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Bioinformatics- Assignment 8

Summary of GTEx track Description of data: A median of gene expression levels was taken from 52 tissues and 2 cell lines, based on RNA-seq data from the GTEx final data release in August 2019. This release was based on data from 17,382 tissue samples obtained from 948 adult post-mortem subjects. Methods: Tissue samples were collected using the GTEx standard operating procedures in partnership with the National Cancer Institute Biorepositories and Biospecimen. All obtained tissue samples were reviewed by pathologists in order to characterize and verify organ sources. That being said, the RNA-seq was conducted by the GTEx Laboratory, Data Analysis, and Coordinating Center. While the sequences were conducted using the STAR v2.5a assisted by the GENCODE 26 transcriptome definition. Finally, gene annotations were produced using a custom isoform collapsing procedure. Subject and Sample Characteristics: The donors of this study and their biospecimen were required to show no evidence of diseas...
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Bioinformatics- Assignment 8| UCSC Genome Browser

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Assignment 8 had me get acquainted with the UCSC genome browser, which is saturated with all different kinds of genomic information. I looked up my protein AMY1B and explored its genetic sequence along with some other loci on the same chromosome. That being said, when I filtered what was displayed in the data track to "NCBI RefSeq" my data track shrunk significantly, only displaying one gene body. When I clicked on the gene body it took me to a new window that listed the specifics of the gene that I had already read about in previous databases used. Taking note of this, it showed me how meticulous these databases strive to be in putting out information. Below is the best image I could get of the initial data track displayed in the UCSC genome browser. 
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Bioinformatics- Assignment 7| CollecTF Database

The three different species of bacteria: - Firmicutes - Clostridia - Clostridiales Ecosystem details: Digestive system -> Large intestine -> Fecal Transcription factor, CsoR.  Motif - Inverted repeat  G/C content - 69.23% Regulatory mode - Activation 0%, Repression 100%, Dual 0%, Not specified 0%. TF conformation - Monomer 0%, Dimer 0%, Tetramer 100%, Other 0%, Not specified 0%. Binding site type - Motif-associated 1, Variable-motif-associated 0, Non-motif-associated 0.  The specific type of gene regulation this transcription factor is involved in I couldn't determine. However, I'm inclined to say, TTHA.
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Bioinformatics- Assignment #6

P04745-Alpha-amylase 1 Uniprot ID: AMY1_HUMAN Protein: Alpha-amylase 1 Gene: AMY1A Diseases associated with alpha-amylase: None to be noted. Catalytic activity: Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides containing three or more (1->4)-alpha-linked D-glucose units. Cofactor: Calcium ion (Ca2+) and Chloride ion (Cl-) Alpha-amylase was found to be rather mildly expressed exclusively in the pancreas. No other organs/regions could be noted.  Some aspects of alpha-amylase I am curious about are, one, why is there such little data about it? Two, why would it be expressed only in the pancreas and not somewhere along the digestive tract?  One project idea I have in mind is further investigating where else alpha-amylase could possibly be expressed, and discovering why it is expressed higher in one region than another. 
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Bioinformatics- Assignment #5 (week 5)

The top three results for the Gene-Disease Associations for my protein were the following: -   Evidence for AMY1B in integumentary system disease                -Association score: 0.508836 -   Evidence for AMY1B in neoplasm of the thorax                            - Association score: 0.5086579             - Evidence for AMY1 in glandular cell neoplasm              - Association score: 0.50802636 The top three diseases:   Title: Salivary Alpha-Amylase Reactivity in Breast Cancer Survivors   Authors: Wan C, Couture-Lalande MÈ, Narain TA, Lebel S, Bielajew C   Summary of Abstract: This study looked at two primary components of the stress system which are the hypothalamic-pituitary-adrenal (HPA) and the sympathetic-adrenal-me...
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Bioinformatics- Assignment #4 (Week 4)

 Hello, Today I explored the website interactome and STRING. While exploring these websites I searched up my assigned protein AMY1B and looked specifically at its different interactions. I first searched up AMY1B in interactomes database and in doing so, found that it interacted with the protein Mucin-7 or MUC7, which functions to promote the clearance of bacteria in the oral cavity. With that being said, I then searched up AMY1B on the website STRING, and it was here I found a series of different interactions with other proteins. Some of which were, H6PD, LCT, MGAM, and BPI just to name some.  After, looking at the two websites I found that they both had very different results. For instance, interactome had only one interaction listed while STRING had a total of eight interactions! However, out of those eight interactions, only four were determined experimentally whereas the other remaining four were from curated databases.  In closing, after exploring interactome and ST...
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Bioinformatics - Assignment #3 (Week 3)

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 Hello, Today I familiarized myself with iTASSER, which is a platform that uses algorithms to construct models of specific proteins that are being investigated. The protein I requested a model of belonged to Deinococcus Radiodurans, D. rad, and had the following locus tag Ga0133345_1136. Below are four images of the protein rotating through space.  
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