Kevin Matthew McKay Week 12

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*GO:0003723-RNA binding-Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
*GO:0003723-RNA binding-Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
==Explanation==
==Explanation==
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*When the cell experiences cold shock, there are numerous effects, depending on how quickly the cold comes on, how quickly it leaves, and how cold the shock actually is.  Consistently, the cell should respond as it would respond to stress.  The cell responds by means of change in gene expression, which is why many of the genes my profile showed significant at less than .05 p value had to do with RNA processing, RNA is directly involved in gene expression and protein synthesis.  The nucleus is where chromosomes are transcribed into mRNA, the beginning of gene expression, this could be why the nucleus term came up in my profile.  A few ribosomal RNA genes came up,and a gene related to ribosome biogenesis. Ribosomes are very involved in the production of protein used in gene expression.  If the cell were to change shape, becoming more or less rigid in response to cold shock, the cytoskeleton would be involved, which explains the non-membrane bound organelle genes used.  Genes involved with the nuclear lumen could have something to do with the cold shock as well.  The liquid in the lumen contains water and other fluids that respond to cold temperature in possible negative ways for the cell, so gene regulation here may be necessary.  The construction of macromolecules at lower temperature would slow down overall, as the cell tries to preserve what energy it has, further explaning the ribosome biogenesiis gene that shows up.
+
*When the cell experiences cold shock, there are numerous effects, depending on how quickly the cold comes on, how quickly it leaves, and how cold the shock actually is.  Consistently, the cell should respond as it would respond to stress.  The cell responds by means of change in gene expression, which is why many of the genes my profile showed significant at less than .05 p value had to do with RNA processing, RNA is directly involved in gene expression and protein synthesis.  The nucleus is where chromosomes are transcribed into mRNA, the beginning of gene expression, this could be why the nucleus term came up in my profile.  A few ribosomal RNA genes came up,and a gene related to ribosome biogenesis. Ribosomes are very involved in the production of protein used in gene expression.  If the cell were to change shape, becoming more or less rigid after cold shock, the cytoskeleton would be involved, which explains the non-membrane bound organelle genes used.  Genes involved with the nuclear lumen could have something to do with the cold shock as well.  The liquid in the lumen contains water and other fluids that respond to cold temperature in possible negative ways for the cell, so gene regulation here may be necessary.  The construction of macromolecules at lower temperature would slow down overall, as the cell tries to preserve what energy it has, further explaning the ribosome biogenesiis gene that shows up.
==Yeastract Questions==
==Yeastract Questions==

Revision as of 14:07, 11 April 2013

Contents

Questions

  • I chose profile 45 because it was the opposite of my partner Laura's, mine was up regulated and then down regulated.
  • 615 Genes were assigned
  • 53.4 Genes were expected
  • p-value was 0
  • At p < .05 209 GO terms were associated with this profile
  • At corrected p < .05 18 GO terms associated with this profile

10 Definitions

  • GO:0005730-Nucleolus-A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
  • GO:0042254-Ribosome biogenesis-A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.
  • GO:0006364-rRNA processing-Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
  • GO:0030529-ribonucleoprotein complex-A macromolecular complex containing both protein and RNA molecules.
  • GO:0016072-rRNA metabolic process-The chemical reactions and pathways involving rRNA, ribosomal RNA, a structural constituent of ribosomes.
  • GO:0031981-nuclear lumen-The volume enclosed by the nuclear inner membrane.
  • GO:0005634-nucleus-A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
  • GO:0010467-gene expression-The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.
  • GO:0043228-nonmembrane bound organelle-Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes.
  • GO:0003723-RNA binding-Interacting selectively and non-covalently with an RNA molecule or a portion thereof.

Explanation

  • When the cell experiences cold shock, there are numerous effects, depending on how quickly the cold comes on, how quickly it leaves, and how cold the shock actually is. Consistently, the cell should respond as it would respond to stress. The cell responds by means of change in gene expression, which is why many of the genes my profile showed significant at less than .05 p value had to do with RNA processing, RNA is directly involved in gene expression and protein synthesis. The nucleus is where chromosomes are transcribed into mRNA, the beginning of gene expression, this could be why the nucleus term came up in my profile. A few ribosomal RNA genes came up,and a gene related to ribosome biogenesis. Ribosomes are very involved in the production of protein used in gene expression. If the cell were to change shape, becoming more or less rigid after cold shock, the cytoskeleton would be involved, which explains the non-membrane bound organelle genes used. Genes involved with the nuclear lumen could have something to do with the cold shock as well. The liquid in the lumen contains water and other fluids that respond to cold temperature in possible negative ways for the cell, so gene regulation here may be necessary. The construction of macromolecules at lower temperature would slow down overall, as the cell tries to preserve what energy it has, further explaning the ribosome biogenesiis gene that shows up.

Yeastract Questions

  • Top 10 transcription factors and percentages are: Ste12p-26.9%; Rap1p-19.3%; Sok2p-13.1%; Sko1p-11.9%; Ino4p-11.6%; Abf1p-10.4%; Skn7p-9.4%; Yap6p-9.3%; Cin5p-8.8%; Fhl1p-7.9%
  • Cin5 is on it-8.8%, Gln3 is as well-2.5%, Zap1-1.0%
  • I would add Ste12, Rap1, Sok2, Ino4, and Abf1. These are the transcription factors that regulated the highest percentage of genes in my cluster which were not alreadyincluded in the model transcription factors.

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