Gene Expression Programming Classifier with Concept Drift Detection Based on Fisher Exact Test

2019 ◽  
pp. 203-211 ◽  
Author(s):  
Joanna Jedrzejowicz ◽  
Piotr Jedrzejowicz
Keyword(s):  
Gene Expression ◽  
Concept Drift ◽  
Gene Expression Programming ◽  
Fisher Exact Test ◽  
Exact Test ◽  
Concept Drift Detection

Mapping cis-acting regulatory variation in recombinant congenic strains

2006 ◽  
Vol 25 (2) ◽  
pp. 294-302 ◽  
Author(s):  
Peter D. Lee ◽  
Bing Ge ◽  
Celia M. T. Greenwood ◽  
Donna Sinnett ◽  
Yannick Fortin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Fisher Exact Test ◽  
Donor Strain ◽  
Exact Test ◽  
Expression Levels ◽  
Cis Acting ◽  
Congenic Strains ◽  
Recombinant Congenic Strains ◽  
Genetic Context

We present an integrated approach for the enriched detection of genes subject to cis-acting variation in the mouse genome. Gene expression profiling was performed with lung tissue from a panel of recombinant congenic strains (RCS) derived from A/J and C57BL/6J inbred mouse strains. A multiple-regression model measuring the association between gene expression level, donor strain of origin (DSO), and predominant strain background identified over 1,500 genes ( P < 0.05) whose expression profiles differed according to the DSO. This model also identified over 1,200 genes whose expression showed dependence on background ( P < 0.05), indicating the influence of background genetic context on transcription levels. Sequences obtained from 1-kb segments of 3′-untranslated regions identified single nucleotide polymorphisms in 64% of genes whose expression levels correlated with DSO status, compared with 29% of genes that displayed no association ( P < 0.01, Fisher exact test). Allelic imbalance was identified in 50% of genes positive for expression-DSO association, compared with 22% of negative genes ( P < 0.05, Fisher exact test). Together, these results demonstrate the utility of RCS mice for identifying the roles of proximal genetic determinants and background genetic context in determining gene expression levels. We propose the use of this integrated experimental approach in multiple tissues from this and other RCS panels as a means for genome-wide cataloging of genetic regulatory mechanisms in laboratory strains of mice.

scholarly journals Whole-Genome mRNA Gene Expression Differs Between Patients With and Without Delirium

2018 ◽  
Vol 31 (4) ◽  
pp. 203-210 ◽  
Author(s):  
Katrina Kalantar ◽  
Sara C. LaHue ◽  
Joseph L. DeRisi ◽  
Hannah A. Sample ◽  
Caitlin A. Contag ◽  
...  
Keyword(s):  
Gene Expression ◽  
Messenger Rna ◽  
Transcriptional Profiling ◽  
Significant Inhibition ◽  
Unknown Etiology ◽  
Fisher Exact Test ◽  
Exact Test ◽  
Mrna Gene ◽  
Transcription Regulators ◽  
Significant Activation

Objective: To identify differences in gene expression between patients with in-hospital delirium from a known etiology (urinary tract infection [UTI]) and patients with delirium from an unknown etiology, as well as from nondelirious patients. Methods: Thirty patients with delirium (8 with UTI) and 21 nondelirious patients (11 with UTI) were included in this prospective case–control study. Transcriptomic profiles from messenger RNA sequencing of peripheral blood were analyzed for gene expression and disease-specific pathway enrichment patterns, correcting for systemic inflammatory response syndrome. Genes and pathways with significant differential activity based on Fisher exact test ( P < .05, |Z score| >2) are reported. Results: Patients with delirium with UTI, compared to patients with delirium without UTI, exhibited significant activation of interferon signaling, upstream cytokines, and transcription regulators, as well as significant inhibition of actin cytoskeleton, integrin, paxillin, glioma invasiveness signaling, and upstream growth factors. All patients with delirium, compared to nondelirious patients, had significant complement system activation. Among patients with delirium without UTI, compared to nondelirious patients without UTI, there was significant activation of elF4 and p7056 K signaling. Conclusions: Differences exist in gene expression between delirious patients due to UTI presence, as well as due to the presence of delirium alone. Transcriptional profiling may help develop etiology-specific biomarkers for patients with delirium.

Gene expression signatures in MLL-rearranged T-lineage and B-precursor acute leukemias: dominance of HOX dysregulation

Blood ◽  
2003 ◽  
Vol 102 (1) ◽  
pp. 262-268 ◽  
Author(s):  
Adolfo A. Ferrando ◽  
Scott A. Armstrong ◽  
Donna S. Neuberg ◽  
Stephen E. Sallan ◽  
Lewis B. Silverman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Hox Genes ◽  
Wilcoxon Test ◽  
Leukemic Cells ◽  
Fisher Exact Test ◽  
Leukemic Transformation ◽  
Acute Leukemias ◽  
Exact Test ◽  
Expression Of Genes ◽  
Thymocyte Differentiation

Abstract Rearrangements of the MLL locus, located on human chromosome 11q23, are frequent in both infant and therapy-related leukemias. Gene expression analysis of MLL-rearranged B-precursor acute lymphoblastic leukemias (MLL B-ALLs) has identified these cases as a unique subtype of leukemia, characterized by the expression of genes associated with both lymphoid and myeloid hematopoietic lineages. Here we show that MLL fusions also generate a distinct genetic subtype of T-lineage ALL (MLL T-ALL), in which leukemic cells are characterized by an early arrest in thymocyte differentiation, with suggestive evidence of commitment to the γδ lineage. Interestingly, multiple genes linked to cell proliferation (eg, PCNA, MYC, CDK2, and POLA) were down-regulated in MLL-fusion samples, relative to those transformed by other T-ALL oncogenes (P &lt; .000 001, Fisher exact test). Overall, MLL T-ALL cases consistently demonstrated increased levels of expression of a subset of major HOX genes—HOXA9, HOXA10, and HOXC6—and the MEIS1 HOX coregulator (P &lt; .008, one-sided Wilcoxon test), a pattern of gene expression that was reiterated in MLL B-ALLs. However, expression of myeloid lineage genes, previously reported in MLL B-ALLs, was not identified in T-lineage cases with this abnormality, suggesting that myeloid gene dysregulation is dispensable in leukemic transformation mediated by MLL fusion proteins. Our findings implicate dysregulation of HOX gene family members as a dominant mechanism of leukemic transformation induced by chimeric MLL oncogenes. (Blood. 2003;102:262-268)

Tenascin-C Is Highly Expressed in T-Cell Non-Hodgkin Lymphomas and Represents an Attractive Target for Radioimmunotherapy

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 4141-4141 ◽  
Author(s):  
Giuseppe Gritti ◽  
Andrea Gianatti ◽  
Fiorella Petronzelli ◽  
Cristina Boschini ◽  
Riccardo Rossi ◽  
...  
Keyword(s):  
Gene Expression ◽  
T Cell ◽  
Poor Prognosis ◽  
Cell Lymphoma ◽  
Large Cell ◽  
Fisher Exact Test ◽  
Chi Square ◽  
Exact Test ◽  
Tenascin C ◽  
Normal Tissues

Abstract Introduction: Tenascins are a family of large glycoproteins present in extracellular matrix, overexpressed in tumors compared to healthy tissues. Tenatumomab (ST2146) is an anti tenascin-C monoclonal antibody that is currently under development for radio immunotherapy (RIT) in tenascin-C expressing cancer. T-cell non-Hodgkin lymphomas (T-NHL) are a heterogeneous and rare group of poor prognosis malignancies lacking of standard treatments. Aim of the study was to evaluate the expression of tenascin-C in a cohort of T-NHL. Material and Methods: Under an IRB-approved protocol, 100 patients with a diagnosis of T-NHL in charge at the Hematology Unit of "Papa Giovanni XXII" Hospital were included in the study. Paraffin-embedded tumor samples were investigated using standard immunohistochemistry (IHC) for tenascin-C expression using tenatumomab antibody. Slides were assessed by two independent investigators. Staining was scored using the four different levels "no staining", "weak", "moderate" and "strong" (0-3). A grading system was used to express the proportion of involved areas in each case, as follows: 0 (0% to 25%), 1 (26% to 50%), 2 (51% to 75%), 3 (76% to 100%). Pattern of expression (stromal, vascular and/or cytoplasmic) was as well recorded. Tenascin C gene expression data were extracted from publicly available datasets. Association among variables was assessed with Chi square or Fisher exact test. Results:Of the 100 patients evaluated, 75 cases were peripheral T-NHL (PTCL) and 25 cutaneous T-NHL (CTCL). Specific diagnosis was, anaplastic large cell lymphoma (ALCL) ALK negative (n=21) or positive (n=19), PTCL-not otherwise specified (NOS, n=20), mycosis fungoides (n=13), angioimmunoblastic T-cell lymphoma (AITL, n=9), CD30+ primary cutaneous T-NHL (n=6) and other subtypes (n=12). Tenatumomab revealed the expression of tenascin-C in all the patients, with a staining that was weak, moderate and strong in 21, 51 and 28 of the cases. There was no significant different distribution among histologies (P=0.334). A high (>50%, grade 2-3) proportion of involved areas in pathologic samples were shown in half of the patients and this proportion was higher in ALCL ALK- (81%), AITL (78%) and ALCL ALK+ (58%) while was lower for PTCL NOS (30%) and CTCL (24%) (P=0.0019). A stromal pattern of expression was present in all the cases, vasculature was stained in 47 patients while in 21 tenascin-C was as well cytoplasmic. Vascular pattern was revealed in 56% of PTCL and 20% of CTCL (P=0.0018). To further evaluate the presence of tenascin C in T-NHL, gene expression datasets from published reports were retrieved and expression values of tenascin-C gene were extracted. Significant overexpression was present in T-NHL compared to normal tissues in both of the two considered datasets (Piccaluga et al., 2007 and Iqbal et al., 2010). Conclusions: Tenatumomab revealedthat tenascin-C is uniformly present in T-NHL with a high proportion of cases showing a strong and diffuse expression. Thus, tenascin-C represent an attractive target for RIT in this category of poor prognosis rare diseases. Disclosures Petronzelli: Sigma Tau S.p.A: Employment.

Concept drift detection based on Fisher’s Exact test

2018 ◽  
Vol 442-443 ◽  
pp. 220-234 ◽  
Author(s):  
Danilo Rafael de Lima Cabral ◽  
Roberto Souto Maior de Barros
Keyword(s):  
Concept Drift ◽  
Exact Test ◽  
Fisher's Exact Test ◽  
Fisher’S Exact Test ◽  
Concept Drift Detection

Venous Thromboembolism and High Grade Gliomas

1993 ◽  
Vol 70 (03) ◽  
pp. 393-396 ◽  
Author(s):  
Mandeep S Dhami ◽  
Robert D Bona ◽  
John A Calogero ◽  
Richard M Hellman
Keyword(s):  
Risk Factors ◽  
Venous Thromboembolism ◽  
Medical Center ◽  
Significant Risk ◽  
Bleeding Complications ◽  
Fisher Exact Test ◽  
High Grade ◽  
Chi Square ◽  
Exact Test ◽  
High Grade Gliomas

SummaryA retrospective study was done to determine the incidence of and the risk factors predisposing to clinical venous thromboembolism (VTE) in patients treated for high grade gliomas. Medical records of 68 consecutive patients diagnosed and treated at Saint Francis Hospital and Medical Center from January 1986 to June 1991 were reviewed. The follow up was to time of death or at least 6 months (up to December 1991). All clinically suspected episodes of VTE were confirmed by objective tests. Sixteen episodes of VTE were detected in 13 patients for an overall episode rate of 23.5%. Administration of chemotherapy (p = 0.027, two tailed Fisher exact test) and presence of paresis (p = 0.031, two tailed Fisher exact test) were statistically significant risk factors for the development of VTE. Thrombotic events were more likely to occur in the paretic limb and this difference was statistically significant (p = 0.00049, chi square test, with Yates correction). No major bleeding complications were seen in the nine episodes treated with long term anticoagulation.We conclude that venous thromboembolic complications are frequently encountered in patients being treated for high grade gliomas and the presence of paresis and the administration of chemotherapy increases the risk of such complications.

Electronic cigarettes: How confident and effective are allergists, pulmonologists, and primary care physicians in their practice behavior?

2020 ◽  
Vol 41 (3) ◽  
pp. 192-197
Author(s):  
Sherry S. Zhou ◽  
Alan P. Baptist
Keyword(s):  
Primary Care ◽  
Primary Care Physicians ◽  
Electronic Cigarettes ◽  
The United States ◽  
Fisher Exact Test ◽  
Exact Test ◽  
Knowledge And Beliefs ◽  
Tobacco Cigarette ◽  
Number Of Patients ◽  
Personal Use

Background: There has been a striking increase in electronic cigarette (EC) use in the United States. The beliefs and practices toward ECs among physicians are unknown. Objective: The purpose of this study was to investigate EC practice patterns among allergists, pulmonologists, and primary care physicians. Methods: An anonymous survey was sent to physicians. The survey contained 32 questions and addressed issues related to demographics, cessation counseling behaviors, personal use, and knowledge and beliefs about ECs. Statistical analysis was performed by using analysis of variance, the Pearson χ2 test, Fisher exact test, and logistic regression. Results: A total of 291 physicians completed the survey (222 primary care physicians, 33 pulmonologists, and 36 allergists) for a response rate of 46%. The allergists asked about tobacco cigarette use as frequently as did the pulmonologists and more than the primary care physicians (p < 0.001), but they rarely asked about EC use. The pulmonologists scored highest on self-reported knowledge on ECs, although all the groups answered <40% of the questions correctly. The allergists did not feel as comfortable about providing EC cessation counseling as did the pulmonologists and primary care physicians (p < 0.001). All three groups were equally unlikely to recommend ECs as a cessation tool for tobacco cigarette users. Conclusion: Allergists lacked knowledge and confidence in providing education and cessation counseling for EC users. As the number of patients who use these products continues to increase, there is an urgent need for all physicians to be comfortable and knowledgeable with counseling about ECs.

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