Abstract：
:The design and analysis of experiments using gene expression microarrays is a topic of considerable current research, and work is beginning to appear on the analysis of proteomics and metabolomics data by mass spectrometry and NMR spectroscopy. The literature in this area is evolving rapidly, and commercial software for analysis of array or proteomics data is rarely up to date, and is essentially nonexistent for metabolomics data. In this paper, I review some of the issues that should concern any biologists planning to use such high-throughput biological assay data in an experimental investigation. Technical details are kept to a minimum, and may be found in the referenced literature, as well as in the many excellent papers which space limitations prevent my describing. There are usually a number of viable options for design and analysis of such experiments, but unfortunately, there are even more non-viable ones that have been used even in the published literature. This is an area in which up-to-date knowledge of the literature is indispensable for efficient and effective design and analysis of these experiments. In general, we concentrate on relatively simple analyses, often focusing on identifying differentially expressed genes and the comparable issues in mass spectrometry and NMR spectroscopy (consistent differences in peak heights or areas for example). Complex multivariate and pattern recognition methods also need much attention, but the issues we describe in this paper must be dealt with first. The literature on analysis of proteomics and metabolomics data is as yet sparse, so the main focus of this paper will be on methods devised for analysis of gene expression data that generalize to proteomics and metabolomics, with some specific comments near the end on analysis of metabolomics data by mass spectrometry and NMR spectroscopy.
journal_name
Semin Cell Dev Bioljournal_title
Seminars in cell & developmental biologyauthors
Rocke DMdoi
10.1016/j.semcdb.2004.09.007subject
Has Abstractpub_date
2004-12-01 00:00:00pages
703-13issue
6eissn
1084-9521issn
1096-3634pii
S1084-9521(04)00093-Xjournal_volume
15pub_type
杂志文章,评审abstract：:The extracellular matrix (ECM) consists of a complex mixture of structural and functional proteins and serves an important role in tissue and organ morphogenesis, maintenance of cell and tissue structure and function, and in the host response to injury. Xenogeneic and allogeneic ECM has been used as a bioscaffold for ...
journal_title：Seminars in cell & developmental biology
pub_type： 杂志文章,评审
doi：10.1016/s1084952102000940
更新日期：2002-10-01 00:00:00
abstract：:It is now well established that the environment to which we are exposed during fetal and neonatal life can have a long-term impact on our health. This has been termed the developmental origins of health and disease. Factors known to have such programming effects include intrauterine nutrient availability (determined b...
journal_title：Seminars in cell & developmental biology
pub_type： 杂志文章,评审
doi：10.1016/j.semcdb.2015.06.006
更新日期：2015-07-01 00:00:00
abstract：:The small ubiquitin-like modifier (SUMO) is covalently attached to lysine residues in target proteins and in doing so changes the properties of the modified protein. Here we examine the role of SUMO modification in transcriptional regulation. SUMO addition to components of the transcriptional apparatus does not have a...
journal_title：Seminars in cell & developmental biology
pub_type： 杂志文章,评审
doi：10.1016/j.semcdb.2003.12.001
更新日期：2004-04-01 00:00:00
abstract：:A system of endoplasmic reticulum (ER) chaperones has evolved to optimize the output of properly folded secretory and membrane proteins. An important player in this network is Glucose Regulated Protein 94 (GRP94). Over the last decade, new structural and functional data have begun to delineate the unique characteristi...
journal_title：Seminars in cell & developmental biology
pub_type： 杂志文章,评审
doi：10.1016/j.semcdb.2010.03.004
更新日期：2010-07-01 00:00:00
abstract：:Yeast prions are atypical genetic elements that are transmitted as heritable protein conformations. [PSI+], [URE3], and [PIN+] are three well-studied prions in the budding yeast, Saccharomyces cerevisiae. In the last three years, several additional prions have been reported in yeast, including [SWI+], [OCT+], [MCA], [...
journal_title：Seminars in cell & developmental biology
pub_type： 杂志文章,评审
doi：10.1016/j.semcdb.2011.03.003
更新日期：2011-07-01 00:00:00
abstract：:In addition to being polarized along their apical/basal axis, cells composing most (if not all) organs are also polarized in a plane vertical to the A/B axis. Recent studies indicate that this so-called planar cell polarity (PCP) plays an essential role in the formation of multiple organ systems regulating directed ce...
journal_title：Seminars in cell & developmental biology
pub_type： 杂志文章,评审
doi：10.1016/j.semcdb.2006.05.003
更新日期：2006-04-01 00:00:00
abstract：:Regulation of Notch signaling is critical to development and maintenance of most eukaryotic organisms. The Notch receptors and ligands are integral membrane proteins and direct cell-cell interactions are needed to activate signaling. Ligand-expressing cells activate Notch signaling through an unusual mechanism involvi...
journal_title：Seminars in cell & developmental biology
pub_type： 杂志文章,评审
doi：10.1016/j.semcdb.2012.01.011
更新日期：2012-06-01 00:00:00
abstract：:Given the large socio-economic burden of cancer, there is an urgent need for in vivo animal cancer models that can provide a rationale for personalised therapeutic regimens that are translatable to the clinic. Recent developments in establishing mouse models that closely resemble human lung cancers involve the applica...
journal_title：Seminars in cell & developmental biology
pub_type： 杂志文章,评审
doi：10.1016/j.semcdb.2014.04.002
更新日期：2014-03-01 00:00:00
abstract：:Wnt signaling is a hallmark of all embryonic development with multiple roles at multiple developmental time points. Wnt signaling is also important in the development of several organs, one of which is the inner ear, where it participates in otic specification, the formation of vestibular structures, and the developme...
journal_title：Seminars in cell & developmental biology
pub_type： 杂志文章,评审
doi：10.1016/j.semcdb.2013.03.008
更新日期：2013-05-01 00:00:00
abstract：:Cellular morphogenesis is a complex process and molecular studies in the last few decades have amassed a large amount of information that is difficult to grasp in any completeness. Fungal systems, in particular the budding and fission yeasts, have been important players in unravelling the basic structural and regulato...
journal_title：Seminars in cell & developmental biology
pub_type： 杂志文章,评审
doi：10.1016/j.semcdb.2008.01.003
更新日期：2008-06-01 00:00:00
abstract：:Viruses are obligate intracellular parasites and have to use the host cell machinery for their replication. Many viruses are able to divert different parts of this machinery to preferentially enhance virus replication at the expense of the cell. The mechanisms by which different viruses do this have, over the years, g...
journal_title：Seminars in cell & developmental biology
pub_type： 杂志文章
doi：10.1006/scdb.1996.0127
更新日期：1997-02-01 00:00:00
abstract：:During development, epithelial cells in some tissues acquire a polarity orthogonal to their apical-basal axis. This polarity, referred to as planar cell polarity (PCP), or tissue polarity, is essential for the normal physiological function of many epithelia. Early studies of PCP focused on insect epithelia (Lawrence, ...
journal_title：Seminars in cell & developmental biology
pub_type： 杂志文章,评审
doi：10.1016/j.semcdb.2009.08.001
更新日期：2009-10-01 00:00:00
abstract：:Axonal projections between two populations of neurons, which preserve neighborhood relationships, are called topographic. They are ubiquitous in the brain. The development of the retinotectal projection, mapping the retinal output onto the roof of the midbrain, has been studied for decades as a model system. The rigid...
journal_title：Seminars in cell & developmental biology
pub_type： 杂志文章,评审
doi：10.1016/j.semcdb.2014.07.010
更新日期：2014-11-01 00:00:00
abstract：:Mitochondria are the key energy-producing organelles and cellular source of reactive species. They are responsible for managing cell life and death by a balanced homeostasis passing through a network of structures, regulated principally via fission and fusion. Herein we discuss about the most advanced findings conside...
journal_title：Seminars in cell & developmental biology
pub_type： 杂志文章,评审
doi：10.1016/j.semcdb.2019.05.022
更新日期：2020-02-01 00:00:00
abstract：:Ontogenetic series of extinct taxa are extremely rare and when preserved often incomplete and difficult to interpret. However, the fossil record of amphibians includes a number of well-preserved ontogenetic sequences for temnospondyl and lepospondyl taxa, which have provided valuable information about the development ...
journal_title：Seminars in cell & developmental biology
pub_type： 杂志文章,评审
doi：10.1016/j.semcdb.2009.11.001
更新日期：2010-06-01 00:00:00
abstract：:In the crowded intranuclear environment, entropic depletion forces between macromolecules are expected to be strong. A review of simulations of linear polymers leads to several predictions about probable conformations of a polynucleosome chain in these conditions. These include a globular conformation, variable compac...
journal_title：Seminars in cell & developmental biology
pub_type： 杂志文章,评审
doi：10.1016/j.semcdb.2007.08.006
更新日期：2007-10-01 00:00:00
abstract：:The urinary collecting system is derived from an epithelial protrusion arising from the Wolffian duct called the ureteric bud (UB) by the signal from its inductive tissue, metanephric mesenchyme (MM). Targeted gene mutation studies have shown that several transcription factors and MM-secreted glial cell line-derived n...
journal_title：Seminars in cell & developmental biology
pub_type： 杂志文章,评审
doi：10.1016/s1084-9521(03)00024-7
更新日期：2003-08-01 00:00:00
abstract：:Research using Xenopus laevis has made enormous contributions to our understanding of vertebrate development, control of the eukaryotic cell cycle and the cytoskeleton. One limitation, however, has been the lack of systematic genetic studies in Xenopus to complement molecular and cell biological investigations. Work w...
journal_title：Seminars in cell & developmental biology
pub_type： 杂志文章,评审
doi：10.1016/j.semcdb.2005.11.009
更新日期：2006-02-01 00:00:00
abstract：:Any type of tubulogenesis is a process that is highly coordinated between large numbers of cells. Like other morphogenetic processes, it is driven to a great extent by complex cell shape changes and cell rearrangements. The formation of the salivary glands in the fly embryo provides an ideal model system to study thes...
journal_title：Seminars in cell & developmental biology
pub_type： 杂志文章,评审
doi：10.1016/j.semcdb.2014.03.020
更新日期：2014-07-01 00:00:00
abstract：:Cardiac chamber walls contain large numbers of non-contractile interstitial cells, including fibroblasts, endothelial cells, pericytes and significant populations of blood lineage-derived cells. Blood cells first colonize heart tissues a few days before birth, although their recruitment from the bloodstream to the car...
journal_title：Seminars in cell & developmental biology
pub_type： 杂志文章,评审
doi：10.1016/j.semcdb.2020.06.008
更新日期：2020-06-23 00:00:00
abstract：:Evidence emerges that redox gradients regulate morphogenesis, inflammation, regeneration, and healing of tissues. At the example of redox signaling during the zebrafish wound response, I briefly discuss current ideas on how such patterns might be sensed and spatially regulated to guide physiological processes over dis...
journal_title：Seminars in cell & developmental biology
pub_type： 杂志文章,评审
doi：10.1016/j.semcdb.2017.07.038
更新日期：2018-08-01 00:00:00
abstract：:The sculpting of embryonic tissues and organs into their functional morphologies involves the spatial and temporal regulation of mechanics at cell and tissue scales. Decades of in vitro work, complemented by some in vivo studies, have shown the relevance of mechanical cues in the control of cell behaviors that are cen...
journal_title：Seminars in cell & developmental biology
pub_type： 杂志文章,评审
doi：10.1016/j.semcdb.2016.03.011
更新日期：2016-07-01 00:00:00
abstract：:Cell signaling is essential for cells to adequately respond to their environment. One of the most evolutionarily conserved signaling pathways is that of the epidermal growth factor receptor (EGFR). Transmembrane receptors with intracellular tyrosine kinase activity are activated by the binding of their corresponding l...
journal_title：Seminars in cell & developmental biology
pub_type： 杂志文章,评审
doi：10.1016/j.semcdb.2018.05.011
更新日期：2019-03-01 00:00:00
abstract：:How limited is the ability of stem cells to generate gametes or differentiated somatic cells? Recent outcomes of research with stem cells from both embryonic and adult origin will be discussed with particular attention to results that challenge conventional wisdom about the presence of reproductive stem cells in adult...
journal_title：Seminars in cell & developmental biology
pub_type： 杂志文章,评审
doi：10.1016/j.semcdb.2006.07.003
更新日期：2006-08-01 00:00:00
abstract：:APOBEC1 is a cytidine deaminase that edits messenger RNAs and was the first enzyme in the APOBEC family to be functionally characterized. Under appropriate conditions APOBEC1 also deaminates deoxycytidine in single-stranded DNA (ssDNA). The other ten members of the APOBEC family have not been fully characterized howev...
journal_title：Seminars in cell & developmental biology
pub_type： 杂志文章,评审
doi：10.1016/j.semcdb.2011.10.004
更新日期：2012-05-01 00:00:00
abstract：:Cancer cachexia is a complex syndrome generated by interaction between the host and tumour cells with a background of treatment effects and toxicity. The complexity of the physiological pathways likely involved in cancer cachexia necessitates a holistic view of the relevant biology. Emergent properties are characteris...
journal_title：Seminars in cell & developmental biology
pub_type： 杂志文章,评审
doi：10.1016/j.semcdb.2015.12.022
更新日期：2016-06-01 00:00:00
abstract：:During the development of vertebrate nervous system, distinct classes of motor neurons and interneurons are generated at distinct dorsoventral positions in the ventral neural tube. The differentiation of these neuronal subtypes is directed by the secreted protein Sonic Hedgehog (Shh). Shh acts in a graded manner to es...
journal_title：Seminars in cell & developmental biology
pub_type： 杂志文章,评审
doi：10.1006/scdb.1999.0295
更新日期：1999-06-01 00:00:00
abstract：:The wide diversity of biogenic minerals that is found in nature, each with its own morphology, mechanical properties and composition, is remarkable. In order to produce minerals that are optimally adapted for their function, biomineralisation usually occurs under strict cellular control. This control is exerted by spe...
journal_title：Seminars in cell & developmental biology
pub_type： 杂志文章,评审
doi：10.1016/j.semcdb.2015.07.004
更新日期：2015-10-01 00:00:00
abstract：:The immune system plays an indispensable role in the process of tissue regeneration following damage as well as during homeostasis. Inflammation and immune cell recruitment are signs of early onset injury. At the wound site, immune cells not only help to clear debris but also secrete numerous signalling molecules that...
journal_title：Seminars in cell & developmental biology
pub_type： 杂志文章,评审
doi：10.1016/j.semcdb.2018.04.002
更新日期：2019-03-01 00:00:00
abstract：:Cells maintain a cholesterol gradient across the secretory system, with the lowest concentrations in the endoplasmic reticulum (ER) and the highest in the plasma membrane (PM). Cholesterol is also heterogeneously distributed in the endocytic pathway. Little is known about how this heterogeneous distribution of cholest...
journal_title：Seminars in cell & developmental biology
pub_type： 杂志文章,评审
doi：10.1016/s1084-9521(02)00048-4
更新日期：2002-06-01 00:00:00
