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    BioInformatics Quiz1 Week10

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    chahoub
    This document provides an overview of ontology and identification of molecular pathways in bioinformatics. It includes readings on gene ontology categories, molecular pathways in KEGG, and evidence codes in GO. It then presents a graded quiz with 6 multiple choice questions testing understanding of gene ontology inferences, identifying which pathways a gene belongs to from KEGG, computational analysis evidence codes in GO, descriptions of KEGG orthology levels and entries, and determining the most statistically enriched pathway from a list of differentially expressed genes using KOBAS.

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    BioInformatics Quiz1 Week10

    Uploaded by

    chahoub
    580 views8 pages
    This document provides an overview of ontology and identification of molecular pathways in bioinformatics. It includes readings on gene ontology categories, molecular pathways in KEGG, and evidence codes in GO. It then presents a graded quiz with 6 multiple choice questions testing understanding of gene ontology inferences, identifying which pathways a gene belongs to from KEGG, computational analysis evidence codes in GO, descriptions of KEGG orthology levels and entries, and determining the most statistically enriched pathway from a list of differentially expressed genes using KOBAS.

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    BioInformatics Quiz1 Week10

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    This document provides an overview of ontology and identification of molecular pathways in bioinformatics. It includes readings on gene ontology categories, molecular pathways in KEGG, and evidence codes in GO. It then presents a graded quiz with 6 multiple choice questions testing understanding of gene ontology inferences, identifying which pathways a gene belongs to from KEGG, computational analysis evidence codes in GO, descriptions of KEGG orthology levels and entries, and determining the most statistically enriched pathway from a list of differentially expressed genes using KOBAS.

    Copyright:

    © All Rights Reserved
    Download as DOCX, PDF, TXT or read online from Scribd
    Download as docx, pdf, or txt
    580 views8 pages

    BioInformatics Quiz1 Week10

    Uploaded by

    chahoub
    This document provides an overview of ontology and identification of molecular pathways in bioinformatics. It includes readings on gene ontology categories, molecular pathways in KEGG, and evidence codes in GO. It then presents a graded quiz with 6 multiple choice questions testing understanding of gene ontology inferences, identifying which pathways a gene belongs to from KEGG, computational analysis evidence codes in GO, descriptions of KEGG orthology levels and entries, and determining the most statistically enriched pathway from a list of differentially expressed genes using KOBAS.

    Copyright:

    © All Rights Reserved
    Download as DOCX, PDF, TXT or read online from Scribd
    Download as docx, pdf, or txt
    of 8
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    The passage discusses ontology and identification of molecular pathways. It provides examples of gene ontology categories and inferences as well as pathways and evidence codes.

    The passage discusses ontology, which is the categorization of genes and gene products, and identification of molecular pathways using tools like KEGG and KOBAS.

    The Retrograde endocannabinoid signaling pathway was found to be the most statistically significantly enriched using KOBAS with the given differential expressed human gene list.

    Bioinformatics: Introduction and Methods 生物信息学: 导论与方法

    Week 10
    Ontology and Identification of Molecular Pathways
    Prev
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       

     

    Quiz: Ontology and Identification of Molecular Pathways

    6 questions

     


    Reading: Readings
    . Duration: 10 minutes10 min


    o

    Reading: Slides

    . Duration: 10 minutes10 min

    Quiz • 30 min

    Ontology and Identification of Molecular Pathways


    Submit your assignment
    Due DateDec 28, 7:59 AM CET
    Attempts3 every 8 hours
    Receive grade
    To Pass80 % or higher
    Grade
    —
    Ontology and Identification of Molecular Pathways
    Graded Quiz • 30 min

    Due Dec 28, 7:59 AM CET

    Ontology and Identification of Molecular Pathways

    Total points 6
    1.
    Question 1

    Which is not the three categories of Gene Ontology?

    Gene Ontology 的三大分类不包括下面中的哪一项？

    1 point

    Molecular Function

    Biological Process

    Biological Regulation

    Cellular Component

    2.
    Question 2

    Which one of the following inferences is right?

    如下哪个推断是正确的？

    1 point

    If A is a B, and B regulates C, then A is a C.

    If A regulates B, and B regulates C, then A regulates C.


    If A is part of B, and B regulates C, then A regulates C.

    If A regulates B, and B is part of C, then A regulates C.

    3.
    Question 3

    Which following pathways do CCR5 (hsa:1234) belong to? (Hint: search from KEGG
    website http://www.genome.jp/kegg/)

    CCR5 (hsa:1234)属于如下哪些条 pathway？ (提示：搜索 KEGG 网站


    http://www.genome.jp/kegg/)

    1 point

    Chemokine signaling pathway

    p53 signaling pathway

    Wnt signaling pathway

    Cytokine-cytokine receptor interaction

    1-2-3-4 1-3-4 1-3

    4.
    Question 4

    Which following GO evidence codes do belong to computational analysis evidence?

    如下哪些 GO 证据代码属于计算分析证据？

    1 point
    expression pattern (IEP)

    direct assay (IDA)

    sequence orthology (ISO)

    key residues (IKR)

    1-2-3-4 1-3-4 1-3 1-2

    5.
    Question 5

    Which of the following statements about KEGG ORTHOLOGY (KO) is right?

    如下哪个关于 KEGG ORTHOLOGY (KO)的陈述是正确的？

    1 point

    KO is a functional hierarchy of five levels

    KO 是一个具有五级的功能层次

    An ortholog group only contains orthologs

    ortholog group 中只包含 ortholog

    The second level of KO contains ortholog groups (KO entries)

    KO 第二层含有 ortholog groups (KO entries)


    The terms in the first level of KO includes Metabolism, Genetic Information
    Processing, and Cellular Processes.

    KO 第一层的 term 包括 Metabolism, Genetic Information Processing, and Cellular


    Processes

    6.
    Question 6

    In an experiment you got the following differential expressed human gene list(in
    Entrez Gene ID format), which KEGG pathway is the most statistically significantly
    enriched one by using KOBAS with default settings?

    在一次实验中得到了如下差异表达人类基因列表（Entrez Gene ID 格式），用


    KOBAS 得到的 KEGG pathway 哪条是统计上最显著富集的（采用默认参数）？

    KOBAS: http://kobas.cbi.pku.edu.cn/

    12

    18

    88

    114

    231

    627

    725

    836

    1124

    1137

    1152

    1267

    1268

    1385

    1428

    1501
    1548

    1813

    1815

    2119

    2166

    2353

    2354

    2565

    2908

    3091

    3164

    3356

    3481

    3916

    4129

    4155

    4353

    4781

    5121

    5126

    5179

    5414

    5602

    5860

    5870
    5999

    6421

    6531

    6532

    6606

    7054

    7086

    7124

    7529

    8288

    9040

    9568

    10399

    10439

    10912

    23236

    23237

    27075

    54704

    79830

    114876

    1 point

    Retrograde endocannabinoid signaling


    Dopaminergic synapse

    Estrogen signaling pathway

    Cocaine addiction

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