Functional Annotation Clustering Research Articles

In Silico Prediction of the Anti-Depression Mechanism of a Herbal Formula (Tiansi Liquid) Containing Morinda officinalis and Cuscuta chinensis.

Purpose: Depression is a sickening psychiatric condition that is prevalent worldwide. To manage depression, the underlying modes of antidepressant effect of herbals are important to be explored for the development of natural drugs. Tiansi Liquid is a traditional Chinese medicine (TCM) that is prescribed for the management of depression, however its underlying mechanism of action is still uncertain. The purpose of this study was to systematically investigate the pharmacological mode of action of a herbal formula used in TCM for the treatment of depression. Methods: Based on literature search, an ingredients-targets database was developed for Tiansi Liquid, followed by the identification of targets related to depression. The interaction between these targets was evaluated on the basis of protein-protein interaction network constructed by STITCH and gene ontology (GO) enrichment analysis using ClueGO plugin. Results: As a result of literature search, 57 components in Tiansi Liquid formula and 106 potential targets of these ingredients were retrieved. A careful screening of these targets led to the identification of 42 potential targets associated with depression. Ultimately, 327 GO terms were found by analysis of gene functional annotation clusters and abundance value of these targets. Most of these terms were found to be closely related to depression. A significant number of protein targets such as IL10, MAPK1, PTGS2, AKT1, APOE, PPARA, MAPK1, MIF, NOS3 and TNF-α were found to be involved in the functioning of Tiansi Liquid against depression. Conclusions: The findings elaborate that Tiansi Liquid can be utilized to manage depression, however, multiple molecular mechanisms of action could be proposed for this effect. The observed core mechanisms could be the sensory perception of pain, regulation of lipid transport and lipopolysaccharide-mediated signaling pathway.

Manganese-Induced Neurotoxicity and Alterations in Gene Expression in Human Neuroblastoma SH-SY5Y Cells.

Manganese (Mn) is an essential trace element required for many physiological functions including proper biochemical and cellular functioning of the central nervous system (CNS). However, exposure to excess level of Mn through occupational settings or from environmental sources has been associated with neurotoxicity. The cellular and molecular mechanism of Mn-induced neurotoxicity remains unclear. In the current study, we investigated the effects of 30-day exposure to a sub-lethal concentration of Mn (100μM) in human neuroblastoma cells (SH-SY5Y) using transcriptomic approach. Microarray analysis revealed differential expression of 1057 transcripts in Mn-exposed SH-SY5Y cells as compared to control cells. Gene functional annotation cluster analysis exhibited that the differentially expressed genes were associated with several biological pathways. Specifically, genes involved in neuronal pathways including neuron differentiation and development, regulation of neurogenesis, synaptic transmission, and neuronal cell death (apoptosis) were found to be significantly altered. KEGG pathway analysis showed upregulation of p53 signaling pathways and neuroactive ligand-receptor interaction pathways, and downregulation of neurotrophin signaling pathway. On the basis of the gene expression profile, possible molecular mechanisms underlying Mn-induced neuronal toxicity were predicted.

Exploring evidence of positive selection signatures in cattle breeds selected for different traits.

Since domestication, the genome landscape of cattle has been changing due to natural and artificial selection forces resulting in several general and specialized cattle breeds of the world. Identifying genomic regions affected due to these forces in livestock gives an insight into the history of selection for economically important traits and genetic adaptation to specific environments of the populations under consideration. This study explores the genes/genomic regions under selection in relation to the phenotypes of Holstein, Hanwoo, and N'Dama cattle breeds using Tajima's D, XP-CLR, and XP-EHH population statistical methods. The whole genomes of 10 Holstein (South Korea), 11 Hanwoo (South Korea), and 10 N'Dama (West Africa-Guinea) cattle breeds re-sequenced to ~11x coverage and retained 37million SNPs were used for the study. Selection signature analysis revealed 441, 512, and 461 genes under selection from Holstein, Hanwoo, and N'Dama cattle breeds, respectively. Among all these, seven genes including ARFGAP3, SNORA70, and other RNA genes were common between the breeds. From each of the gene lists, significant functional annotation cluster terms including milk protein and thyroid hormone signaling pathway (Holstein), histone acetyltransferase activity (Hanwoo), and renin secretion (N'Dama) were enriched. Genes that are related to the phenotypes of the respective breeds were also identified. Moreover, significant breed-specific missense variants were identified in CSN3, PAPPA2 (Holstein), C1orf116 (Hanwoo), and COMMD1 (N'Dama) genes. The genes identified from this study provide an insight into the biological mechanisms and pathways that are important in cattle breeds selected for different traits of economic significance.

Structure and functional impact of seed region variant in MIR-499 gene family in bronchial asthma

BackgroundSmall non-coding RNAs (microRNAs) have been evolved to master numerous cellular processes. Genetic variants within microRNA seed region might influence microRNA biogenesis and function. The study aimed at determining the role of microRNA-499 (MIR-499) gene family polymorphism as a marker for susceptibility and progression of bronchial asthma and to analyze the structural and functional impact of rs3746444 within the seed region.MethodsGenotyping for 192 participants (96 patients and 96 controls) in the discovery phase and 319 subjects (115 patients and 204 controls) in the replication phase was performed via Real Time-Polymerase Chain Reaction technology. Patients underwent the methacholine challenge test and biochemical analysis. Gene structural and functional analysis, target prediction, annotation clustering, and pathway enrichment analysis were executed. Predicted functional effect of rs37464443 SNP was analyzed.ResultsmiR-499 gene family is highly implicated in inflammation-related signaling pathways. Rs374644 (A > G) in MIR499A and MIR499B within the seed region could disrupt target genes and create new genes. The G variant was associated with high risk of developing asthma under all genetic association models (G versus A: OR = 3.27, 95% CI = 2.53–4.22; GG versus AA: OR = 9.52, 95% CI = 5.61–16.5; AG versus AA: OR = 2.13, 95% CI = 1.24–3.46; GG + AG versus AA: OR = 4.43, 95% CI = 2.88–6.82). GG genotype was associated with poor pre-bronchodilator FEV1 (p = 0.047) and the worst bronchodilator response after Salbutamol inhalation, represented in low peaked expiratory flow rate (p = 0.035).ConclusionsmiR-499 rs3746444 (A > G) polymorphism was associated with asthma susceptibility and bronchodilator response in Egyptian children and adolescents. Further functional analysis is warranted to develop more specific theranostic agents for selecting targeted therapy.

Mapping the STK4/Hippo signaling network in prostate cancer cell.

Dysregulation of MST1/STK4, a key kinase component of the Hippo-YAP pathway, is linked to the etiology of many cancers with poor prognosis. However, how STK4 restricts the emergence of aggressive cancer remains elusive. Here, we investigated the effects of STK4, primarily localized in the cytoplasm, lipid raft, and nucleus, on cell growth and gene expression in aggressive prostate cancer. We demonstrated that lipid raft and nuclear STK4 had superior suppressive effects on cell growth in vitro and in vivo compared with cytoplasmic STK4. Using RNA sequencing and bioinformatics analysis, we identified several differentially expressed (DE) genes that responded to ectopic STK4 in all three subcellular compartments. We noted that the number of DE genes observed in lipid raft and nuclear STK4 cells were much greater than cytoplasmic STK4. Our functional annotation clustering showed that these DE genes were commonly associated with oncogenic pathways such as AR, PI3K/AKT, BMP/SMAD, GPCR, WNT, and RAS as well as unique pathways such as JAK/STAT, which emerged only in nuclear STK4 cells. These findings indicate that MST1/STK4/Hippo signaling restricts aggressive tumor cell growth by intersecting with multiple molecular pathways, suggesting that targeting of the STK4/Hippo pathway may have important therapeutic implications for cancer.

A system-level mechanistic investigation of traditional Chinese medicine, Yinlai Decoction, for related diseases

Purpose: To systemically explore the pharmacological mechanisms of traditional Chinese medicine, Yinlai Decoction (YD), used in the clinical management of pediatric diseases such as pneumonia and recurrent respiratory tract infections.Methods: An ingredient-target-disease database of YD was constructed using Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP). First, the molecular targets related to lung and stomach diseases were searched and screened to avoid duplication. Second, the associations between these molecular targets were evaluated via Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) and Gene Ontology (GO) and Pathway enrichment analysis in STRING.Results: A total of 627 chemical ingredients and 654 protein targets in YD were obtained. After further screening, 38 molecular targets linked to respiratory diseases, inflammatory responses and various infections were identified. Finally, 576 GO terms and 75 KEGG pathway terms were obtained by analyzing gene functional annotation clusters and abundance value of these targets. Most of these terms were closely related to the inflammatory response.Conclusion: Based on these in silico findings, the use of YD for treating respiratory diseases, inflammation and various infections, most probably via the suppression of inflammation, has been established. The approach adopted in this study can serve as a model methodology to develop an innovative TCM candidate drug at a network pharmacology level.Keywords: Yinlai Decoction, Network (System) pharmacology, Inflammation, Interacting genes/proteins, Gene ocntology, Pathway enrichment analysis

A large scale Plasmodium vivax- Saimiri boliviensis trophozoite-schizont transition proteome.

Plasmodium vivax is a complex protozoan parasite with over 6,500 genes and stage-specific differential expression. Much of the unique biology of this pathogen remains unknown, including how it modifies and restructures the host reticulocyte. Using a recently published P. vivax reference genome, we report the proteome from two biological replicates of infected Saimiri boliviensis host reticulocytes undergoing transition from the late trophozoite to early schizont stages. Using five database search engines, we identified a total of 2000 P. vivax and 3487 S. boliviensis proteins, making this the most comprehensive P. vivax proteome to date. PlasmoDB GO-term enrichment analysis of proteins identified at least twice by a search engine highlighted core metabolic processes and molecular functions such as glycolysis, translation and protein folding, cell components such as ribosomes, proteasomes and the Golgi apparatus, and a number of vesicle and trafficking related clusters. Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.8 enriched functional annotation clusters of S. boliviensis proteins highlighted vesicle and trafficking-related clusters, elements of the cytoskeleton, oxidative processes and response to oxidative stress, macromolecular complexes such as the proteasome and ribosome, metabolism, translation, and cell death. Host and parasite proteins potentially involved in cell adhesion were also identified. Over 25% of the P. vivax proteins have no functional annotation; this group includes 45 VIR members of the large PIR family. A number of host and pathogen proteins contained highly oxidized or nitrated residues, extending prior trophozoite-enriched stage observations from S. boliviensis infections, and supporting the possibility of oxidative stress in relation to the disease. This proteome significantly expands the size and complexity of the known P. vivax and Saimiri host iRBC proteomes, and provides in-depth data that will be valuable for ongoing research on this parasite’s biology and pathogenesis.

Differences of RNA Expression in the Tendon According to Anatomic Outcomes in Rotator Cuff Repair

Background: Despite increased understanding of the pathophysiology of rotator cuff tears and the evolution of rotator cuff repair, healing failure remains a substantial problem. The critical roles played by biological factors have been emphasized, but little is known of the implications of gene expression profile differences at the time of repair. Purpose: To document the relationship between the perioperative gene expression of healed and unhealed rotator cuffs by RNA microarray analysis. Study Design: Case-control study; Level of evidence, 3. Methods: Superior (supraspinatus involvement) and posterosuperior (supraspinatus and infraspinatus involvement) tears were included in the study. Samples of rotator cuff tendons were prospectively collected during rotator cuff surgery. Three samples were harvested at the tendon ends of tears from the anterior, middle (apex), and posterior parts using an arthroscopic punch. Seven patients with an unhealed rotator cuff were matched one-to-one with patients with a healed rotator cuff by sex, age, tear size, and fatty degeneration of rotator cuff muscles. mRNA microarray analysis was used to identify genetic differences between healed and unhealed rotator cuff tendons. Gene ontology and gene association files were obtained from the Gene Ontology Consortium, and the Gene Ontology system in DAVID was used to identify enhanced biological processes. Results: Microarray analyses identified 262 genes that were differentially expressed by at least 1.5-fold between the healed and unhealed groups. Overall, in the healed group, 103 genes were significantly downregulated, and 159 were significantly upregulated. DAVID Functional Annotation Cluster analysis showed that in the healed group, the genes most upregulated were related to the G protein–coupled receptor protein signaling pathway and to the neurological system. On the other hand, the genes most downregulated were related to immune and inflammatory responses. BMP5 was the gene most upregulated in the healed group, and the majority of downregulated genes were involved in the immune/inflammatory response. Conclusion: The downregulation of inflammatory response genes and the upregulation of cell differentiation genes in torn rotator cuffs at the time of surgery are related to rotator cuff healing. These results provide useful baseline information for future biological studies on rotator cuff healing.

130 The convergence and divergence of molecular pathways in lv hypertrophy defined by ecg voltage versus lv mass in patients with aortic stenosis

BackgroundLeft ventricular hypertrophy (LVH) assessment by ECG voltage or image based mass volume is commonly used in clinical practice and research. Our previous study of LVH regression after AVR for...

128 Genomic insights of ecg strain patten in aortic stenosis: t wave inversion and st-segment depression are underlined by different molecular pathways

BackgroundECG strain pattern is frequently presented in AS patients as a marker of LV hypertrophy and is emerging as one of the predictors for AVR. Our previous study had demonstrated...

Altered erythropoiesis and decreased number of erythrocytes in children with neuroblastoma.

Neuroblastoma (NB) is a pediatric tumor presenting at diagnosis either as localized or metastatic disease, which mainly involves the bone marrow (BM). The physical occupancy of BM space by metastatic NB cells has been held responsible for impairment of BM function. Here, we investigated whether localized or metastatic NB may alter hematopoietic lineages’ maturation and release of mature cells in the periphery, through gene expression profiling, analysis of BM smears, cell blood count and flow cytometry analysis.Gene ontology and disease-associated analysis of the genes significantly under-expressed in BM resident cells from children with localized and metastatic NB, as compared to healthy children, indicated anemia, blood group antigens, and heme and porphyrin biosynthesis as major functional annotation clusters. Accordingly, in children with NB there was a selective impairment of erythrocyte maturation at the ortho-chromic stage that resulted in reduced erythrocyte count in the periphery, regardless of the presence of metastatic cells in the BM. By considering all NB patients, low erythrocyte count at diagnosis associated with worse survival. Moreover, in the subset of metastatic patients, low erythrocyte count, hemoglobin and hematocrit and high red cell distribution width at follow-up also associated with worse outcome.These observations provide an alternative model to the tenet that infiltrating cells inhibit BM functions due to physical occupancy of space and may open a new area of research in NB to understand the mechanism(s) responsible for such selective impairment.

Exploring the Genetic Resistance to Gastrointestinal Nematodes Infection in Goat Using RNA-Sequencing.

Gastrointestinal nematodes (GINs) are one of the most economically important parasites of small ruminants and a major animal health concern in many regions of the world. However, the molecular mechanisms of the host response to GIN infections in goat are still little known. In this study, two genetically distinct goat populations, one relatively resistant and the other susceptible to GIN infections, were identified in Yichang goat and then four individuals in each group were chosen to compare mRNA expression profiles using RNA-seq. Field experiment showed lower worm burden, delayed and reduced egg production in the relatively resistant group than the susceptible group. The analysis of RNA-seq showed that 2369 genes, 1407 of which were up-regulated and 962 down-regulated, were significantly (p < 0.001) differentially expressed between these two groups. Functional annotation of the 298 genes more highly expressed in the resistant group yielded a total of 46 significant (p < 0.05) functional annotation clusters including 31 genes (9 in innate immunity, 13 in immunity, and 9 in innate immune response) related to immune biosynthetic process as well as transforming growth factor (TGF)-β, mitogen-activated protein kinase (MAPK), and cell adhesion molecules (CAMs) pathways. Our findings provide insights that are immediately relevant for the improvement of host resistance to GIN infections and which will make it possible to know the mechanisms underlying the resistance of goats to GIN infections.

Hyperglycaemic memory affects the neurovascular unit of the retina in a diabetic mouse model.

The aim of this study was to evaluate damage to the neurovascular unit in a mouse model of hyperglycaemic memory. A streptozotocin-induced mouse model of diabetes (C57BL/6J background) received insulin-releasing pellets and pancreatic islet-cell transplantation. Damage to the neurovascular unit was studied by quantitative retinal morphometry for microvascular changes and microarray analysis, with subsequent functional annotation clustering, for changes of the retinal genome. Sustained microvascular damage was confirmed by persistent loss of pericytes in the retinal vasculature (PC/mm2): compared with healthy controls (1981±404 PC/mm2), the pericyte coverage of the retinal vasculature was significantly reduced in diabetic mice (1571±383 PC/mm2, p<0.001) and transplanted mice (1606±268 PC/mm2, p<0.001). Genes meeting the criteria for hyperglycaemic memory were attributed to the cytoskeletal and nuclear cell compartments of the neurovascular unit. The most prominent regulated genes in the cytoskeletal compartment were Ddx51, Fgd4, Pdlim7, Utp23, Cep57, Csrp3, Eml5, Fhl3, Map1a, Mapk1ip1, Mnda, Neil2, Parp2, Myl12b, Dynll1, Stag3 and Sntg2, and in the nuclear compartment were Ddx51, Utp23, Mnda, Kmt2e, Nr6a1, Parp2, Cdk8, Srsf1 and Zfp326. We demonstrated that changes in gene expression and microvascular damage persist after euglycaemic re-entry, indicating memory. The datasets generated during and/or analysed during the current study are available in the GEO repository, GSE87433, www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=idmbysgctluxviv&acc=GSE87433 .

Immunoproteomic identification and characterization of Ni2+-regulated proteins implicates Ni2+ in the induction of monocyte cell death

Nickel allergy is the most common cause of allergic reactions worldwide, with cutaneous and systemic effects potentially affecting multiple organs. Monocytes are precursors of not only macrophages but also dendritic cells, the most potent activators of nickel hypersensitivity. Monocytes are themselves important antigen-presenting cells, capable of nickel-specific T-cell activation in vivo and in vitro, in addition to being important for immediate innate immune inflammation. To elucidate early Ni2+-dependent inflammatory molecular mechanisms in human monocytes, a Ni2+-specific proteomic approach was applied. Quantitative two-dimensional (2D) differential gel electrophoresis and Delta2D software analyses coupled with matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) revealed that Ni2+ significantly regulated 56 protein species, of which 36 were analyzed by MALDI-MS. Bioinformatics analyses of all identified proteins resulted in Ni2+-associated functional annotation clusters, such as cell death, metal ion binding, and cytoskeletal remodeling. The involvement of Ni2+ in the induction of monocyte cell death, but not T-cell death, was observed at Ni2+ concentrations at or above 250 μM. Examination of caspase activity during Ni2+-mediated cell death revealed monocytic cell death independent of caspase-3 and -7 activity. However, confocal microscopy analysis demonstrated Ni2+-triggered cytoskeletal remodeling and nuclear condensation, characteristic of cellular apoptosis. Thus, Ni2+-specific peripheral blood mononuclear cell stimulation suggests monocytic cell death at Ni2+ concentrations at or above 250 μM, and monocytic effects on immune regulation at lower Ni2+ concentrations.

Multilocus genetic analysis implicates neurodevelopment and immune system in the etiology of schizophrenia

Schizophrenia is a severe psychiatric disorder of poorly understood etiology, characterized by high heritability, multifactorial inheritance and high heterogeneity. Multilocus associaton methods may reduce the genetic heterogeneity and improve the probability of replication between analyses. The aims of our study were twofold: 1. To analyse genetic risk factors of schizophrenia by using multilocus genetic tests. 2. To assess the replication probability attributable to the various multilocus tests. Subjects - Discovery set: case-parent trios of unaffected parents and affected probands with a DSM-IV schizophrenia diagnosis (n=16); replication set: schizophrenia cases and unaffected controls (n=5337). Associations of single nucleotide and indel markers were transferred to gene- and geneset-based associations, furthermore to geneset-enrichment tests and functional annotation cluster analyses in a two-staged designs. Associations with p<0.1 from the discovery set were tested in the replication sample. Familywise p-value correction for multiple comparisons were performed during the replication step. After correction for multiplicity, no significant association or enrichment were detected for gene-based nor canonical pathway analyses, but significant association of the 14q31 cytoband and enrichments of the 5q31 and Xq13 cytobands were found (p_corr: 0.002, 0.006 and 0.048, respectively). Functional annotation clustering yielded statistically significant enrichment scores for clusters of splicing/alternative splicing, neurodevelopment and embryonic development. Improvements in replication probability were found with increased test complexity (P_rep: 0, 0.015, 0.21). Our results corroborate the involvement of neurodevelopment, synaptic plasticity and immune mechanisms in the etiology of schizophrenia. Also, our findings indicated improvement of replication probability by using multilocus genetic analyses.

Microarray Analysis of microRNAs Expression Profiles in Adult and Aged Mice Hippocampus

Purpose: To analyze the miRNA expression profiles in C57 mice ageing hippocampus in detail, and investigate the functional information of these hippocampus specific miRNAs and the related regulatory networks. Methods: Microarrays were used to analyze miRNA expression profiles in adult and aged hippocampi, and bioinformatics analysis methods, such as three public datasets (Mirbase, Miranda, and Mirdb), DAVID online tools and KEGG pathway tools were used to study in detail the target genes of the differentially expressed miRNAs. Results: 26 differentially expressed miRNAs were identified by greater than 1.5-fold change (intersection of two sets), of which 16 were up-regulated and 10 were down-regulated. DAVID Functional Annotation Cluster (FAC) analysis of the 132 predicted target genes of up-regulated miRNAs revealed confident enrichment scores for synaptic function and apoptosis etc. (Figure 1), indicating the functional significance and importance of these miRNAs during hippocampal ageing. Conclusions: Bioinformatic analyses of the differentially expressed miRNAs have identified a number of miRNAs with putative involvement in the hippocampus ageing process. This study lays a solid foundation for further studies to clarify the important regulation function of miRNAs in ageing process of brain tissue.

MiR-124 Promotes Newborn Olfactory Bulb Neuron Dendritic Morphogenesis and Spine Density.

Using microarray analysis, we detected microRNA-124 (miR-124) to be abundantly expressed in the olfactory bulb (OB). miR-124 regulates adult neurogenesis in the subventricular zone (SVZ). However, much less is known about its role in newborn OB neurons. Here, using both gain-of-function and loss-of-function approaches, we demonstrate that brain-specific miR-124 affects dendritic morphogenesis and spine density in newborn OB neurons. Functional Annotation Clustering of miR-124 targets was enriched in "cell morphogenesis involved in neuron differentiation."

Association of MITF loci with coat color spotting patterns in Ethiopian cattle

The genetics of coat color have been the focus of investigation for decades because beyond its aesthetic values, coat color is associated with thermo-tolerance, production and health traits. Despite the fascinating coat color phenotypes observed in Ethiopian cattle populations, up to now, there are no studies performed to identify and characterize polymorphisms associated with such variation at the genome level. In an attempt to identify and map the genetic basis of coat color variation in Ethiopian cattle, a genome-wide association study (GWAS), selection signatures test and network analysis were performed in 187 cattle populations genotyped on Illumina high-density chip. Loci significant at the genome-wide level (P ≤ 8.29 × 10−7) and show selection signals (F ST − 5SNP window = 0.13) were mainly localized on BTA22 (31.53–31.99) within the MITF gene. Network and functional annotation clustering analyses revealed that the candidate genes are involved in important pathways including melanogenesis. The results of the present study suggest a role of the MITF gene and its interaction with other genes in determining the spotting patterns observed in the Begait and Fogera cattle populations.

Integrative analysis for identification of shared markers from various functional cells/tissues for rheumatoid arthritis.

Rheumatoid arthritis (RA) is a systemic autoimmune disease. So far, it is unclear whether there exist common RA-related genes shared in different tissues/cells. In this study, we conducted an integrative analysis on multiple datasets to identify potential shared genes that are significant in multiple tissues/cells for RA. Seven microarray gene expression datasets representing various RA-related tissues/cells were downloaded from the Gene Expression Omnibus (GEO). Statistical analyses, testing both marginal and joint effects, were conducted to identify significant genes shared in various samples. Followed-up analyses were conducted on functional annotation clustering analysis, protein-protein interaction (PPI) analysis, gene-based association analysis, and ELISA validation analysis in in-house samples. We identified 18 shared significant genes, which were mainly involved in the immune response and chemokine signaling pathway. Among the 18 genes, eight genes (PPBP, PF4, HLA-F, S100A8, RNASEH2A, P2RY6, JAG2, and PCBP1) interact with known RA genes. Two genes (HLA-F and PCBP1) are significant in gene-based association analysis (P=1.03E-31, P=1.30E-2, respectively). Additionally, PCBP1 also showed differential protein expression levels in in-house case-control plasma samples (P=2.60E-2). This study represented the first effort to identify shared RA markers from different functional cells or tissues. The results suggested that one of the shared genes, i.e., PCBP1, is a promising biomarker for RA.

Analysis of protein profiling studies of β-thalassemia/Hb E disease.

A number of studies have used global protein profiling technologies on a range of patient samples to detect proteins that are differentially expressed in β-thalassemia/Hb E as an aid for understanding the physiopathology of this disease. Seven studies have identified a total of 111 unique, differentially expressed proteins. Seven proteins (prothrombin, alpha-1-antichymotrypsin, fibrinogen beta chain, hemoglobin beta, selenium-binding protein, microtubule-actin cross-linking factor and adenomatous polyposis coli protein 2) have been identified in two independent studies, whereas two proteins (carbonic anhydrase 1 and peroxiredoxin-2) have been identified in three independent studies. Both of these latter two proteins were consistently upregulated in the studies that identified them. Ontological analysis of all differentially regulated proteins identified "response to inorganic substances" as the most significant functional annotation cluster, which is consistent with iron overload being a major pathological consequence of this disease. Despite the range of samples investigated and the relatively small number of studies undertaken, a coherent picture of the mediators of the pathological consequences of β-thalassemia/Hb E disease is starting to emerge.