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Table 12 Highly significantly over- and under-represented peptides across LEA Protein Groups

From: LEAping to conclusions: A computational reanalysis of late embryogenesis abundant proteins and their possible roles

Grp

Threshold Pr

Representation

Sample of Significant Peptides (negative p-values indicate under-representation)

1

3.9e-07

over

G (2.6e-49), E (7.9e-36), Q (2.6e-10), R (4.2e-08), GG (5.8e-47), KGG (1.6e-41), EMG (9.5e-33), QMG (2.1e-19)

  

under

I (-3.7e-16), V (-1.1e-14), P (-1.7e-14), F (-7.4e-14), N (-1.3e-12), L (-4.2e-11), C (-6.6e-11), W (-1.7e-09)

2

1.1e-10

over

G (0), TG (0), H (7.4e-291), GG (6.4e-178), T (6.8e-122), K (1.4e-59), Q (8.7e-28), HG (5.6e-187), KLP (2.8e-170), EK (1.1e-120), YG (4.7e-101), SSS (2.0e-43)

  

under

L (-5.6e-123), F (-2.2e-81), I (-1.1e-52), V (-9.8e-47), N (-3.7e-43), R (-3.8e-39), C (-1.0e-36), W (-1.7e-35), S (-5.2e-25),

3

4.3e-08

over

A (3.6e-246), K (7.3e-140), T (3.2e-48), E (2.9e-37), Q (7.8e-32), KD (1.6e-93), AKD (1.6e-83), AKE (2.4e-45), KDY (2.1e-46), EK (1.8e-45)

  

under

L (-1.2e-89), I (-3.9e-61), P (-2.8e-51), F (-6.1e-35), W (-8.3e-27), C (-4.2e-19), N (-1.5e-14), R (-2.3e-12)

4

4.1e-04

over

TG (1.9e-17), G (4.7e-14), T (9.5e-12), GH (8.7e-09), A (7.8e-08), AKA (1.9e-07), EK (8.6e-07), AA (3.8e-05)

  

under

L (-5.1e-19), I (-4.8e-09), F (-1.4e-08), V (-5.6e-06), C (-4.6e-05), W (-1.8e-04), S (-8.5e-04)

5

6.2e-04

over

AKE (1.2e-17), K (9.2e-13), A (4.1e-10), E (1.0e-08), EK (2.7e-05)

  

under

L (-5.2e-11), P (-4.3e-08), I (-1.5e-06)

6

8.4e-04

over

A (6.5e-30), AA (3.1e-18), AT (1.7e-08), AE (1.8e-07), QS (2.2e-06), GV (3.7e-06), GG (8.6e-06), Q (4.1e-05), V (1.6e-04), QSA (2e-13)

  

under

L (-2.2e-10), F (-8.9e-09), C (-7.9e-07), Y (-6.0e-06), I (-3.5e-05), K (-3.3e-04), W (-3.0e-04)

Lea5

1.2e-03

over

A (4.4e-05), GA (4.1e-05), GY (8.8e-05), SS (1.3e-04), R (2.6e-04), S (6.9e-04)

  

under

Q (-4.9e-04)

Lea14

1.3e-03

over

IP (1.1e-07), D (7.7e-05), K (3.3e-04), I (1.2e-03)

  

under

R (-4.1e-06), Q (-8.0e-06), F (-3.3e-03)

  1. Applying popp_create.py to each group of LEA protein sequence taken as a whole, the table lists a sample of the peptides that are highly over-represented or highly under-represented, i.e. their probabilities are more stringent than the thresholds listed in the second column. The different thresholds arise due to differences in the numbers of sequences, hence differing amino acid counts, corresponding to each Group.
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