Analysis of Four Types of Leukemia Using Gene Ontology Term and Kyoto Encyclopedia of Genes and Genomes Pathway Enrichment Scores

2020 ◽  
Vol 23 (4) ◽  
pp. 295-303
Author(s):  
Jing Lu ◽  
YuHang Zhang ◽  
ShaoPeng Wang ◽  
Yi Bi ◽  
Tao Huang ◽  
...  
Keyword(s):  
Gene Ontology ◽  
Lymphoblastic Leukemia ◽  
Feature Selection Method ◽  
Lymphocytic Leukemia ◽  
Myelogenous Leukemia ◽  
Ontology Term ◽  
Kegg Pathways ◽  
Different Types ◽  
First Time ◽  
Go Terms

Aim and Objective: Leukemia is the second common blood cancer after lymphoma, and its incidence rate has an increasing trend in recent years. Leukemia can be classified into four types: acute lymphoblastic leukemia (ALL), acute myeloid leukemia (AML), chronic lymphocytic leukemia (CLL), and chronic myelogenous leukemia (CML). More than forty drugs are applicable to different types of leukemia based on the discrepant pathogenesis. Therefore, the identification of specific drug-targeted biological processes and pathways is helpful to determinate the underlying pathogenesis among such four types of leukemia. Methods: In this study, the gene ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways that were highly related to drugs for leukemia were investigated for the first time. The enrichment scores for associated GO terms and KEGG pathways were calculated to evaluate the drugs and leukemia. The feature selection method, minimum redundancy maximum relevance (mRMR), was used to analyze and identify important GO terms and KEGG pathways. Results: Twenty Go terms and two KEGG pathways with high scores have all been confirmed to effectively distinguish four types of leukemia. Conclusion: This analysis may provide a useful tool for the discrepant pathogenesis and drug design of different types of leukemia.

scholarly journals Analysis of Important Gene Ontology Terms and Biological Pathways Related to Pancreatic Cancer

2016 ◽  
Vol 2016 ◽  
pp. 1-10 ◽  
Author(s):  
Hang Yin ◽  
ShaoPeng Wang ◽  
Yu-Hang Zhang ◽  
Yu-Dong Cai ◽  
Hailin Liu
Keyword(s):  
Pancreatic Cancer ◽  
Gene Ontology ◽  
Feature Selection Method ◽  
Selection Method ◽  
Biological Processes ◽  
Kegg Pathways ◽  
Extensive Analysis ◽  
The World ◽  
Serious Disease ◽  
Go Terms

Pancreatic cancer is a serious disease that results in more than thirty thousand deaths around the world per year. To design effective treatments, many investigators have devoted themselves to the study of biological processes and mechanisms underlying this disease. However, it is far from complete. In this study, we tried to extract important gene ontology (GO) terms and KEGG pathways for pancreatic cancer by adopting some existing computational methods. Genes that have been validated to be related to pancreatic cancer and have not been validated were represented by features derived from GO terms and KEGG pathways using the enrichment theory. A popular feature selection method, minimum redundancy maximum relevance, was employed to analyze these features and extract important GO terms and KEGG pathways. An extensive analysis of the obtained GO terms and KEGG pathways was provided to confirm the correlations between them and pancreatic cancer.

Differences in oncogenic potency but not target cell specificity distinguish the two forms of the BCR/ABL oncogene

1991 ◽  
Vol 11 (9) ◽  
pp. 4710-4716
Author(s):  
M Kelliher ◽  
A Knott ◽  
J McLaughlin ◽  
O N Witte ◽  
N Rosenberg
Keyword(s):  
Philadelphia Chromosome ◽  
Lymphocytic Leukemia ◽  
Myelogenous Leukemia ◽  
Hematopoietic Stem ◽  
Hematological Diseases ◽  
Aggressive Disease ◽  
Disease Patterns ◽  
Cell Specificity ◽  
Different Types ◽  
Indolent Disease

Two forms of activated BCR/ABL proteins, P210 and P185, that differ in BCR-derived sequences, are associated with Philadelphia chromosome-positive leukemias. One of these diseases is chronic myelogenous leukemia, an indolent disease arising in hematopoietic stem cells that is almost always associated with the P210 form of BCR/ABL. Acute lymphocytic leukemia, a more aggressive malignancy, can be associated with both forms of BCR/ABL. While it is virtually certain that BCR/ABL plays a central role in both of these diseases, the features that determine the association of a particular form with a given disease have not been elucidated. We have used the bone marrow reconstitution leukemogenesis model to test the hypothesis that BCR sequences influence the ability of activated ABL to transform different types of hematopoietic cells. Our studies reveal that both P185 and P210 induce a similar spectrum of hematological diseases, including granulocytic, myelomonocytic, and lymphocytic leukemias. Despite the similarity of the disease patterns, animals given P185-infected marrow developed a more aggressive disease after a shorter latent period than those given P210-infected marrow. These data demonstrate that the structure of the BCR/ABL oncoprotein does not affect the type of disease induced by each form of the oncogene but does control the potency of the oncogenic signal.

scholarly journals Gene Ontology and KEGG Enrichment Analyses of Genes Related to Age-Related Macular Degeneration

2014 ◽  
Vol 2014 ◽  
pp. 1-10 ◽  
Author(s):  
Jian Zhang ◽  
ZhiHao Xing ◽  
Mingming Ma ◽  
Ning Wang ◽  
Yu-Dong Cai ◽  
...  
Keyword(s):  
Gene Ontology ◽  
Feature Selection ◽  
Macular Degeneration ◽  
Classification System ◽  
Underlying Disease ◽  
Age Related Macular Degeneration ◽  
Disease Genes ◽  
Kegg Pathways ◽  
Age Related ◽  
Go Terms

Identifying disease genes is one of the most important topics in biomedicine and may facilitate studies on the mechanisms underlying disease. Age-related macular degeneration (AMD) is a serious eye disease; it typically affects older adults and results in a loss of vision due to retina damage. In this study, we attempt to develop an effective method for distinguishing AMD-related genes. Gene ontology and KEGG enrichment analyses of known AMD-related genes were performed, and a classification system was established. In detail, each gene was encoded into a vector by extracting enrichment scores of the gene set, including it and its direct neighbors in STRING, and gene ontology terms or KEGG pathways. Then certain feature-selection methods, including minimum redundancy maximum relevance and incremental feature selection, were adopted to extract key features for the classification system. As a result, 720 GO terms and 11 KEGG pathways were deemed the most important factors for predicting AMD-related genes.

scholarly journals Expression of leukocyte alkaline phosphatase gene in normal and leukemic cells: regulation of the transcript by granulocyte colony- stimulating factor

Blood ◽  
1990 ◽  
Vol 76 (12) ◽  
pp. 2565-2571 ◽  
Author(s):  
A Rambaldi ◽  
M Terao ◽  
S Bettoni ◽  
ML Tini ◽  
R Bassan ◽  
...  
Keyword(s):  
Alkaline Phosphatase ◽  
Lymphoblastic Leukemia ◽  
Lymphocytic Leukemia ◽  
Myelogenous Leukemia ◽  
Leukemic Cells ◽  
Polymorphonuclear Cells ◽  
Granulocyte Colony Stimulating Factor ◽  
Colony Stimulating Factor ◽  
Leukocyte Alkaline Phosphatase ◽  
Stimulating Factor

Abstract The levels of leukocyte alkaline phosphatase (LAP) messenger RNA (mRNA) are evaluated in B and T lymphocytes, monocytes, and polymorphonuclear cells (PMNs), and this transcript is found to be present only in PMNs. Precursors of the myelomonocytic pathway, represented by leukemic cells isolated from several cases of chronic myelogenous leukemia (CML) in its stable and blastic phase and acute myelogenous leukemia (AML), are devoid of LAP transcript. These data support the notion that LAP is a marker of the granulocyte terminal differentiation. Despite the absence of LAP mRNA in both the myeloid and the lymphoid precursors, nuclear run-on experiments show constitutive transcription of the LAP gene in leukemic cells obtained from AML, CML, as well as acute lymphoblastic leukemia (ALL) and B-cell chronic lymphocytic leukemia (B-CLL). In CML and in chronic myelo-monocytic leukemia (CMML) PMNs, granulocyte colony- stimulating factor (G-CSF) specifically accumulates LAP mRNA without showing a substantial increase in the rate of transcription of the LAP gene. Once increased by G-CSF, LAP mRNA is very stable, showing a half- life of more than 4 hours in the presence of actinomycin-D. G-CSF is suggested to play a pivotal role in the modulation of LAP transcript in PMNs.

scholarly journals Transcriptome Analysis of Porcine PBMCs Reveals the Immune Cascade Response and Gene Ontology Terms Related to Cell Death and Fibrosis in the Progression of Liver Failure

2018 ◽  
Vol 2018 ◽  
pp. 1-8
Author(s):  
YiMin Zhang ◽  
Li Shao ◽  
Ning Zhou ◽  
JianZhou Li ◽  
Yu Chen ◽  
...  
Keyword(s):  
Cell Death ◽  
Gene Ontology ◽  
Liver Failure ◽  
Transcriptome Analysis ◽  
Receptor Interaction ◽  
Failure Group ◽  
Kegg Pathways ◽  
Gene Sets ◽  
Baseline Group ◽  
Go Terms

Background. The key gene sets involved in the progression of acute liver failure (ALF), which has a high mortality rate, remain unclear. This study aims to gain a deeper understanding of the transcriptional response of peripheral blood mononuclear cells (PBMCs) following ALF. Methods. ALF was induced by D-galactosamine (D-gal) in a porcine model. PBMCs were separated at time zero (baseline group), 36 h (failure group), and 60 h (dying group) after D-gal injection. Transcriptional profiling was performed using RNA sequencing and analysed using DAVID bioinformatics resources. Results. Compared with the baseline group, 816 and 1,845 differentially expressed genes (DEGs) were identified in the failure and dying groups, respectively. A total of five and two gene ontology (GO) term clusters were enriched in 107 GO terms in the failure group and 154 GO terms in the dying group. These GO clusters were primarily immune-related, including genes regulating the inflammasome complex and toll-like receptor signalling pathways. Specifically, GO terms related to cell death, including apoptosis, pyroptosis, and autophagy, and those related to fibrosis, coagulation dysfunction, and hepatic encephalopathy were enriched. Seven Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, cytokine-cytokine receptor interaction, hematopoietic cell lineage, lysosome, rheumatoid arthritis, malaria, and phagosome and pertussis pathways were mapped for DEGs in the failure group. All of these seven KEGG pathways were involved in the 19 KEGG pathways mapped in the dying group. Conclusion. We found that the dramatic PBMC transcriptome changes triggered by ALF progression was predominantly related to immune responses. The enriched GO terms related to cell death, fibrosis, and so on, as indicated by PBMC transcriptome analysis, seem to be useful in elucidating potential key gene sets in the progression of ALF. A better understanding of these gene sets might be of preventive or therapeutic interest.

scholarly journals Computational Approach to Investigating Key GO Terms and KEGG Pathways Associated with CNV

2018 ◽  
Vol 2018 ◽  
pp. 1-9
Author(s):  
YuanYuan Luo ◽  
Yan Yan ◽  
Shiqi Zhang ◽  
Zhen Li
Keyword(s):  
Elderly Population ◽  
Feature Selection Method ◽  
The Elderly ◽  
Selection Method ◽  
Eye Disease ◽  
Extensive Literature ◽  
Biological Mechanisms ◽  
Computational Tools ◽  
Kegg Pathways ◽  
Go Terms

Choroidal neovascularization (CNV) is a severe eye disease that leads to blindness, especially in the elderly population. Various endogenous and exogenous regulatory factors promote its pathogenesis. However, the detailed molecular biological mechanisms of CNV have not been fully revealed. In this study, by using advanced computational tools, a number of key gene ontology (GO) terms and KEGG pathways were selected for CNV. A total of 29 validated genes associated with CNV and 17,639 nonvalidated genes were encoded based on the features derived from the GO terms and KEGG pathways by using the enrichment theory. The widely accepted feature selection method—maximum relevance and minimum redundancy (mRMR)—was applied to analyze and rank the features. An extensive literature review for the top 45 ranking features was conducted to confirm their close associations with CNV. Identifying the molecular biological mechanisms of CNV as described by the GO terms and KEGG pathways may contribute to improving the understanding of the pathogenesis of CNV.

scholarly journals Plasma and urine cyclic nucleotide levels in patients with acute and chronic leukemia

Blood ◽  
1983 ◽  
Vol 61 (3) ◽  
pp. 429-434 ◽  
Author(s):  
M Peracchi ◽  
L Lombardi ◽  
AT Maiolo ◽  
F Bamonti-Catena ◽  
V Toschi ◽  
...  
Keyword(s):  
Chronic Myelogenous Leukemia ◽  
Cyclic Nucleotide ◽  
Lymphoblastic Leukemia ◽  
Normal Subjects ◽  
Lymphocytic Leukemia ◽  
Myelogenous Leukemia ◽  
Response To Treatment ◽  
Deficiency Anemia ◽  
Additional Parameter ◽  
Acute Myelogenous

Abstract Plasma and urine levels of cyclic adenosine 3′,5′-monophosphate (cAMP) and of cyclic guanosine 3′,5′-monophosphate (cGMP) were measured in 35 normal subjects, in 24 patients with nonneoplastic diseases (iron deficiency anemia, peptic ulcer, and cholelithiasis), and in 50 leukemic patients. The leukemic group included patients with acute lymphoblastic leukemia, acute myelogenous leukemia, chronic lymphocytic leukemia, and chronic myelogenous leukemia. All patients were recently diagnosed and untreated, except for 5 patients with blastic transformation of chronic myelogenous leukemia who had been previously treated. There were no significant differences in plasma and urine cyclic nucleotide levels between normal subjects and patients with nonneoplastic diseases. In leukemic patients, plasma and urine cAMP levels were similar to those of normal subjects, whereas plasma and urine cGMP levels were markedly elevated. There were no significant differences in cGMP values between the various types of leukemia. After starting treatment, plasma cyclic nucleotide levels were periodically measured in 21 of the patients with acute leukemia; cGMP levels were normalized in all the 16 subjects who attained complete remission, whereas both cAMP and cGMP levels were apparently unaffected in the patients who did not respond to treatment. This suggests that plasma or urine cGMP could be used as an additional parameter to monitor the patient's response to treatment.

scholarly journals Prediction and Analysis of Retinoblastoma Related Genes through Gene Ontology and KEGG

2013 ◽  
Vol 2013 ◽  
pp. 1-8 ◽  
Author(s):  
Zhen Li ◽  
Bi-Qing Li ◽  
Min Jiang ◽  
Lei Chen ◽  
Jian Zhang ◽  
...  
Keyword(s):  
Gene Ontology ◽  
Disease Free Survival ◽  
Computational Method ◽  
The Other ◽  
Free Survival ◽  
Kegg Pathways ◽  
Incremental Feature Selection ◽  
Optimal Feature ◽  
Go Terms ◽  
Disease Free

One of the most important and challenging problems in biomedicine is how to predict the cancer related genes. Retinoblastoma (RB) is the most common primary intraocular malignancy usually occurring in childhood. Early detection of RB could reduce the morbidity and promote the probability of disease-free survival. Therefore, it is of great importance to identify RB genes. In this study, we developed a computational method to predict RB related genes based on Dagging, with the maximum relevance minimum redundancy (mRMR) method followed by incremental feature selection (IFS). 119 RB genes were compiled from two previous RB related studies, while 5,500 non-RB genes were randomly selected from Ensemble genes. Ten datasets were constructed based on all these RB and non-RB genes. Each gene was encoded with a 13,126-dimensional vector including 12,887 Gene Ontology enrichment scores and 239 KEGG enrichment scores. Finally, an optimal feature set including 1061 GO terms and 8 KEGG pathways was obtained. Analysis showed that these features were closely related to RB. It is anticipated that the method can be applied to predict the other cancer related genes as well.

scholarly journals Changes of Dentition State in Leukemic Patients during Chemotherapy

2021 ◽  
Vol 18 (15) ◽  
pp. 8193
Author(s):  
Maja Ptasiewicz ◽  
Paweł Maksymiuk ◽  
Renata Chałas
Keyword(s):  
Dental Treatment ◽  
Case Reports ◽  
Lymphoblastic Leukemia ◽  
Hematological Parameters ◽  
Blood Parameters ◽  
Lymphocytic Leukemia ◽  
Myelogenous Leukemia ◽  
University Hospital ◽  
Treatment Needs ◽  
Systemic Complications

A number of systemic diseases including hematological disorders have manifestations in the oral cavity region. These manifestations may often represent early signs of the underlying hematopoietic disease and occur frequently in leukemia. Despite the fact that leukemia has long been known to be associated with oral health deterioration, the available literature on this topic consists mostly of case reports, without data to conclude these. The aim of the study was to assess dentition state in leukemic patients during one cycle of chemotherapy and its correlation with blood parameters. The study included 102 adults treated because of leukemia at the Clinic of Haemato-Oncology and Bone Marrow Transplantation at the university hospital in Lublin, Poland. The sample group consisted of 51 women and 51 men aged 22 to 72 (54.07 ± 10.33) with following diagnoses: Acute myelogenous leukemia (AML)—55 patients (53.92%), Chronic lymphocytic leukemia (CLL)—17 patients (16.67%), Acute lymphoblastic leukemia (ALL)—16 patients (15.69%), Chronic myelogenous leukemia (CML)—10 patients (9.80%), Acute promyelocytic leukemia (APL) —3 patients (2.94%), Chronic hairy cell leukemia (HCL)—1 patient (0.98%). DMFT index was used to assess dentition state. After the cycle of chemotherapy, their dentition state changed in terms of decayed, missing and filled teeth and correlated with hematological parameters. Adult patients with leukemia have high dental treatment needs, and high number of missing teeth; thus, a comprehensive and fast dental treatment is necessary to avoid systemic complications and ensure better quality of life.

scholarly journals Expression of leukocyte alkaline phosphatase gene in normal and leukemic cells: regulation of the transcript by granulocyte colony- stimulating factor

Blood ◽  
1990 ◽  
Vol 76 (12) ◽  
pp. 2565-2571 ◽  
Author(s):  
A Rambaldi ◽  
M Terao ◽  
S Bettoni ◽  
ML Tini ◽  
R Bassan ◽  
...  
Keyword(s):  
Alkaline Phosphatase ◽  
Lymphoblastic Leukemia ◽  
Lymphocytic Leukemia ◽  
Myelogenous Leukemia ◽  
Leukemic Cells ◽  
Polymorphonuclear Cells ◽  
Granulocyte Colony Stimulating Factor ◽  
Colony Stimulating Factor ◽  
Leukocyte Alkaline Phosphatase ◽  
Stimulating Factor

The levels of leukocyte alkaline phosphatase (LAP) messenger RNA (mRNA) are evaluated in B and T lymphocytes, monocytes, and polymorphonuclear cells (PMNs), and this transcript is found to be present only in PMNs. Precursors of the myelomonocytic pathway, represented by leukemic cells isolated from several cases of chronic myelogenous leukemia (CML) in its stable and blastic phase and acute myelogenous leukemia (AML), are devoid of LAP transcript. These data support the notion that LAP is a marker of the granulocyte terminal differentiation. Despite the absence of LAP mRNA in both the myeloid and the lymphoid precursors, nuclear run-on experiments show constitutive transcription of the LAP gene in leukemic cells obtained from AML, CML, as well as acute lymphoblastic leukemia (ALL) and B-cell chronic lymphocytic leukemia (B-CLL). In CML and in chronic myelo-monocytic leukemia (CMML) PMNs, granulocyte colony- stimulating factor (G-CSF) specifically accumulates LAP mRNA without showing a substantial increase in the rate of transcription of the LAP gene. Once increased by G-CSF, LAP mRNA is very stable, showing a half- life of more than 4 hours in the presence of actinomycin-D. G-CSF is suggested to play a pivotal role in the modulation of LAP transcript in PMNs.

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