Differentially expressed genes in preimplantation human embryos: potential candidate genes for blastocyst formation and implantation

Muscle tissue is involved with every stage of life activities and has roles in biological processes. For example, the blood circulation system needs the heart muscle to transport blood to all parts, and the movement cannot be separated from the participation of skeletal muscle. However, the process of muscle development and the regulatory mechanisms of muscle development are not clear at present. In this study, we used bioinformatics techniques to identify differentially expressed genes specifically expressed in multiple muscle tissues of mice as potential candidate genes for studying the regulatory mechanisms of muscle development. Mouse tissue microarray data from 18 tissue samples was selected from the GEO database for analysis. Muscle tissue as the treatment group, and the other 17 tissues as the control group. Genes expressed in the muscle tissue were different to those in the other 17 tissues and identified 272 differential genes with highly specific expression in muscle tissue, including 260 up-regulated genes and 12 down regulated genes. is the genes were associated with the myofibril, contractile fibers, and sarcomere, cytoskeletal protein binding, and actin binding. KEGG pathway analysis showed that the differentially expressed genes in muscle tissue were mainly concentrated in pathways for AMPK signaling, cGMP PKG signaling calcium signaling, glycolysis, and, arginine and proline metabolism. A PPI protein interaction network was constructed for the selected differential genes, and the MCODE module used for modular analysis. Five modules with Score > 3.0 are selected. Then the Cytoscape software was used to analyze the tissue specificity of differential genes, and the genes with high degree scores collected, and some common genes selected for quantitative PCR verification. The conclusion is that we have screened the differentially expressed gene set specific to mouse muscle to provide potential candidate genes for the study of the important mechanisms of muscle development.

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Network-based analysis of differentially expressed genes in cerebrospinal fluid (CSF) and blood reveals new candidate genes for multiple sclerosis

PeerJ ◽

10.7717/peerj.2775 ◽

2016 ◽

Vol 4 ◽

pp. e2775 ◽

Cited By ~ 15

Author(s):

Nahid Safari-Alighiarloo ◽

Mostafa Rezaei-Tavirani ◽

Mohammad Taghizadeh ◽

Seyyed Mohammad Tabatabaei ◽

Saeed Namaki

Keyword(s):

Multiple Sclerosis ◽

Cerebrospinal Fluid ◽

Candidate Genes ◽

Differentially Expressed Genes ◽

Expression Profiles ◽

Biological Pathways ◽

Differentially Expressed ◽

Potential Candidate ◽

Functional Modules ◽

Ppi Networks

BackgroundThe involvement of multiple genes and missing heritability, which are dominant in complex diseases such as multiple sclerosis (MS), entail using network biology to better elucidate their molecular basis and genetic factors. We therefore aimed to integrate interactome (protein–protein interaction (PPI)) and transcriptomes data to construct and analyze PPI networks for MS disease.MethodsGene expression profiles in paired cerebrospinal fluid (CSF) and peripheral blood mononuclear cells (PBMCs) samples from MS patients, sampled in relapse or remission and controls, were analyzed. Differentially expressed genes which determined only in CSF (MSvs.control) and PBMCs (relapsevs.remission) separately integrated with PPI data to construct the Query-Query PPI (QQPPI) networks. The networks were further analyzed to investigate more central genes, functional modules and complexes involved in MS progression.ResultsThe networks were analyzed and high centrality genes were identified. Exploration of functional modules and complexes showed that the majority of high centrality genes incorporated in biological pathways driving MS pathogenesis. Proteasome and spliceosome were also noticeable in enriched pathways in PBMCs (relapsevs.remission) which were identified by both modularity and clique analyses. Finally, STK4, RB1, CDKN1A, CDK1, RAC1, EZH2, SDCBP genes in CSF (MSvs.control) and CDC37, MAP3K3, MYC genes in PBMCs (relapsevs.remission) were identified as potential candidate genes for MS, which were the more central genes involved in biological pathways.DiscussionThis study showed that network-based analysis could explicate the complex interplay between biological processes underlying MS. Furthermore, an experimental validation of candidate genes can lead to identification of potential therapeutic targets.

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Screening and identification of muscle-specific candidate genes via mouse microarray data analysis

10.1101/2021.08.11.456020 ◽

2021 ◽

Author(s):

Sayed Haidar Abbas Raza ◽

Chengcheng Liang ◽

Wang Guohua ◽

Linsen Zan

Keyword(s):

Candidate Genes ◽

Differentially Expressed Genes ◽

Muscle Tissue ◽

Microarray Data ◽

Muscle Development ◽

The Other ◽

Differentially Expressed ◽

Regulatory Mechanisms ◽

Potential Candidate ◽

Differential Genes

Muscle tissue is involved with every stage of life activities and has roles in biological processes. For example, the blood circulation system needs the heart muscle to transport blood to all parts, and the movement cannot be separated from the participation of skeletal muscle. However, the process of muscle development and the regulatory mechanisms of muscle development are not clear at present. In this study, we used bioinformatics techniques to identify differentially expressed genes specifically expressed in multiple muscle tissues of mice as potential candidate genes for studying the regulatory mechanisms of muscle development. Mouse tissue microarray data from 17 tissue samples was selected from the GEO database for analysis. Muscle tissue as the treatment group, and the other 16 tissues as the control group. Genes expressed in the muscle tissue were different to those in the other 16 tissues and identified 272 differential genes with highly specific expression in muscle tissue, including 260 up-regulated genes and 12 down regulated genes. is the genes were associated with the myofibril, contractile fibers, and sarcomere, cytoskeletal protein binding, and actin binding. KEGG pathway analysis showed that the differentially expressed genes in muscle tissue were mainly concentrated in pathways for AMPK signaling, cGMP PKG signaling calcium signaling, glycolysis, and, arginine and proline metabolism. A PPI protein interaction network was constructed for the selected differential genes, and the MCODE module used for modular analysis. Five modules with Score > 3.0 are selected. Then the Cytoscape software was used to analyze the tissue specificity of differential genes, and the genes with high degree scores collected, and some common genes selected for quantitative PCR verification. The conclusion is that we have screened the differentially expressed gene set specific to mouse muscle to provide potential candidate genes for the study of the important mechanisms of muscle development.

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Analysis of Differentially Expressed Genes and Signaling Pathways Related to Intramuscular Fat Deposition in Skeletal Muscle of Sex-Linked Dwarf Chickens

BioMed Research International ◽

10.1155/2014/724274 ◽

2014 ◽

Vol 2014 ◽

pp. 1-7 ◽

Cited By ~ 3

Author(s):

Yaqiong Ye ◽

Shumao Lin ◽

Heping Mu ◽

Xiaohong Tang ◽

Yangdan Ou ◽

...

Keyword(s):

Gene Expression ◽

Skeletal Muscle ◽

Signaling Pathways ◽

Candidate Genes ◽

Differentially Expressed Genes ◽

Molecular Mechanisms ◽

Muscle Development ◽

Intramuscular Fat ◽

Differentially Expressed ◽

Potential Candidate

Intramuscular fat (IMF) plays an important role in meat quality. However, the molecular mechanisms underlying IMF deposition in skeletal muscle have not been addressed for the sex-linked dwarf (SLD) chicken. In this study, potential candidate genes and signaling pathways related to IMF deposition in chicken leg muscle tissue were characterized using gene expression profiling of both 7-week-old SLD and normal chickens. A total of 173 differentially expressed genes (DEGs) were identified between the two breeds. Subsequently, 6 DEGs related to lipid metabolism or muscle development were verified in each breed based on gene ontology (GO) analysis. In addition, KEGG pathway analysis of DEGs indicated that some of them (GHR, SOCS3, and IGF2BP3) participate in adipocytokine and insulin signaling pathways. To investigate the role of the above signaling pathways in IMF deposition, the gene expression of pathway factors and other downstream genes were measured by using qRT-PCR and Western blot analyses. Collectively, the results identified potential candidate genes related to IMF deposition and suggested that IMF deposition in skeletal muscle of SLD chicken is regulated partially by pathways of adipocytokine and insulin and other downstream signaling pathways (TGF-β/SMAD3 and Wnt/catenin-βpathway).

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Identifying Candidate Genes for Hypoxia Adaptation of Tibet Chicken Embryos by Selection Signature Analyses and RNA Sequencing

Genes ◽

10.3390/genes11070823 ◽

2020 ◽

Vol 11 (7) ◽

pp. 823

Author(s):

Xiayi Liu ◽

Xiaochen Wang ◽

Jing Liu ◽

Xiangyu Wang ◽

Haigang Bao

Keyword(s):

Candidate Genes ◽

Rna Sequencing ◽

Differentially Expressed Genes ◽

Gallus Gallus ◽

Differentially Expressed ◽

Tibet Plateau ◽

Embryonic Liver ◽

Selection Signature ◽

Chicken Embryos ◽

Hypoxia Adaptation

The Tibet chicken (Gallus gallus) lives on the Qinghai–Tibet Plateau and adapts to the hypoxic environment very well. The objectives of this study was to obtain candidate genes associated with hypoxia adaptation in the Tibet chicken embryos. In the present study, we used the fixation index (Fst) and cross population extended haplotype homozygosity (XPEHH) statistical methods to detect signatures of positive selection of the Tibet chicken, and analyzed the RNA sequencing data from the embryonic liver and heart with HISAT, StringTie and Ballgown for differentially expressed genes between the Tibet chicken and White leghorn (Gallus gallus, a kind of lowland chicken) embryos hatched under hypoxia condition. Genes which were screened out by both selection signature analysis and RNA sequencing analysis could be regarded as candidate genes for hypoxia adaptation of chicken embryos. We screened out 1772 genes by XPEHH and 601 genes by Fst, and obtained 384 and 353 differentially expressed genes in embryonic liver and heart, respectively. Among these genes, 89 genes were considered as candidate genes for hypoxia adaptation in chicken embryos. ARNT, AHR, GSTK1 and FGFR1 could be considered the most important candidate genes. Our findings provide references to elucidate the molecular mechanism of hypoxia adaptation in Tibet chicken embryos.

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Identification and characterization of differentially expressed genes in Caenorhabditis elegans in response to pathogenic and nonpathogenic Stenotrophomonas maltophilia

10.21203/rs.2.14106/v2 ◽

2019 ◽

Author(s):

Leah J Radeke ◽

Michael Herman

Keyword(s):

Candidate Genes ◽

Differentially Expressed Genes ◽

Stenotrophomonas Maltophilia ◽

Defense Mechanisms ◽

Virulent Strain ◽

Differentially Expressed ◽

Transcriptional Responses ◽

Transcriptomic Response ◽

C Elegans ◽

Realistic Interaction

Abstract Background: Stenotrophomonas maltophilia is an emerging nosocomial pathogen that causes infection in immunocompromised patients. S. maltophilia isolates are genetically diverse, contain diverse virulence factors, and are variably pathogenic within several host species. Members of the Stenotrophomonas genus are part of the native microbiome of C. elegans , being found in greater relative abundance within the worm than its environment, suggesting that these bacteria accumulate within C. elegans . Thus, study of the C. elegans-Stenotrophomonas interaction is of both medical and ecological significance. To identify host defense mechanisms, we analyzed the C. elegans transcriptomic response to S. maltophilia strains of varying pathogenicity: K279a, an avirulent clinical isolate, JCMS, a virulent strain isolated in association with soil nematodes near Manhattan, KS, and JV3, an even more virulent environmental isolate. Results: Overall, we found 145 genes that are commonly differentially expressed in response to pathogenic S. maltophilia strains, 89% of which are upregulated, with many even further upregulated in response to JV3 as compared to JCMS. There are many more JV3-specific differentially expressed genes (225, 11% upregulated) than JCMS-specific differentially expressed genes (14, 86% upregulated), suggesting JV3 has unique pathogenic mechanisms that could explain its increased virulence. We used connectivity within a gene network model to choose pathogen-specific and strain-specific differentially expressed candidate genes for functional analysis. Mutations in 13 of 22 candidate genes caused significant differences in C. elegans survival in response to at least one S. maltophilia strain, although not always the strain that induced differential expression, suggesting a dynamic response to varying levels of pathogenicity. Conclusions: Variation in observed pathogenicity and differences in host transcriptional responses to S. maltophilia strains reveal that strain-specific mechanisms play important roles in S. maltophilia pathogenesis. Furthermore, utilizing bacteria closely related to strains found in C. elegans natural environment provides a more realistic interaction for understanding host-pathogen response.

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Peer Review #2 of "Network-based analysis of differentially expressed genes in cerebrospinal fluid (CSF) and blood reveals new candidate genes for multiple sclerosis (v0.1)"

10.7287/peerj.2775v0.1/reviews/2 ◽

2016 ◽

Keyword(s):

Multiple Sclerosis ◽

Cerebrospinal Fluid ◽

Peer Review ◽

Candidate Genes ◽

Differentially Expressed Genes ◽

Differentially Expressed

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Trascriptome Analysis of Bone Marrow CD14+ Monocytes Revealed Differential Expression Profiles in Symptomatic Multiple Myeloma (MM) Compared to Smoldering MM and Monoclonal Gammopathy of Undetermined Significance

Blood ◽

10.1182/blood.v120.21.1811.1811 ◽

2012 ◽

Vol 120 (21) ◽

pp. 1811-1811

Author(s):

Marco Peronaci ◽

Paola Storti ◽

Domenica Ronchetti ◽

Luca Agnelli ◽

Marina Bolzoni ◽

...

Keyword(s):

Multiple Myeloma ◽

Bone Marrow ◽

Differentially Expressed Genes ◽

Monoclonal Gammopathy ◽

Conflicts Of Interest ◽

Expression Profiles ◽

Differentially Expressed ◽

Potential Candidate ◽

Molecular Alterations ◽

Potential Candidate Gene

Abstract Abstract 1811 Symptomatic multiple myeloma (MM), smoldering MM (SMM) and monoclonal gammopathy of uncertain significance (MGUS) are well known different pathological and clinical entities of plasma cell (PC) disorders. Nevertheless molecular studies performed on clonal CD138+ PC do not clear distinguished these disorders that share common alterations. Studies focusing on the presence of potential molecular alterations in the microenvironment cells are ongoing. Because monocytes are the cells primarily involved in osteoclastogenesis, angiogenesis and immune system disfuction, that are the hallmark of symptomatic MM compared to SMM and MGUS, in this study we have analyzed the transcriptional profile of the bone marrow (BM) CD14+ cells in these settings of patients. BM CD14+ monocytes were purified from a total cohort of 36 patients with PC disorders including 21 patients with symptomatic MM, 8 patients with SMM and 7 patients with MGUS. CD14+ cells were isolated from the CD138 negative fraction of BM samples of patients by immunomagnetic method with anti-CD14 monoclonal antibody conjugated with microbeads. The presence of potential haemopoietic and CD138+ contaminating cells was excluded by FACS analysis. Only samples with CD14 purity greater than 95% were analyzed by microarrays by GeneChip® HG-U133Plus 2.0 arrays (Affymetrix®) (13 MM, 8 SMM and 7 MGUS). Data obtained were then validated on selected genes by Real-Time quantitative PCR. A multiclass analysis identified 14 differentially expressed genes, which characterized MGUS vs SMM vs symptomatic MM. A supervised analysis between symptomatic MM vs. SMM and MGUS samples identified 101 genes differentially expressed in CD14+ (58 genes up-regulated in MM vs SMM and MGUS and 43 genes donwregulated). Interestingly, among the differentially expressed genes we found that cytokines and cytokine receptors (IL21, IL21R, IL15, IL15R), chemokines (CXCL10, CXCL11) and interferon-inducible proteins (IFI27, IFI44) were up-regulated in CD14+ of MM patients as compared to SMM and MGUS. A supervised analysis between MM and MGUS identified 6 differentially expressed genes in CD14+ whereas 37 genes distinguished MM and SMM patients. Notably the SLAMF7 (CS1) gene recently indentified as a therapeutic target in CD138+ MM cells was up-regulated in CD14+ monocytes of MM patients as compared either to MGUS alone or to MGUS plus SMM could be a potential candidate gene. Overall our preliminary results indicate that a different transcriptional fingerprint may be identified in BM CD14+ cells of patients with symptomatic MM as compared to those with indolent PC disorders such as SMM and MGUS with a greater number of differentially expressed genes between symptomatic MM and SMM patient rather than between MM and MGUS. Disclosures: No relevant conflicts of interest to declare.

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Integrated metabolomic and transcriptomic analysis of the anthocyanin regulatory networks in Salvia miltiorrhiza Bge. flowers

10.21203/rs.3.rs-25292/v1 ◽

2020 ◽

Author(s):

Tao Jiang ◽

Meide Zhang ◽

Chunxiu Wen ◽

Xiaoliang Xie ◽

Wei Tian ◽

...

Keyword(s):

Candidate Genes ◽

Differentially Expressed Genes ◽

Regulatory Networks ◽

Anthocyanin Biosynthesis ◽

Salvia Miltiorrhiza ◽

Flower Color ◽

Differentially Expressed ◽

Integrated Analysis ◽

Anthocyanin Content ◽

Transcriptomics Data

Abstract Background: The study objectives were to reveal the anthocyanin biosynthesis metabolic pathway in white and purple flowers of Salvia miltiorrhiza using metabolomics and transcriptomics, to identify different anthocyanin metabolites, and to analyze the differentially expressed genes involved in anthocyanin biosynthesis . Results: We analyzed the metabolomics and transcriptomics data of Salvia miltiorrhiza flowers. A total of 1994 differentially expressed genes and 84 flavonoid metabolites were identified between the white and purple flowers of Salvia miltiorrhiza . Integrated analysis of transcriptomic and metabolomics showed that cyanidin 3,5-O-diglucoside, malvidin 3,5-diglucoside, and cyanidin 3-O-galactoside were mainly responsible for the purple flower color of Salvia miltiorrhiza. A total of 100 unigenes encoding 10 enzymes were identified as candidate genes involved in anthocyanin biosynthesis in Salvia miltiorrhiza flowers. The low expression of the ANS gene decreased the anthocyanin content but enhanced the accumulation of flavonoids in Salvia miltiorrhiza flowers. Conclusions: Our results provide valuable information on the anthocyanin metabolites and the candidate genes involved in the anthocyanin biosynthesis pathways in Salvia miltiorrhiza .

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Analysis of BMP15-Induced Transcriptome in Human Granulosa Cells for the Identification of Novel Candidate Genes for Primary Ovarian Insufficiency

Journal of the Endocrine Society ◽

10.1210/jendso/bvab048.1553 ◽

2021 ◽

Vol 5 (Supplement_1) ◽

pp. A763-A764

Author(s):

Raffaella Rossetti ◽

Marco Fornili ◽

Silvia Moleri ◽

Ilaria Ferrari ◽

Davide Gentilini ◽

...

Keyword(s):

Candidate Genes ◽

Differentially Expressed Genes ◽

Granulosa Cells ◽

Transcriptome Analysis ◽

Primary Ovarian Insufficiency ◽

Differentially Expressed ◽

Incomplete Penetrance ◽

Sequencing Analysis ◽

Ovarian Insufficiency ◽

Human Granulosa Cells

Abstract Primary Ovarian Insufficiency (POI) is a female fertility disorder which affects 1% of women before 40 years of age and manifests with amenorrhea, elevation of serum gonadotrophins and low estrogens. POI has a strong genetic component with incomplete penetrance. Several candidate genes have been described so far, however, its etiopathogenesis is mostly unknown. In order to discover the POI-related causative mechanisms, microarray transcriptome analysis in human granulosa cells (hGCs) stimulated with recombinant human BMP15 (rhBMP15) and next generation sequencing analysis (NGS) on the identified differentially expressed genes in a selected group of patients with POI were conducted on NGS Illumina platform. In the present study, we obtained 19 differentially expressed genes upon rhBMP15 stimulation in hGCs. Results: showed that all identified genes were upregulated and associated to pluripotency, inhibition of apoptosis, cell proliferation, BMP signaling and apoptosis. Moreover, we identified nine POI patients bearing six rare variants in 5 of the BMP15-induced genes (SAMD11, SMAD6, ID1, USP35, GPCR137C). The BMP15-induced transcriptome analysis in hGCs contributed the understanding of BMP15 role as transcriptional regulator, through the activation of transcriptional repressors, by inducing pathways inhibiting the ovarian follicle maturation, thus possibly maintaining an undifferentiated state of hGCs. These findings lead to the identification of novel candidate genes for POI.

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