Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Human gene expression atlas of 5372 samples representing 369 different cell and tissue types, disease states and cell lines

ABSTRACT: The experiment contains systematically annotated and consistently normalized human gene expression data matrix of 5372 samples integrated from 206 public experiments of a HG-U133A array platform. The dataset is a subset of a larger pool of 9004 samples gathered from ArrayExpress and GEO websites and checked for quality assessment and suitability for data co-analysis as described by Bolstad et al 2005. The sample annotations have been subject to semiautomatic curation and manual generalization of 369 biological groups which have been additionally organized into blood/non-blood, 14 and 15 meta-classes.

ORGANISM(S): Homo sapiens

DISEASE(S): "colon adenocarcinoma, acterial infection"

SUBMITTER: Margus Lukk

PROVIDER: E-MTAB-62 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Multiple receptor tyrosine kinases promote the in vitro phenotype of metastatic human osteosarcoma cell lines.

Rettew A N AN Young E D ED Lev D C DC Kleinerman E S ES Abdul-Karim F W FW Getty P J PJ Greenfield E M EM

Oncogenesis 20121119

The survival rate for osteosarcoma patients with localized disease is 70% and only 25% for patients with metastases. Therefore, novel therapeutic and prognostic tools are needed. In this study, extensive screening and validation strategies identified Axl, EphB2, FGFR2, IGF-1R and Ret as specific receptor tyrosine kinases (RTKs) that are activated and promote the in vitro phenotype of two genetically different metastatic osteosarcoma cell lines. Initial phosphoproteomic screening identified twelv ...[more]

PMID: 23552467

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Project description:Tomato (Solanum lycopersicum) is a model species for studying fruit development, wounding, herbivory, and pathogen attack. Despite tomato’s world-wide economic importance and the role of chloroplasts as metabolic hubs and integrators of environmental cues, little is known about the stromal proteome of tomato. Using a high-yielding protocol for chloroplast and stromal protein isolation, MudPIT nano-LC-MS/MS analyses, a robust in-house protein database (the Atlas) for predicting the plastid localization of tomato proteins, and rigorous selection criteria for inclusion/exclusion in the stromal proteome, we identified 1,254 proteins of the tomato stromal proteome. We provide one of the most robust stromal proteomes available to date with empirical evidence for 550 and 105 proteins not previously described for tomato plastids and the Arabidopsis stroma, respectively. The relative abundance of tomato stromal proteins was determined using the exponentially modified protein abundance index (emPAI). Comparison of the abundance of tomato and Arabidopsis stromal proteomes provided evidence for the species-specific nature of stromal protein homeostasis. The manual curation of the tomato stromal proteome classified proteins into ten functional categories resulting in an accessible compendium of tomato chloroplast proteins. After curation, only 88 proteins remained as unknown, uncharacterized or as enzymes with unknown functions. The curation of the tomato stromal proteins also indicated that tomato has a number of paralogous proteins, not present in Arabidopsis, which accumulated to different levels in chloroplasts. As some of these proteins function in key metabolic pathways or in perceiving or transmitting signals critical for plant adaptation to biotic and abiotic stress, these data suggest that tomato may modulate the bidirectional communication between chloroplasts and nuclei in a novel manner. The stromal proteome provides a fertile ground for future mechanistic studies in the field of tomato chloroplast-nuclear signaling and are foundational for our goal of elucidating the dynamics of the stromal proteome controlled by the solanaceous-specific, stromal, and wound-inducible leucine aminopeptidase A of tomato.

Dataset Information

Human gene expression atlas of 5372 samples representing 369 different cell and tissue types, disease states and cell lines

Publications

Multiple receptor tyrosine kinases promote the in vitro phenotype of metastatic human osteosarcoma cell lines.

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