Top-10-Studied-Genes

Comparative Sequence Analysis of Top 10 Studied Genes

• Compare their DNA sequence and Protein (Amino Acid) sequence

  • GC Content
  • Analysis of protein sequence
  • Freq of Each Amino Acids

• Find similarity between them

  • Alignment
  • hamming distance

• 3D structure of each

The idea

An article from nature

Datasource

• RCSB PDB
• NCBI
• Biopython
• Py3Dmol

Fasta Files

• 1.TP53
• 2.TNF
• 3.EGFR
• 4.VEGFA
• 5.APOE
• 6.IL6
• 7.TGFB1
• 8.MTHFR
• 9.ESR1
• 10.AKT1

Comparative Analysis of Top 10 Genes

GC Contents In DNA

• GC-content (or guanine-cytosine content) is the percentage of nitrogenous bases in a DNA or RNA molecule that are either guanine (G) or cytosine (C)

Usefulness

• In polymerase chain reaction (PCR) experiments, the GC-content of short oligonucleotides known as primers is often used to predict their annealing temperature to the template DNA.
• A higher GC-content level indicates a relatively higher melting temperature.
• DNA with low GC-content is less stable than DNA with high GC-content AKT1 have the most number of GC -> 73.07% then APOE with 65.06%

Protein Sequence analysis

ESR1 have the most protein length with 158.49k

EGFR protein length 64.204k

Check for the Count of Amino Acids

Most Common amino acids

• TP53 -> (L, 674), (S, 616), (G, 477), (P, 464), (R, 421)

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• TNF -> (L, 96), (S, 91), (G, 79), (R, 73), (P, 72)

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• EGFR -> (L, 6982), (S, 5916), (P, 3914), (G, 3695), (V, 3457)

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• VEGFA -> (L, 589), (G, 577), (S, 567), (P, 541), (R, 404)

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• APOE -> (G, 131), (P, 130), (S, 127), (R, 119), (A, 117)

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• IL6 -> (L, 226), (S, 191), (P, 141), (G, 130), (K, 125)

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• TGFB1 -> (L, 806), (S, 749), (G, 659), (P, 637), (R, 597)

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• MTHFR -> (L, 715), (S, 649), (G, 609), (P, 603), (A, 508)

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• ESR1 -> (L, 18225), (S, 14142), (F, 10419), (I, 9754), (*, 8724)

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• AKT1 -> (G, 1211), (P, 1005), (L, 846), (A, 801), (R, 720)

Find similarity between them

Narative

• similarity between APOE and IL6 is 78.54%
• similarity between TNF and APOE is 71%
• similarity between MTHFR and VEGFA is 70.9%
• similarity between TGFB1 and AKT1 is 67%
• similarity between TP53 and MTHFR is 66.5%
• similarity between TP53 and VEGFA is 0.35%

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similarity between EGFR and ESR1 for the first 35000 is 63.82%

3D Structure

you can see them in the code