Project name: NOPP-gigas-ploidy-temp
Funding source: National Oceanographic Partnership Program
Species: Crassostrea gigas
variable: ploidy, elevated seawater temperature, desiccation
Github repo: NOPP-gigas-ploidy-temp

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Tagseq analysis - Generate Gene Tables

Using the following R script:

  1. I imported the significant (p<0.05, lfc>1.5) genes generated from DESeq2 using the apeglm shrinkage estimator for each comparison,
  2. sorted by whether the LOCID were characterized or uncharacterized, and
  3. generated gene tables w/ descriptions

Here are the results:

VOLCANO PLOTS: Multiple comparisons by treatment

comparison control single-stressor multi-stressor
ploidy

VOLCANO PLOTS: significant genes by ploidy

comparison diploid triploid
single-stressor v control
multi-stressor v control

DEG LISTS: summary stats

35% - 60% of identified DEGS were uncharacterized (LOCID w/o annotation) across treatments (SS = single stressor; MS = multi-stressor)

ploidy treatment total known unknown percent_unknown
both control v control 109 44 65 60%
both SS v SS 343 182 161 46.9%
both MS v MS 138 60 78 56.5%
diploid SS v control 316 174 142 45%
diploid MS v control 72 45 27 37.5%
triploid SS v control 92 59 33 36%
triploid MS v control 62 40 22 35%

Direction of log2fold change expression for DEGs.

comparison total positive negative percent_negative percent_positive
control_ploidy 109 80 29 26.6 73.4
SS_ploidy 344 290 54 15.7 84.3
MS_ploidy 138 81 57 41.3 58.7
diploid_SS 317 90 227 71.6 28.4
diploid_MS 74 46 28 37.8 62.2
triploid_SS 94 35 59 62.8 37.2
triploid_MS 62 33 29 46.8 53.2

DEG LISTS: links to lists

Links to lists of all and significant DEGs. SS = single stressor; MS = multi-stressor.

ploidy treatment DEG_all DEG_sig
both control v control X X
both SS v SS X X
both MS v MS X X
diploid SS v control X X
diploid MS v control X X
triploid SS v control X X
triploid MS v control X X

DAVID: GOterm analysis