Bioinformatic Methods for Finding Differentially Expressed Genes in cDNA Libraries, Applied to the Identification of Tumour Vascular Targets

2011 ◽  
pp. 99-119 ◽  
Author(s):  
John M. J. Herbert ◽  
Dov J. Stekel ◽  
Manuela Mura ◽  
Michail Sychev ◽  
Roy Bicknell
Keyword(s):  
Differentially Expressed Genes ◽  
Differentially Expressed ◽  
Cdna Libraries

scholarly journals De Novo Assembly and Transcriptome Profiling of Ethiopian Lowland Bamboo Oxytenanthera Abyssinica (A. rich) Munro Under Drought and Salt Stresses

2019 ◽  
Vol 13 (1) ◽  
pp. 6-17
Author(s):  
Muhamed Adem ◽  
Dereje Beyene ◽  
Tileye Feyissa ◽  
Kai Zhao ◽  
Tingbo Jiang
Keyword(s):  
Differentially Expressed Genes ◽  
De Novo ◽  
Transcriptome Profiling ◽  
Global Gene Expression ◽  
Perennial Grasses ◽  
Differentially Expressed ◽  
Cdna Libraries ◽  
Protein Families ◽  
Sequencing Platform ◽  
Genome Wide

Background: Bamboos are perennial grasses classified under family Poaceae and subfamily Bambusoideae and are among the fastest growing plants on earth. Despite ecological and economic significances, Ethiopian lowland bamboo (O. abyssinica) lacks global gene expression under abiotic stress. Methods: Plastic pot germinated seedlings of O. abyssinica were subjected to 200 µm NaCl and 25% PEG-6000 (Poly Ethylene glycol) to induce salt and drought stress, respectively. Using the Illumina sequencing platform, fifteen cDNA libraries were constructed and sequenced to generate the first drought and salt stress transcriptome profiling of the species so as to elucidate genome-wide transcriptome changes in response to such stresses. Results: Following quality control, 754,444,646 clean paired-ends reads were generated, and then de novo assembled into 406,181 unigenes. Functional annotation against the public databases presented annotation of 217,067 (53.4%) unigenes, where NCBI-Nr 203,777, Swissport 115,741, COG 81,632 and KEGG 80,587. Prediction of Transcripts Factors (TFs) have generated 4,332 TFs organized into 64 TF families. Analysis of Differentially Expressed Genes (DEGs) provided 65,471 genes where 569 genes belong to all stresses. Protein families with a higher number of differentially expressed genes include bZIP (49), WRKY (43), MYB (38), AP2/ERF (30), HD-ZIP (25) and MYB related (21). Conclusion: In addition to revealing the genome-wide level appraisal of transcriptome resources of the species, this study also uncovered the comprehensive understanding of key stress responsive protein-coding genes, protein families and pathways which could be used as the basis for further studies.

Subtraction suppressive hybridisation analysis of differentially expressed genes associated with puberty in the goat hypothalamus

2016 ◽  
Vol 28 (11) ◽  
pp. 1781 ◽  
Author(s):  
G. L. Cao ◽  
T. Feng ◽  
M. X. Chu ◽  
R. Di ◽  
Y. L. Zhang ◽  
...  
Keyword(s):  
Oxidative Phosphorylation ◽  
Differentially Expressed Genes ◽  
Matched Control ◽  
Protein Translation ◽  
Differentially Expressed ◽  
Cdna Libraries ◽  
Control Group ◽  
Group A ◽  
Subtracted Cdna Libraries ◽  
Group B

The cost of developing replacement nanny goats could be reduced by decreasing the age at puberty because this way nanny goats could be brought into production at an earlier age. The aim of the present study was to screen genes related to puberty to investigate the molecular mechanisms of puberty. Subtracted cDNA libraries were constructed for hypothalami from juvenile (Group A), pubertal (Group B) and age-matched control pubertal (Group E) Jining grey (JG) and Liaoning cashmere (LC) goats using suppression subtractive hybridisation (SSH). Differentially expressed genes were analysed by bioinformatics methods. There were 203 expressed sequence tags (ESTs) in the subtracted cDNA libraries that were differentially expressed between JG and LC goats at the juvenile stage, 226 that were differentially expressed at puberty and 183 that were differentially expressed in the age-matched control group. The differentially expressed ESTs in each subtracted cDNA library were classified as known gene, known EST and unknown EST according to sequence homology in the GenBank non-redundant (NR) and EST database. According to gene function analysis in the COG (Cluster of Orthologous Groups) database, the known genes were grouped into 10 subdivisions in Group A, into seven subdivisions in Group E and into nine subdivisions in Group B under three categories: cellular processes and signalling, information storage and processing, and metabolism. Pathway analysis in the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway database of known genes revealed that the three pathways that most differentially expressed genes were involved in were metabolic pathways, Parkinson’s disease and oxidative phosphorylation. Protein interaction analysis of the high homology genes revealed the most dominant network to be structure of ribosome/protein translation, oxidative phosphorylation and carbohydrate metabolism. The results reveal that the onset of puberty is a complex event involving multiple genes in multiple biological processes. The differentially expressed genes include genes related to both neuroendocrine and energy metabolism.

scholarly journals Identification and analysis of differentially expressed genes in immune tissues of Atlantic cod stimulated with formalin-killed, atypicalAeromonas salmonicida

2009 ◽  
Vol 37 (3) ◽  
pp. 149-163 ◽  
Author(s):  
Charles Y. Feng ◽  
Stewart C. Johnson ◽  
Tiago S. Hori ◽  
Marlies Rise ◽  
Jennifer R. Hall ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Atlantic Cod ◽  
Head Kidney ◽  
Differentially Expressed ◽  
Cdna Libraries ◽  
Bacterial Antigen ◽  
Functional Annotations ◽  
Antigen Stimulation ◽  
Bacterial Antigens ◽  
Immune Tissues

Physiological changes, elicited in animal immune tissues by exposure to pathogens, may be studied using functional genomics approaches. We created and characterized reciprocal suppression subtractive hybridization (SSH) cDNA libraries to identify differentially expressed genes in spleen and head kidney tissues of Atlantic cod ( Gadus morhua) challenged with intraperitoneal injections of formalin-killed, atypical Aeromonas salmonicida. Of 4,154 ESTs from four cDNA libraries, 10 genes with immune-relevant functional annotations were selected for QPCR studies using individual fish templates to assess biological variability. Genes confirmed by QPCR as upregulated by A. salmonicida included interleukin-1β, interleukin-8, a small inducible cytokine, interferon regulatory factor 1 (IRF1), ferritin heavy subunit, cathelicidin, and hepcidin. This study is the first large-scale discovery of bacteria-responsive genes in cod and the first to demonstrate upregulation of IRF1 in fish immune tissues as a result of bacterial antigen stimulation. Given the importance of IRF1 in vertebrate immune responses to viral and bacterial pathogens, the full-length cDNA sequence of Atlantic cod IRF1 was obtained and compared with putative orthologous sequences from other organisms. Functional annotations of assembled SSH library ESTs showed that bacterial antigen stimulation caused changes in many biological processes including chemotaxis, regulation of apoptosis, antimicrobial peptide production, and iron homeostasis. Moreover, differences in spleen and head kidney gene expression responses to the bacterial antigens pointed to a potential role for the cod spleen in blood-borne pathogen clearance. Our data show that Atlantic cod immune tissue responses to bacterial antigens are similar to those seen in other fish species and higher vertebrates.

scholarly journals 211 TEMPORAL AND SPATIAL EXPRESSION PROFILE OF THE UTERINE MILK PROTEIN — A MEMBER OF THE SERINE PROTEASE INHIBITOR SUPERFAMILY — IN THE BOVINE ENDOMETRIUM

2005 ◽  
Vol 17 (2) ◽  
pp. 256
Author(s):  
S. Bauersachs ◽  
S.E. Ulbrich ◽  
K. Gross ◽  
S. Schmidt ◽  
H. Wenigerkind ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Milk Protein ◽  
Statistical Significance ◽  
Cdna Array ◽  
Serine Proteinase ◽  
Differentially Expressed ◽  
Expression Level ◽  
Cdna Libraries ◽  
The Us ◽  
Array Hybridization

A combination of subtracted cDNA libraries and cDNA array hybridization was applied to identify differentially expressed genes in the bovine intercaruncular endometrium at estrus and diestrus. Six cyclic Simmental heifers were cycle-synchronized and slaughtered the morning after standing heat occurred (n = 3) or 12 days after estrus (n = 3), respectively. The uterus was divided into seven sections: corpus, plus the caudal, middle, and cranial parts of both uterine horns. Samples were collected from the epithelial layer of the lamina propria of the intercaruncular endometrium. Two subtracted libraries were prepared and analyzed by array hybridization with probes produced from the 42 tissue samples. More than 130 differentially expressed genes were identified. Among these genes, the mRNA for the uterine milk protein (UTMP) showed a much higher expression level at estrus versus diestrus. Furthermore, the expression level differed markedly between the uterus sections. Statistical significance was tested using ANOVA and Student Newman Keuls post-hoc test (GeneSpring® version 6.1, Silicon Genetics, Redwood City, CA, USA). There was a pronounced expression gradient from both cranial uterine horns (highest) to the corpus (lowest) at estrus. UTMP mRNA level was highest in the ipsilateral cranial horn. A more accurate quantification was done by quantitative real-time RT-PCR using the same RNA samples as for array hybridization and, in addition, samples from further time points of the estrous cycle and early pregnancy. The results obtained by array hybridization were clearly confirmed. UTMPs, also known as uterine serpins (US), were previously shown to be the major products secreted by the uteri of cattle, sheep, and pigs during pregnancy. The US are glycoproteins belonging to the serpin (serine proteinase inhibitor) superfamily of proteins. However, no inhibitory activity to any serine proteinase has been found. The ovine uterine serpin (OvUS) has been shown to inhibit a wide variety of immune responses, including mixed lymphocyte reaction, T cell-dependent antibody production, and NK (natural killer)-like activity, indicating a major role in protecting the conceptus from maternal immune reactions. The four members of the US family form a clade distinct from other serpins, which have probably adopted important biological functions in the reproductive biology of Artiodactyla. Therefore, the identified expression gradient of the UTMP mRNA at estrus may be of particular importance, e.g. for sperm selection, and deserves further investigation at the protein level and in functional studies. This work was supported by the Deutsche Forschungsgemeinschaft (Research Unit “Mechanisms of Embryo-Maternal Communication”; FOR 478/1).

scholarly journals Transcriptomic Analyses of the Hypothalamic-Pituitary-Gonadal Axis Identify Candidate Genes Related to Egg Production in Xinjiang Yili Geese

Animals ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 90
Author(s):  
Yingping Wu ◽  
Xiaoyu Zhao ◽  
Li Chen ◽  
Junhua Wang ◽  
Yuqing Duan ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Differentially Expressed Genes ◽  
Egg Production ◽  
Molecular Mechanisms ◽  
Egg Laying ◽  
Differentially Expressed ◽  
Cdna Libraries ◽  
Receptor Interaction ◽  
Sequencing Data ◽  
Pituitary Glands

The study was conducted to investigate the transcriptomic differences of the hypothalamic-pituitary-gonadal axis between Xinjiang Yili geese with high and low egg production and to find candidate genes regulating the egg production of Xinjiang Yili geese. The 8 selected Xinjiang Yili Geese with high or low egg production (4 for each group) were 3 years old, with good health, and under the same feeding condition. High-throughput sequencing technology was used to sequence cDNA libraries of the hypothalami, pituitary glands, and ovaries. The sequencing data were compared and analyzed, and the transcripts with significant differences were identified and analyzed with bioinformatics. The study showed that the transcriptome sequencing data of the 24 samples contained a total of 1,176,496,146 valid reads and 176.47 gigabase data. Differential expression analyses identified 135, 56, and 331 genes in the hypothalami, pituitary glands, and ovaries of Xinjiang Yili geese with high and low egg production. Further annotation of these differentially expressed genes in the non-redundant protein sequence database (Nr) revealed that 98, 52, and 309 genes were annotated, respectively. Through the annotations of GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) databases, 30 candidate genes related to the egg production of Xinjiang Yili geese were preliminarily selected. The gap junction, focal adhesion, and ECM-receptor interaction signaling pathways were enriched with the hypothalamic, pituitary, and ovarian differentially expressed genes, and the calcium signaling pathway was enriched with the pituitary and ovarian differentially expressed genes. Thus, these pathways in the hypothalamic-pituitary-gonadal axis may play an important role in regulating egg production of Xinjiang Yili geese. The results provided the transcriptomic information of the hypothalamic-pituitary-gonadal axis of Xinjiang Yili geese and laid the theoretical basis for revealing the molecular mechanisms regulating the egg-laying traits of Xinjiang Yili geese.

scholarly journals Discovery of differentially expressed genes in human breast cancer using subtracted cDNA libraries and cDNA microarrays

Oncogene ◽  
2002 ◽  
Vol 21 (14) ◽  
pp. 2270-2282 ◽  
Author(s):  
Yuqiu Jiang ◽  
Susan L Harlocker ◽  
David A Molesh ◽  
David C Dillon ◽  
John A Stolk ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Differentially Expressed Genes ◽  
Human Breast Cancer ◽  
Cdna Microarrays ◽  
Differentially Expressed ◽  
Cdna Libraries ◽  
Human Breast ◽  
Subtracted Cdna Libraries

scholarly journals Gonadal transcriptome sequencing of the critically endangered Acipenser dabryanus to discover candidate sex-related genes

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5389 ◽  
Author(s):  
Yeyu Chen ◽  
Ya Liu ◽  
Quan Gong ◽  
Jiansheng Lai ◽  
Mingjiang Song ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Sexual Development ◽  
Transcriptome Sequencing ◽  
Sex Differentiation ◽  
Differentially Expressed ◽  
Cdna Libraries ◽  
Nucleotide Polymorphisms ◽  
Significant Similarity ◽  
Clusters Of Orthologous Groups ◽  
History Of

Background Acipenser dabryanus, an endemic Chinese species, has been listed as a first-class protected animal in China. Sturgeons are among the oldest and most primitive group of existing fish in the world and occupy a special place in the evolutionary history of fish. Thus, a study of the reproduction and sex differentiation of sturgeon will be of great value for fish as well as the whole vertebrate group. Methods In this study, we conducted comparative analysis of the testes and ovaries transcriptomes of A. dabryanus to screen for sex-differentiation and sexual development-related genes. Results The transcriptome sequencing of six cDNA libraries generated 265 million clean reads, encompassing 79 Gb of sequences. The N50 and mean length of the identified 91,375 unigenes were 1,718 and 989 bp, respectively. A total of 6,306, 9,961, 13,170, 15,484, and 23,588 unigenes were annotated in the clusters of orthologous groups, gene ontology categories, Kyoto Encyclopedia of Genes and Genomes Pathway, euKaryotic orthologous groups, and NCBI non-redundant protein databases, respectively. A total of 5,396 differentially expressed genes were found between the two sexes, with 1,938 predicted to be up-regulated in ovaries and 3,458 in testes. A total of 73 candidate genes known to be involved in sex differentiation and sexual development were searched in the transcriptome of A. dabryanus of which 52 showed significant similarity. We highlighted six genes that are differentially expressed between the two sexes and may play important roles in sex differentiation and gonad maintenance. In addition, 24,271 simple sequence repeats (SSRs) and 550,519 single-nucleotide polymorphisms (SNPs) were detected. Discussion This work represents the first transcriptome study comparing the ovary and testis in A. dabryanus. The putative differentially expressed genes between the gonads provide an important source of information for further study of the sex-differentiation related genes and the sex-differentiation mechanism in sturgeons. The SSRs or SNPs identified in this study will be helpful in the discovery of sex-related markers in A. dabryanus.

scholarly journals Generation of Full-Length cDNA Libraries Enriched for Differentially Expressed Genes for Functional Genomics

BioTechniques ◽  
2001 ◽  
Vol 30 (3) ◽  
pp. 512-520 ◽  
Author(s):  
B. Zhumabayeva ◽  
C. Chang ◽  
J. McKinley ◽  
L. Diatchenko ◽  
P.D. Siebert
Keyword(s):  
Functional Genomics ◽  
Differentially Expressed Genes ◽  
Full Length ◽  
Differentially Expressed ◽  
Cdna Libraries ◽  
Full Length Cdna

scholarly journals Global Transcriptomic Analysis Reveals Differentially Expressed Genes Involved in Embryogenic Callus Induction in Drumstick (Moringa oleifera Lam.)

2021 ◽  
Vol 22 (22) ◽  
pp. 12130
Author(s):  
Endian Yang ◽  
Mingyang Zheng ◽  
Xuan Zou ◽  
Xiaoling Huang ◽  
Heyue Yang ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Callus Induction ◽  
Embryogenic Callus ◽  
Cell Mass ◽  
Differentially Expressed ◽  
Cdna Libraries ◽  
Auxin Signaling ◽  
Embryogenic Cell ◽  
New Genes ◽  
Embryogenic Callus Induction

The plant embryogenic callus (EC) is an irregular embryogenic cell mass with strong regenerative ability that can be used for propagation and genetic transformation. However, difficulties with EC induction have hindered the breeding of drumstick, a tree with diverse potential commercial uses. In this study, three drumstick EC cDNA libraries were sequenced using an Illumina NovaSeq 6000 system. A total of 7191 differentially expressed genes (DEGs) for embryogenic callus development were identified, of which 2325 were mapped to the KEGG database, with the categories of plant hormone signal transduction and Plant-pathogen interaction being well-represented. The results obtained suggest that auxin and cytokinin metabolism and several embryogenesis-labeled genes are involved in embryogenic callus induction. Additionally, 589 transcription factors from 20 different families were differentially expressed during EC formation. The differential expression of 16 unigenes related to auxin signaling pathways was validated experimentally by quantitative real time PCR (qRT-PCR) using samples representing three sequential developmental stages of drumstick EC, supporting their apparent involvement in drumstick EC formation. Our study provides valuable information about the molecular mechanism of EC formation and has revealed new genes involved in this process.

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