malignancies in women. However, currently there are no clinical or pathologic parameters available that can reliably predict clinical outcome. In a previously published pilot study we explored the performance of microarrays in predicting clinical behaviour of ovarian tumours. For this purpose we performed microarray analysis on 20 patients and estimated that we could predict disease stage with 100% accuracy and the response to platin-based chemotherapy with 76.92% accuracy using leave-one-out cross validation techniques in combination with Least Squares Support Vector Machines (LS-SVMs). In the current study we prospectively evaluate models, built on the pilot data set, on a set of 49 new patients. Principal component analysis showed that the gene expression data from stage I, platin-sensitive advanced stage and platin-resistant advanced stage tumours in the prospective study did not correspond to their respective classes in the pilot study. Additionally, LS-SVM models built using the data from the pilot study, only misclassified one of four stage I tumours and correctly classified all 45 advanced stage tumours but this model was not able to predict resistance to platin-based chemotherapy. We discuss possible reasons for prospective failure of these models and conclude that existing results based on gene expression patterns of ovarian tumours need to be thoroughly scrutinized before this technology could be considered ready for clinical use.

2007-12-31 | E-MEXP-995 | biostudies-arrayexpress

Transcription profiling of leaves from different developmental stages of Arabidopsis plants

Project description:Transcriptome analysis of A.thaliana cy5 labeled versus oligos reference mix cy3 labeled.

2007-01-27 | E-CAGE-198 | biostudies-arrayexpress