Correlating Technical Replicates Part 10

The end of a saga

I think I’m at a point where I kind of trust my new dataset with bad samples removed. Within each peptide, all transitions show a consistent expression pattern between sites. Peptides within a protein, however, have different expression. This could be due to alternative splicing.

There are three different patterns I saw with my protein expression data:

  • Puget Sound sites had similar expression values, but Willapa Bay had higher expressoin
  • There’s a U-shape (CI –> FB –> PG (minimum) –> SK –> WB)
  • All five expression values are similar

For my future reference, I’m going to paste my boxplots from one transition per peptide below. I’ve sorted proteins by their functions.

Oxidative Stress (4 proteins)

**CHOYP_BRAFLDRAFT_119799.1.1 m.23765**: Peroxiredoxin-5, mitochondrial (EC 1.11.1.15)

choyp_brafldraft_119799 1 1 m 23765 vnsgelfgk y4

choyp_brafldraft_119799 1 1 m 23765 vpavdlfek y6

**CHOYP_BRAFLDRAFT_122807.1.1 m.3729**: Thioredoxin reductase 3 (EC 1.8.1.9)

choyp_brafldraft_122807 1 1 m 3729 daiqdyigslnwgyr y8

choyp_brafldraft_122807 1 1 m 3729 igdymevegvk y7

choyp_brafldraft_122807 1 1 m 3729 viglhvlgpnageitqgyavamr y5

**CHOYP_CATA.1.3 m.11120**: Catalase (EC 1.11.1.6)

choyp_cata 1 3 m 11120 iqimtpeqaek y6

choyp_cata 1 3 m 11120 lqahldsvsnvsk y5

choyp_cata 1 3 m 11120 lvenignhlintqk y4

**CHOYP_CATA.3.3 m.21642**: Catalase (EC 1.11.1.6)

choyp_cata 3 3 m 21642 tdqgiqnlsaaeanr y7

Heat shock (1 protein)

**CHOYP_HS12A.25.33 m.60352**: Heat shock 70 kDa protein 12B

choyp_hs12a 25 33 m 60352 apttlllepdgk y4

choyp_hs12a 25 33 m 60352 giaeaisssk y4

Acid-base balance (1 protein)

**CHOYP_CAH2.1.1 m.42306**: Carbonic anhydrase 2 (EC 4.2.1.1)

choyp_cah2 1 1 m 42306 iqeagssvk y4

choyp_cah2 1 1 m 42306 naevsntgssik y7

choyp_cah2 1 1 m 42306 qspidistk y4

Drug resistance (1 protein)

**CHOYP_MRP1.5.10 m.34368**: Multidrug resistance-associated protein 1 (ATP-binding cassette sub-family C member 1)

choyp_mrp1 5 10 m 34368 dstvltiahr y4

choyp_mrp1 5 10 m 34368 lyawepsfqdk y6

Fatty acid metabolism (1 protein)

**CHOYP_ACAA2.1.1 m.30666**: 3-ketoacyl-CoA thiolase, mitochondrial (EC 2.3.1.16)

x elglnnditnmnggaialghplaasgtr y8

x itghlahelqr y5

x qynltplar y4

Carbohydrate metabolism (2 proteins)

**CHOYP_G6PD.2.2 m.46923**: Glucose-6-phosphate 1-dehydrogenase (G6PD) (EC 1.1.1.49)

choyp_g6pd 2 2 m 46923 sdelyeawr y4

choyp_g6pd 2 2 m 46923 tyfigyar y3

**CHOYP_LOC100883864.1.1 m.41791**: Glycogen phosphorylase, muscle form (EC 2.4.1.1)

choyp_loc100883864 1 1 m 41791 dyylslahtvr y5

choyp_loc100883864 1 1 m 41791 iedgwqveepdewlr y6

choyp_loc100883864 1 1 m 41791 vlypndnffsgk y7

Cell growth and maintenance (5 proteins)

**CHOYP_BRAFLDRAFT_275870.1.1 m.12895**: Protein phosphatase 1B (EC 3.1.3.16)

choyp_brafldraft_275870 1 1 m 12895 gmpemvsgedk y5

choyp_brafldraft_275870 1 1 m 12895 tgflqldek y4

**CHOYP_LOC100633041.1.1 m.35428**: NAD(P) transhydrogenase, mitochondrial (EC 1.6.1.2)

choyp_loc100633041 1 1 m 35428 avveaannfgr y5

choyp_loc100633041 1 1 m 35428 sltnvilggygtk y7

**CHOYP_PDIA1.1.1 m.5297**: Protein disulfide-isomerase (PDI) (EC 5.3.4.1)

choyp_pdia1 1 1 m 5297 gsqqvvdynger y6

choyp_pdia1 1 1 m 5297 litlgedmtk y3

choyp_pdia1 1 1 m 5297 tspeivnwlr y5

**CHOYP_PDIA3.1.1 m.60223**: Protein disulfide-isomerase A3 (EC 5.3.4.1)

choyp_pdia3 1 1 m 60223 agefseeyggpr y7

choyp_pdia3 1 1 m 60223 iffavsnsk y4

choyp_pdia3 1 1 m 60223 vadamstdlk y5

**CHOYP_PSA.1.1 m.27259**: Puromycin-sensitive aminopeptidase (PSA) (EC 3.4.11.14)

choyp_psa 1 1 m 27259 agmistvdvlk y3

choyp_psa 1 1 m 27259 sendlpedstwk y4

choyp_psa 1 1 m 27259 yfqiayplpk y4

Written on November 1, 2017