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PubMed2003

The human pituitary proteome: the characterization of differentially expressed proteins in an adenoma compared to a control.

In order to clarify the basic molecular mechanisms that participate in the formation of human pituitary macroadenomas, this study, for the first time, describes the comparative proteomics between a pituitary adenoma tissue and a control tissue. A vertical, two-dimensional polyacrylamide gel electrophoresis system and PDQuest image analysis software were used to provide a high level of between-gel reproducibility and electrophoretic separation to accurately locate each differentially expressed protein. Mass spectrometry (MALDI-TOF and LC-ESI-Q-IT) and protein databases were used to characterize each differentially expressed protein. A total of 137 differential gel spots (37 increased spot volumes, 39 decreased, 19 new and 42 lost) were found when we compared an adenoma proteome to a control proteome. Seventy-one spots (20 increased, 27 decreased, 13 new, 11 lost), representing 39 differentially regulated proteins, were identified. Five differentially regulated proteins (prolactin, cellular retinoic acid-binding protein II, G-protein beta subunit 3, secretagogin and calreticulin) were also validated with results from a comparative transcriptomics study of pituitary adenomas and controls. The functional characteristics of these differentially expressed proteins provide a differential proteomic profile between a pituitary adenoma and a control.

Adenoma↗
PubMed2006

Alternative splicing of G6PC2, the gene coding for the islet-specific glucose-6-phosphatase catalytic subunit-related protein (IGRP), results in differential expression in human thymus and spleen compared with pancreas.

AIMS/HYPOTHESIS: Autoimmunity to insulin, glutamic acid decarboxylase and the tyrosine-phosphatase-like protein IA-2 is associated with type 1 diabetes. The production of self-molecules in thymus and secondary lymphoid tissues is critical for self-tolerance; reduced levels may impair tolerance and predispose to autoimmunity, as shown for insulin. Alternative splicing causes differential expression of IA-2 gene (PTPRN) transcripts and IA-2 protein in human thymus and spleen compared with pancreas. IA-2 sequences not present in lymphoid tissues become autoimmune targets in type 1 diabetes. The beta cell molecule islet-specific glucose-6-phosphatase catalytic subunit-related protein (IGRP) is an autoantigen in the non-obese diabetic (NOD) mouse, a model of type 1 diabetes. IGRP is a candidate autoantigen in the human disease, but robust assays for IGRP autoantibodies and/or autoreactive T cells are not available. Both full-length and IGRP splice variants encoded by the G6PC2 gene are expressed in the pancreas. In this study we tested the hypothesis that IGRP splice variants could be differentially expressed in thymus and spleen compared with the pancreas. METHODS: We evaluated the expression of G6PC2 transcripts in matched human thymus, spleen and pancreas specimens by RT-PCR. RESULTS: Alternative splicing results in differential expression of G6PC2 transcripts in thymus and spleen compared with pancreas. The full-length transcript is expressed in human pancreas but not in thymus or spleen. Five alternative spliced forms are always expressed in pancreas but those lacking exons 2, 3 and 4, alone or in combination, were rarely detected in thymus or spleen. CONCLUSIONS/INTERPRETATION: Differential tissue expression might favour autoimmune responses to IGRP in humans; target epitopes may be encoded by exons 3 and 4, or at the junctions of the conserved exons in the spliced transcripts. This information may aid in designing synthetic peptides for the identification of IGRP-specific autoreactive T cells in patients with type 1 diabetes.

Alternative Splicing↗
PubMed2006

The loss in power when the test of differential expression is performed under a wrong scale.

One of the most common and important goals of microarray studies is to identify genes that are differentially expressed between cells of different conditions. T-test and ANOVA models on the expression data are common practices to gauge the significance of the observed difference in expression levels. Transformation of the microarray data is often applied in order to satisfy the model assumptions being entertained. However, the distributional properties of the expression are gene specific, and it is impractical to find a single transformation that is universally optimal for all the genes. This difficulty results in the situation that some genes have to violate the assumptions of the model (e.g., homogeneity in variance, normality). It is thus the interest of this paper to evaluate the impact on the inference of differential expression when the test is performed under an inappropriate scale. Particularly, we quantitatively assess the loss of power when the test is performed under a wrong scale. Normal distribution and log-normal distribution of the expression data are considered. The loss in power is investigated in two scenarios: a transformation is misused, or a transformation fails to be applied. Log transformation and power transformation are particularly considered due to the fact that Box-Cox types of transformation are commonly used in practice. The impact of using a wrong scale is investigated analytically and based on simulations. The loss in power is assessed both as a function of the degree to which the assumptions are violated and as a function of the effect size. Simulations are conducted to quantitatively assess the power loss when tests are performed under a wrong scale. A public experimental microarray dataset is used to illustrate the impact of transformation on the results of testing differential expression. The results show that the loss of power is a function of CV and fold-change (effect size). The loss in power depends on the true model and on how severely the assumptions are violated.

Databases, Genetic↗
PubMed2001

Identification of differentially expressed genes in hepatocellular carcinoma and metastatic liver tumors by oligonucleotide expression profiling.

BACKGROUND: The characterization of differentially expressed genes between cancerous and normal tissues is an important step in the understanding of tumorigenesis. Global gene expression profiling with microarrays has now offered a powerful tool to measure the changes of thousands of genes in any carcinoma tissues in an effort to identify these key disease-related genes. To compare the gene expression of a primary liver carcinoma, metastatic carcinoma to the liver, and normal liver, the authors analyzed tissue from six primary hepatocellular carcinomas (HCCs), five colorectal adenocarcinoma metastases to the liver, and eight normal livers. METHODS: Samples were processed from total RNA to fragmented cRNA and hybridized onto Affymetrix GeneChip(R) expression arrays. Analyses were performed to determine the consensus pattern of gene expression for primary liver carcinoma, metastatic liver carcinoma, and normal liver tissue and their changes in expression level. RESULTS: In hepatocellular carcinoma, 842 genes were overexpressed, and 393 genes were underexpressed in comparison with genes of normal liver tissue. Of note, 7 of the 20 most increased identified known genes previously have been associated with liver carcinoma or other types of cancers. The 13 additional identified genes until now have not previously shown strong association with cancers. Furthermore, the authors identified 42 genes and 24 expressed sequence tags that are expressed at a significant level in both HCC and metastastic tumors, presenting a list of marker genes indicative of cancerous liver tissue. CONCLUSIONS: In this study, genes that can be involved in the production of and maintenance of hepatic carcinomas were identified. These data offer new insight into genes that are potentially important in the pathogenesis of liver carcinoma, as well as additional targets for new strategies for cancer therapy and treatment.

Adult↗
PubMed2003

[Indentification of differentially expressed genes in proliferating and involuting hemangiomas by cDAN microarray analysis of gene-expression profiles].

OBJECTIVE: To investigate the differentially expressed genes of proliferating and involuting hemangiomas by cDNA microarray analysis of gene-expression profiles in an effort to identify the key disease-related genes. METHODS: Samples were processed from total RNA and purified to mRNA, which was reverse-transcripted and hybridized onto Biodoor Genechip expression microarrays. Analyses were performed to determine the consensus pattern of gene expression in the proliferating and involuting stages of the same hemangioma and the changes in the expression level. RESULTS: In proliferating hemangioma, 79 genes were overexpressed, and 115 genes were underexpressed in comparison with the involuting hemangioma. Some cytokines and growth factors such as neurotensin, Nov, CYR6, keratinocyte growth factor, interleukin-10 were overexpressed in proliferative hemangioma. In involuting hemangioma, apoptotic factors such as bcl-2 binding component, cytochrome C were overexpressed. The overexpression of Nov, CYR6, c-myc implied that angiogenesis and oncogenes might participate in the pathogenesis of hemangiomas. Mitochondria activated apoptotic passage (cytokines, bcl-2, cytochrome C) and Wnt/beta-catenin passage(Frizzled, beta-catenin, c-myc) were involved. CONCLUSION: The development of hemangiomas may be the results of imbalance of cell proliferation and apoptosis.

Apoptosis↗
PubMed2004

A generalized likelihood ratio test to identify differentially expressed genes from microarray data.

MOTIVATION: Microarray technology emerges as a powerful tool in life science. One major application of microarray technology is to identify differentially expressed genes under various conditions. Currently, the statistical methods to analyze microarray data are generally unsatisfactory, mainly due to the lack of understanding of the distribution and error structure of microarray data. RESULTS: We develop a generalized likelihood ratio (GLR) test based on the two-component model proposed by Rocke and Durbin to identify differentially expressed genes from microarray data. Simulation studies show that the GLR test is more powerful than commonly used methods, like the fold-change method and the two-sample t-test. When applied to microarray data, the GLR test identifies more differentially expressed genes than the t-test, has a lower false discovery rate and shows more consistency over independently repeated experiments. AVAILABILITY: The approach is implemented in software called GLR, which is freely available for downloading at http://www.cc.utah.edu/~jw27c60

Algorithms↗
PubMed2004

Identification of differentially expressed genes from spinal cord after firearm injury to rabbit sciatic nerves.

OBJECTIVE: Peripheral nerve regeneration depends on gene regulation by central neurons. To search for more effective treatment methods to improve the regeneration of wounded peripheral nerves, gene expression profile of spinal cord after firearm injury to rabbit sciatic nerves are studied with DNA micro-array technique. METHODS: A total of 54 rabbits were randomly divided into 4 groups: Groups d1, d3, d7 and normal control group. Lumbar spinal cords were sampled. RNA and mRNA were extracted, labeled by Cy3 and Cy5, and analyzed by mouse_8192S gene chips. RESULTS: A total of 1367, 923, and 61 genes with differential expression were found on day 1, day 3, and day 7 after trauma respectively. Five expressed sequence tag (EST) sequences demonstrated differential expression during 7 days after trauma. CONCLUSIONS: There is complex gene profile with differential expression after firearm nerve injury, among which AW701496, U84291, W13926, X04017 and AW822394 EST sequences may be important regulation factors that involved in regeneration of peripheral nerve injury.

Animals↗
PubMed1998

Differentially expressed genes in cultured aortic smooth muscle cells by cholesterol-loading.

Differentially expressed genes generated by cholesterol-loading in the culture medium of aortic smooth muscle cells (SMC) were screened using the DDRT-PCR technique in order to identify the genes that are possibly involved in the pathogenesis of atherosclerosis in the artery. Twenty-eight genes were initially isolated and three differentially expressed cDNAs were finally selected by Northern blot analysis. All three cDNAs were up-regulated (designated CRGSM-1 through -3) by the cholesterol-loading. Upon nucleotide sequencing and homology search in the databases, the first cDNA (CRGSM-1) had a high homology (97%) with the corresponding segment of the acyl-CoA synthetase II gene from rat brain, which participates in fatty acid synthesis. The second one (CRGSM-2) had a high homology (91%) with a part of Mus musculus (mouse) LIM protein 1, and with human skeletal muscle LIM-protein 1 genes (80%) and the third gene (CRGSM-3) had no significant homology match in the database. A full size cDNA isolated from the cDNA library of rat aortic smooth muscle cell using the CRGSM-2 as a probe was identified to have a high homology with muscle LIM protein (MLP). The isolated cDNA contained a segment of DNA that encodes for a zinc-finger motif and two LIM domains. Proteins bearing the LIM domain, defined as a unique double zinc-finger structure associated with a subclass of proteins involved in the determination of cell identity, cell differentiation and control of cell growth, have previously been suggested to play an important role in the pathogenesis of atherosclerosis by others.

Amino Acid Sequence↗
PubMed2001

Screening of differentially expressed genes in 5-fluorouracil-resistant human gastrointestinal tumor cells.

To identify genes differentially expressed in association with resistance to 5-fluorouracil (5FU), an mRNA differential display (DD) analysis was used to compare transcripts from the NUGC-3 human gastric tumor cell line and the NUGC-3 / 5FU / L line, which had acquired 208-fold resistance as a consequence of repeated exposure to escalating concentrations of 5FU. The 110 cDNA fragments differentially expressed in the DD analysis of either the NUGC-3 or NUGC-3 / 5FU / L cells were sequenced and subjected to a homology search, and 29 overexpressed and 22 underexpressed genes were identified in NUGC-3 / 5FU / L as a result. To confirm whether the changes in the gene expression levels in the NUGC-3 / 5FU / L cells were shared by other 5FU-resistant cells, 35 genes were analyzed by northern hybridization in 3 pairs of parent / 5FU-resistant human gastrointestinal tumor cell lines. The analysis revealed 20 overexpressed and 10 underexpressed genes in at least one of the three 5FU-resistant cells as compared with those in the parent cells. Among them, P-glycoprotein, equilibrative nucleoside transporter 1, and methylenetetrahydrofolate dehydrogenase were highly expressed in two of the three 5FU-resistant cells and cytidine deaminase and integrin alpha3 were underexpressed. The acquisition of resistance to 5FU by tumor cells may result from multiple changes in cellular functions.

Antimetabolites, Antineoplastic↗
PubMedDate not supplied

Isolation of differentially expressed genes from contaminant exposed European flounder by suppressive, subtractive hybridisation.

Commercially farmed European flounder (Platichthys flesus) were treated with benzo[a]pyrene or cadmium under controlled laboratory conditions. In addition, animals were collected from the polluted Tyne and relatively clean Alde estuaries in the UK. Potential differentially expressed genes were isolated from liver tissue by means of suppressive, subtractive hybridisation. A total of 284 different mRNAs were identified as having the potential for being differentially expressed, of which 84 could be tentatively identified by homology with database sequences. These clones will form part of a flounder cDNA array for validation and future applications, with full identification being pursued for those expressed sequence tags for which differential expression can be confirmed by array technology.

Animals↗
PubMed2003

Differentially expressed proteins of gamma-ray irradiated mouse intestinal epithelial cells by two-dimensional electrophoresis and MALDI-TOF mass spectrometry.

AIM: To identify the differentially expressed proteins involved in ionizing radiation in mice and to explore new ways for studying radiation-related proteins. METHODS: Bal B/c mice grouped as sham-irradiation, 3 h and 72 h irradiation were exposed to 9.0 Gy single dose of gamma-irradiation. Intestinal epithelia were isolated from mice, and total proteins were extracted with urea containing solution. A series of methods were used, including two-dimensional electrophoresis, PDQuest 2-DE software analysis, peptide mass fingerprinting based on matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) and SWISS-PROT database searching, to separate and identify the differential proteins. Western blotting and RT-PCR were used to validate the differentially expressed proteins. RESULTS: Mouse intestine was severely damaged by 9.0 Gy gamma-irradiation. Image analysis of two-dimensional gels revealed that averages of 638 +/- 39, 566 +/- 32 and 591 +/- 29 protein spots were detected in 3 groups, respectively, and the majority of these protein spots were matched. About 360 protein spots were matched between normal group and 3 h irradiation group, and the correlation coefficient was 0.78 by correlation analysis of gels. Also 312 protein spots matched between normal group and 72 h irradiation group, and 282 protein spots between 3 h and 72 h irradiation groups. Twenty-eight differential protein spots were isolated from gels, digested with trypsin, and measured with MALDI-TOF-MS. A total of 25 spots yielded good spectra, and 19 spots matched known proteins after database searching. These proteins were mainly involved in anti-oxidation, metabolism, signal transduction, and protein post-translational processes. Western-blotting confirmed that enolase was up-regulated by gamma-irradiation. Up-regulation of peroxiredoxin I was verified by applying RT-PCR technique, but no change occurred in Q8VC72. CONCLUSION: These differentially expressed proteins might play important roles when mouse intestine was severely injured by gamma-irradiation. It is suggested that differential proteomic analysis may be a useful tool to study the proteins involved in radiation damage of mouse intestinal epithelia.

Animals↗
PubMed1997

[Detection of differentially expressed genes in head-neck carcinomas].

BACKGROUND: Carcinogenesis is generally considered a multistage process based on many alterations of the genetic substance. These alterations lead to many qualitative and quantitative changes in gene expression with subsequent malignant transformation of the cell. Only a few of these genetic alterations are identified yet. METHODS: The differential display reverse transcriptase polymerase chain reaction was employed to detect differentially expressed genes in head and neck cancer. The mRNA expression of cultivated keratinocytes of the upper aerodigestive tract was compared to the one of cultivated squamous cell carcinoma cells of the larynx, hypopharynx, and floor of the mouth. RESULTS: A total of 116 differentially expressed gene fragments were identified. They were either solely expressed by the malignant cells or the keratinocytes or in just one carcinoma cell entity. Forty-three of the 116 DNA fragments were sequenced successfully. In four cases the specific differential expression was confirmed by Northern blot hybridisation in comparison to keratinocytes, normal mucosa, and 3 benign tumors from the head and neck region. A gene bank search revealed in three cases a homology of less than 20% to already known human, animal, bacterial or viral gene sequences and in one case a homology of 98% with a human gene sequence. CONCLUSIONS: The detected for squamous cell carcinoma of the head and neck specific genes or gene fragments are the basis for further investigations to better understand carcinogenesis.

Carcinoma, Squamous Cell↗
PubMed2006

Genes from Chagas susceptibility loci that are differentially expressed in T. cruzi-resistant mice are candidates accounting for impaired immunity.

Variation between inbred mice of susceptibility to experimental Trypanosoma cruzi infection has frequently been described, but the immunogenetic background is poorly understood. The outcross of the susceptible parental mouse strains C57BL/6 (B6) and DBA/2 (D2), B6D2F1 (F1) mice, is highly resistant to this parasite. In the present study we show by quantitative PCR that the increase of tissue parasitism during the early phase of infection is comparable up to day 11 between susceptible B6 and resistant F1 mice. A reduction of splenic parasite burdens occurs thereafter in both strains but is comparatively retarded in susceptible mice. Splenic microarchitecture is progressively disrupted with loss of follicles and B lymphocytes in B6 mice, but not in F1 mice. By genotyping of additional backcross offspring we corroborate our earlier findings that susceptibility maps to three loci on Chromosomes 5, 13 and 17. Analysis of gene expression of spleen cells from infected B6 and F1 mice with microarrays identifies about 0.3% of transcripts that are differentially expressed. Assuming that differential susceptibility is mediated by altered gene expression, we propose that the following differentially expressed transcripts from these loci are strong candidates for the observed phenotypic variation: H2-Ealpha, H2-D1, Ng23, Msh5 and Tubb5 from Chromosome 17; and Cxcl11, Bmp2k and Spp1 from Chromosome 5. Our results indicate that innate mechanisms are not of primary relevance to resistance of F1 mice to T. cruzi infection, and that differential susceptibility to experimental infection with this protozoan pathogen is not paralleled by extensive variation of the transcriptome.

Animals↗
PubMed2002

Detection of differentially expressed genes in healing mouse corneas, using cDNA microarrays.

PURPOSE: To identify differentially expressed genes in healing mouse corneas by using cDNA microarrays. METHODS: Transepithelial excimer laser ablations were performed on mouse corneas, and the wounds were allowed to heal partially in vivo for 18 to 22 hours. Total RNA was isolated from both normal and healing corneas and was used for synthesis of cDNA probes. 33P-labeled exponential cDNA probes were hybridized to mouse cDNA nylon arrays. RESULTS: Of the 1176 genes on the nylon arrays, the expression of 37 was upregulated and that of 27 was downregulated more than fivefold in the healing corneas compared with the normal, uninjured corneas. Interleukin (IL)-1beta, laminin-5, and thrombospondin-1, which have been shown to be upregulated in healing corneas, were all found to be induced in the corneas in response to excimer laser treatment. Many genes were identified for the first time to be differentially regulated during corneal wound healing. Among the upregulated genes were intercellular adhesion molecule (ICAM)-1, macrophage inflammatory proteins, suppressors of cytokine signaling proteins (SOCS), IL-10 receptor, and galectin-7. Among the downregulated genes were connexin-31, a gap junction protein; ZO1 and occludin, tight junction proteins; and Smad2, a key component in the TGFbeta signaling pathway. Microarray data were validated on a limited number of genes by semiquantitative RT-PCR and Western blot analyses. CONCLUSIONS: Gene array technology was used to identify for the first time many genes that are differentially regulated during corneal wound healing. These differentially expressed genes have not previously been investigated in the context of wound healing and represent novel factors for further study of the mechanism of wound healing.

Animals↗
PubMed1999

Differential expression of prostaglandin endoperoxide H synthase-2 and formation of activated beta-catenin-LEF-1 transcription complex in mouse colonic epithelial cells contrasting in Apc.

Mutations in Apc underlie the intestinal lesions in familial adenomatous polyposis and are found in >85% of sporadic colon cancers. They are frequently associated with overexpression of prostaglandin endoperoxide H synthase-2 (PGHS-2) in colonic adenomas. It has been suggested that Apc mutations are linked mechanistically to increased PGHS-2 expression by elevated nuclear accumulation of beta-catenin-Tcf-LEF transcription complex. In the present study, we show that PGHS-2 is differentially expressed in mouse colonic epithelial cells with distinct Apc status. Cells with a mutated Apc expressed markedly higher levels of PGHS-2 mRNA and protein and produced significantly more prostaglandin E2 than cells with normal Apc. Using electrophoretic mobility shift assays, we demonstrate that DNA-beta-catenin-LEF-1 complex formation is differentially induced in these two cell lines in an Apc-dependent manner. Our data indicate that the differential induction of beta-catenin-LEF-1 complex correlates closely with differential expression of PGHS-2. These findings support the hypothesis that the differential expression of PGHS-2 is mediated through the proposed beta-catenin/Tcf-LEF signaling pathway.

Alleles↗
PubMed2004

[Isolation of differentially expressed cDNA sequences in human gastric carcinoma by cDNA microarray].

BACKGROUND & OBJECTIVE: Some gastric carcinoma-related genes haven't been identified yet. The study was designed to isolate and identify differentially expressed cDNA sequences in gastric carcinoma, and further clone gastric carcinoma-related genes. METHODS: The differences of gene expression profile between 30 gastric carcinoma tissues and their adjacent normal tissues were analyzed by cDNA microarray which representing about 4 892 cDNA sequences, the differentially expressed cDNA sequences were analyzed by bioinformatics, and selected cDNA sequences were confirmed by reverse transcripase-polymerase chain reaction (RT-PCR). RESULTS: A total of 33 differentially expressed cDNA sequences were identified in gastric carcinoma, among which 18 up-regulated in gastric carcinoma,while 15 down-regulated. MDSCBC11 clone,represented a novel gene, located in chromosome band 1p35-36, and significantly down-regulated in 13 of 30 (43%) gastric carcinomas. CONCLUSIONS: Some gastric carcinoma-related cDNA sequences have been identified,they might be involved in pathogenesis of gastric carcinoma. This study provides a useful clue for further clone gastric carcinoma-related genes.

Adult↗
PubMed1999

Identification of multiple, differentially expressed messenger RNAs in dermal fibroblasts from patients with systemic sclerosis.

OBJECTIVE: To simultaneously identify several genes whose expression is altered in dermal fibroblasts from patients with systemic sclerosis (SSc). METHODS: Total RNA was prepared from fibroblasts derived from clinically affected and unaffected skin of patients with SSc. The RNA samples were analyzed using differential-display reverse transcription-polymerase chain reaction (DDRT-PCR). Complementary DNA (cDNA) fragments corresponding to differentially expressed messenger RNAs (mRNAs) were eluted, cloned, and sequenced. The differential expression of the corresponding mRNAs was confirmed by ribonuclease protection assay. RESULTS: We identified 21 differentially expressed mRNAs. Their corresponding cDNAs were sequenced and the sequences obtained were compared with those of known genes entered into the EMBL/GenBank database. Three of the sequences corresponded to transcripts of yet-unidentified genes. Some of the mRNAs shared partial homology with extracellular matrix components, cellular receptors, enzymes, and nuclear factors. Others corresponded to known mRNAs such as those of fibronectin, fibronectin receptor, laminin receptor homolog, beta-tubulin, insulin-like growth factor binding protein 5, KIAA0179 protein, and protease nexin 1. CONCLUSION: The application of DDRT-PCR to scleroderma research has identified many mRNAs whose altered expression in scleroderma has not yet been described, thus providing new information for further investigation and potential targets for the development of novel therapies.

Clone Cells↗
PubMed2005

Identification by suppression subtractive hybridization of genes that are differentially expressed between near-isogenic maize lines in association with sugarcane mosaic virus resistance.

The molecular mechanisms underlying the development and progression of sugarcane mosaic virus (SCMV) infection in maize are poorly understood. A study of differential expression was conducted to identify genes involved in resistance to SCMV. In this study, we combined suppression subtractive hybridization and macroarray hybridization to identify genes that are differently expressed in the near isogenic lines F7+ (SCMV resistant) and F7 (susceptible). Altogether, 302 differentially expressed genes were identified in four comparisons based on constitutively expressed and inducible genes, and on compatible and incompatible plant-virus interactions. Apart from genes related to metabolism, most of the functionally classified genes identified belonged to three pathogenesis-related categories: cell rescue, defense, cell death and ageing, signal transduction, and transcription. The latter three groups accounted for 56-66% of the genes classified. Some 19% (60 of 302) of the identified genes had previously been assigned to 29 bins distributed over all ten maize chromosomes. Among the mapped genes, 31% (18 of 58) were located within the Scmv2 and Scmv1 regions on chromosomes 3 and 6, respectively, which have been associated with resistance to SCMV. Promising candidate genes for Scmv1 have been identified, such as AA661457 (receptor-like kinase Xa21-binding protein 3). The implications of the genomic distribution of differentially expressed genes identified by this isogenic comparison are discussed in the context of breeding for resistance.

Chromosome Mapping↗