De novo Transcriptome Reveals Gene Changes in the Development of the Endosperm Chalazal Haustorium in Taxillus chinensis (DC.) Danser

Loranthus (Taxillus chinensis) is a facultative, hemiparasite and stem parasitic plant that attacks other plants for living. Transcriptome sequencing and bioinformatics analysis were applied in this study to identify the gene expression profiles of fresh seeds (CK), baby (FB), and adult haustoria tissues (FD). We assembled 160,571 loranthus genes, of which 64,926, 35,417, and 47,249 were aligned to NR, GO, and KEGG pathway databases, respectively. We identified 14,295, 15,921, and 16,402 genes in CK, FB, and FD, respectively. We next identified 5,480 differentially expressed genes (DEGs) in the process, of which 258, 174, 81, and 94 were encoding ribosomal proteins (RP), transcription factors (TF), ubiquitin, and disease resistance proteins, respectively. Some DEGs were identified to be upregulated along with the haustoria development (e.g., 68 RP and 26 ubiquitin genes). Notably, 36 RP DEGs peak at FB; 10 ER, 5 WRKY, 6 bHLH, and 4 MYB TF genes upregulated only in FD. Further, we identified 4 out of 32 microRNA genes dysregulated in the loranthus haustoria development. This is the first haustoria transcriptome of loranthus, and our findings will improve our understanding of the molecular mechanism of haustoria.

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Non‑small-cell lung cancer pathological subtype‑related gene selection and bioinformatics analysis based on gene expression profiles

Molecular and Clinical Oncology ◽

10.3892/mco.2017.1516 ◽

2017 ◽

Cited By ~ 1

Author(s):

Jiangpeng Chen ◽

Xiaoqi Dong ◽

Xun Lei ◽

Yinyin Xia ◽

Qing Zeng ◽

...

Keyword(s):

Gene Expression ◽

Lung Cancer ◽

Gene Selection ◽

Bioinformatics Analysis ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Small Cell ◽

Related Gene ◽

Small Cell Lung ◽

Pathological Subtype

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Why Polyphenols have Promiscuous Actions? An Investigation by Chemical Bioinformatics

Natural Product Communications ◽

10.1177/1934578x1601100525 ◽

2016 ◽

Vol 11 (5) ◽

pp. 1934578X1601100

Author(s):

Guang-Yan Tang

Keyword(s):

Redox Potential ◽

Bioinformatics Analysis ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Critical Factor ◽

Structural Features ◽

Molecular Structures ◽

Pharmacological Effects ◽

Protein Targets ◽

Structure Activity

Despite their diverse pharmacological effects, polyphenols are poor for use as drugs, which have been traditionally ascribed to their low bioavailability. However, Baell and co-workers recently proposed that the redox potential of polyphenols also plays an important role in this, because redox reactions bring promiscuous actions on various protein targets and thus produce non-specific pharmacological effects. To investigate whether the redox reactivity behaves as a critical factor in polyphenol promiscuity, we performed a chemical bioinformatics analysis on the structure-activity relationships of twenty polyphenols. It was found that the gene expression profiles of human cell lines induced by polyphenols were not correlated with the presence or not of redox moieties in the polyphenols, but significantly correlated with their molecular structures. Therefore, it is concluded that the promiscuous actions of polyphenols are likely to result from their inherent structural features rather than their redox potential.

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De Novo Transcriptome Study Identifies Candidate Genes Involved in Resistance to Austropuccinia psidii (Myrtle Rust) in Syzygium luehmannii (Riberry)

Phytopathology ◽

10.1094/phyto-09-17-0298-r ◽

2018 ◽

Vol 108 (5) ◽

pp. 627-640 ◽

Cited By ~ 5

Author(s):

Peri A. Tobias ◽

David I. Guest ◽

Carsten Külheim ◽

Robert F. Park

Keyword(s):

De Novo ◽

Expression Profiles ◽

Interleukin 1 ◽

Gene Expression Profiles ◽

Early Gene ◽

De Novo Transcriptome ◽

Myrtle Rust ◽

Wide Range ◽

The Family ◽

Austropuccinia Psidii

Austropuccinia psidii, causal agent of myrtle rust, was discovered in Australia in 2010 and has since become established on a wide range of species within the family Myrtaceae. Syzygium luehmannii, endemic to Australia, is an increasingly valuable berry crop. Plants were screened for responses to A. psidii inoculation, and specific resistance, in the form of localized necrosis, was determined in 29% of individuals. To understand the molecular basis underlying this response, mRNA was sequenced from leaf samples taken preinoculation, and at 24 and 48 h postinoculation, from four resistant and four susceptible plants. Analyses, based on de novo transcriptome assemblies for all plants, identified significant expression changes in resistant plants (438 transcripts) 48 h after pathogen exposure compared with susceptible plants (three transcripts). Most significantly up-regulated in resistant plants were gene homologs for transcription factors, receptor-like kinases, and enzymes involved in secondary metabolite pathways. A putative G-type lectin receptor-like kinase was exclusively expressed in resistant individuals and two transcripts incorporating toll/interleukin-1, nucleotide binding site, and leucine-rich repeat domains were up-regulated in resistant plants. The results of this study provide the first early gene expression profiles for a plant of the family Myrtaceae in response to the myrtle rust pathogen.

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Gene Expression Profiles in Acute Myeloid Leukemia (AML): From Diagnosis to Prognosis.

Blood ◽

10.1182/blood.v106.11.2996.2996 ◽

2005 ◽

Vol 106 (11) ◽

pp. 2996-2996

Author(s):

Sanggyu Lee ◽

Jianjun Chen ◽

Goulin Zhou ◽

Run Shi ◽

Masha Kocherginsky ◽

...

Keyword(s):

Gene Expression ◽

De Novo ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Major Change ◽

Molecular Signature ◽

Human Leukemia ◽

Prognostic Information ◽

Myeloid Progenitor Cells ◽

Novel Transcripts

Abstract Chromosome translocations are among the most common genetic abnormalities in human leukemia. The abnormally expressed genes from each translocation can be used to identify specific markers for clinical diagnosis of each translocation. Microarrays have identified genes differentially expressed in different translocations but the results between laboratories are not always compatible. We used SAGE to quantitate gene expression in bone marrow(BM) samples from 22 patients with four types of AML, [de novo AML M2 with t(8;21), AML M3 or M3V with t(15;17), AML M4Eo with inv(16), AML M5 with t(9;11) or secondary t(9;11)].We made SAGE libraries from CD15+ leukemic myeloid progenitor cells, collecting over 106 SAGE tags, of which 209,486 were unique tags; 136,010 were known genes and ESTs, and 73,476 were novel transcripts. SAGE tags for further analysis were selected based on a 5-fold difference between patient’s samples and normal CD15+ BM; they were also statistically significantly different at the 5% level. Using these strict criteria, we identified 2,381 unique tags, of which 2,053 were known genes and ESTs, and 328 were novel transcripts that were either specific for each translocation or were common(55) SAGE tags for all 4 translocations. The major change in all translocations was a decrease in expression in leukemia cells compared with normal cells; the decrease was least in the t(8;21) cells. Changes in expression of these known genes, which fall into different gene ontology functional categories, varied by translocation. Those associated with macromolecular biosynthesis, transport and transcription were most altered in the t(8;21); those related to defense response and apoptosis were altered in the t(15;17); cell proliferation genes were most affected by the t(9;11). From this analysis, we identified the functional molecular signature of each translocation. We designed a custom microarray to validate our SAGE data analysis. Our initial microarray contained 349 probes including 212 known genes, 61 ESTs, 28 novel sequences based on our data and 48 genes reported by others. We have now included 65 additional probes that appeared to be correlated with survival. Using 63 samples with the four translocations [16 inv(16), 4 t(9;11), 20 t(15;17), 4 t(8;21) and 19 other translocations], we are validating which genes provide a robust, reproducible “fingerprint” for each translocation, for all translocations, and which ones provide reliable information related to prognosis and survival. Our results will provide new insights into genes that collaborate with each translocation to lead to a fully leukemic phenotype as well as which genes appear to provide valid prognostic information.

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Gammaherpesvirus Lytic Gene Expression as Characterized by DNA Array

Journal of Virology ◽

10.1128/jvi.76.12.6244-6256.2002 ◽

2002 ◽

Vol 76 (12) ◽

pp. 6244-6256 ◽

Cited By ~ 46

Author(s):

Joo Wook Ahn ◽

Kenneth L. Powell ◽

Paul Kellam ◽

Dagmar G. Alber

Keyword(s):

Gene Expression ◽

De Novo ◽

Expression Profiles ◽

Cdna Array ◽

Gene Expression Profiles ◽

Hierarchical Cluster ◽

Murine Gammaherpesvirus ◽

Transcription Profiles ◽

A Genome

ABSTRACT Gammaherpesviruses are associated with a number of diseases including lymphomas and other malignancies. Murine gammaherpesvirus 68 (MHV-68) constitutes the most amenable animal model for this family of pathogens. However experimental characterization of gammaherpesvirus gene expression, at either the protein or RNA level, lags behind that of other, better-studied alpha- and beta-herpesviruses. We have developed a cDNA array to globally characterize MHV-68 gene expression profiles, thus providing an experimental supplement to a genome that is chiefly annotated by homology. Viral genes started to be transcribed as early as 3 h postinfection (p.i.), and this was followed by a rapid escalation of gene expression that could be seen at 5 h p.i. Individual genes showed their own transcription profiles, and most genes were still being expressed at 18 h p.i. Open reading frames (ORFs) M3 (chemokine-binding protein), 52, and M9 (capsid protein) were particularly noticeable due to their very high levels of expression. Hierarchical cluster analysis of transcription profiles revealed four main groups of genes and allowed functional predictions to be made by comparing expression profiles of uncharacterized genes to those of genes of known function. Each gene was also categorized according to kinetic class by blocking de novo protein synthesis and viral DNA replication in vitro. One gene, ORF 73, was found to be expressed with α-kinetics, 30 genes were found to be expressed with β-kinetics, and 42 genes were found to be expressed with γ-kinetics. This fundamental characterization furthers the development of this model and provides an experimental basis for continued investigation of gammaherpesvirus pathology.

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Gene expression profiles and bioinformatics analysis of human umbilical vein endothelial cells exposed to PM 2.5

Chemosphere ◽

10.1016/j.chemosphere.2017.05.153 ◽

2017 ◽

Vol 183 ◽

pp. 589-598 ◽

Cited By ~ 7

Author(s):

Hejing Hu ◽

Collins Otieno Asweto ◽

Jing Wu ◽

Yanfeng Shi ◽

Lin Feng ◽

...

Keyword(s):

Gene Expression ◽

Endothelial Cells ◽

Bioinformatics Analysis ◽

Umbilical Vein ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Human Umbilical Vein ◽

Pm 2.5 ◽

Umbilical Vein Endothelial Cells

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De novo characterization of the Lycium ruthenicum transcriptome and analysis of its digital gene expression profiles during fruit development and ripening

Archives of Biological Sciences ◽

10.2298/abs160123125p ◽

2017 ◽

Vol 69 (1) ◽

pp. 181-190 ◽

Cited By ~ 1

Author(s):

Yong Peng ◽

Huiqin Ma ◽

Shangwu Chen

Keyword(s):

Gene Expression ◽

Developmental Stages ◽

De Novo ◽

Expression Profiles ◽

Expression Patterns ◽

Gene Expression Profiles ◽

Digital Gene Expression ◽

Orthologous Group ◽

Functional Studies ◽

Lycium Ruthenicum

Lycium ruthenicum Murr., which belongs to the family Solanaceae, is a resource plant for Chinese traditional medicine and nutraceutical foods. In this study, RNA sequencing was applied to obtain raw reads of L. ruthenicum fruit at different stages of ripening, and a de novo assembly of its sequence was performed. Approximately 52.45 million 100-bp paired-end raw reads were generated from the samples by deep RNA-seq analysis. These short reads were assembled to obtain 164814 contigs, and the contigs were assembled into 84968 non-redundant unigenes using the Trinity method. Assembled sequences were annotated with gene descriptions, gene ontology, clusters of orthologous group and KEGG (Kyoto Encyclopedia of Genes and Genomes)pathway terms. Digital gene expression analysis was applied to compare gene-expression patterns at different fruit developmental stages. These results contribute to existing sequence resources for Lycium spp. during the fruit-ripening stages, which is valuable for further functional studies of genes involved in L. ruthenicum fruit nutraceutical quality.

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Comprehensive Clinical and Molecular Characterization of KRASG12C-Mutant Colorectal Cancer

JCO Precision Oncology ◽

10.1200/po.20.00256 ◽

2021 ◽

pp. 613-621

Author(s):

Jason T. Henry ◽

Oluwadara Coker ◽

Saikat Chowdhury ◽

John Paul Shen ◽

Van K. Morris ◽

...

Keyword(s):

Colorectal Cancer ◽

Clinical Trials ◽

De Novo ◽

Expression Profiles ◽

Single Gene ◽

Gene Expression Profiles ◽

Progression Free Survival ◽

Cancer Center ◽

Data Set ◽

External Data

PURPOSE KRAS p.G12C mutations occur in approximately 3% of metastatic colorectal cancers (mCRC). Recently, two allosteric inhibitors of KRAS p.G12C have demonstrated activity in early phase clinical trials. There are no robust studies examining the behavior of this newly targetable population. METHODS We queried the MD Anderson Cancer Center data set for patients with colorectal cancer who harbored KRAS p.G12C mutations between January 2003 and September 2019. Patients were analyzed for clinical characteristics, overall survival (OS), and progression-free survival (PFS) and compared against KRAS nonG12C. Next, we analyzed several internal and external data sets to assess immune signatures, gene expression profiles, hypermethylation, co-occurring mutations, and proteomics. RESULTS Among the 4,632 patients with comprehensive molecular profiling, 134 (2.9%) were found to have KRAS p.G12C mutations. An additional 53 patients with single gene sequencing were included in clinical data but excluded from prevalence analysis allowing for 187 total patients. Sixty-five patients had de novo metastatic disease and received a median of two lines of chemotherapy without surgical intervention. For the first three lines of chemotherapy, the median PFS was 6.4 months (n = 65; 95% CI, 5.0 to 7.4 months), 3.9 months (n = 47; 95% CI, 2.9 to 5.9 months), and 3.0 months (n = 21; 95% CI, 2.0 to 3.4 months), respectively. KRAS p.G12C demonstrated higher rates of basal EGFR activation compared with KRAS nonG12C. When compared with an internal cohort of KRAS nonG12C, KRAS p.G12C patients had worse OS. CONCLUSION PFS is poor for patients with KRAS p.G12C metastatic colorectal cancer. OS was worse in KRAS p.G12C compared with KRAS nonG12C patients. Our data highlight the innate resistance to chemotherapy for KRAS p.G12C patients and serve as a historical comparator for future clinical trials.

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