In my transcriptomics analysis, there are some genes that I am interested are significantly different, but not differentially expressed.
I am in confusion if I really understand the concept behind what is exactly DEGs means now
In my DEG pipeline parameters were;

pval_adj_method <- 'BH'
pval_cut <- 0.01
l2fc_cut <- 1

I have 3 time course - 0/12/24 hrs
4 genotypes - WT, 3 mutants (aox1/2/3)
I compared each mutants to it's WT values at given time point
e.g.

aox1_0h-WT_0h
aox2_0h-WT_0h

aox1_12h-WT_12h

etc.

From this output, only a few combinations showed they are DEGs

**Gene1_** aox2_0h.WT_0h    down-regulated
**Gene2-** aox3_0h.WT_0h    up-regulated
**Gene6_** aox2_12h.WT_12h  down-regulated

However, once I plotted original values, I see other mutants also statistically different compared to their WT

What does it mean?

Does DEG (pval_cut = 0.01 l2fc_cut = 1) mean at a given time point comparisions'sor
does it compare across all the time course?

For example, inf Gene 2, if aox3 considered as DEG why not the other 2 mutants?
This is what confusing to me
Would be grateful if someone could explain this kindly.

structure(list(AGI = c("Gene_1", "Gene_2", "Gene_3", "Gene_4", 
"Gene_5", "Gene_6"), aox1_0h_1.tsv = c(12.19671398, 215.2944799, 
16.44462648, 494.4740158, 231.5254774, 72.57597906), aox1_0h_4.tsv = c(20.483339, 
309.7008485, 24.97567468, 692.9926789, 363.0050461, 123.5888977
), aox1_0h_5.tsv = c(12.02356715, 99.9827504, 11.36592332, 276.0989805, 
142.2411187, 58.85580698), aox1_12h_4.tsv = c(15.40599103, 72.92196194, 
19.36412892, 376.7248056, 269.677545, 99.21985896), aox1_12h_5.tsv = c(14.1934073, 
79.71249677, 32.45167316, 356.2905953, 196.2274429, 89.37924571
), aox1_12h_6.tsv = c(24.80343931, 95.02515421, 34.05358939, 
440.896732, 346.8153177, 127.4466926), aox1_24h_4.tsv = c(6.184604587, 
196.0341138, 25.18641024, 258.9801928, 223.9545066, 33.84484312
), aox1_24h_6.tsv = c(6.883819431, 98.05429052, 2.021393634, 
112.1958862, 139.6212486, 28.75295204), aox2_0h_3.tsv = c(25.53690512, 
175.1041763, 28.87826692, 459.5438353, 433.4289707, 137.3774675
), aox2_0h_4.tsv = c(10.18876629, 280.2141447, 32.48869835, 624.7432893, 
323.5662966, 87.89508861), aox2_0h_5.tsv = c(12.34945421, 312.5272061, 
28.36719904, 848.7432271, 469.8874526, 158.9474865), aox2_12h_1.tsv = c(19.08287299, 
137.9990764, 29.84418565, 377.4153307, 314.9721922, 95.42395784
), aox2_12h_2.tsv = c(7.890962701, 74.2399241, 15.29254776, 236.4643073, 
135.7776899, 26.49812298), aox2_12h_3.tsv = c(3.678221008, 62.60983209, 
11.67625132, 200.3733542, 100.7079901, 31.6012183), aox2_24h_1.tsv = c(11.2162246, 
149.1030715, 30.70364462, 321.8824458, 234.0832479, 67.24515005
), aox2_24h_4.tsv = c(13.99519719, 902.6355571, 41.48997933, 
501.303002, 772.8283795, 350.2515435), aox2_24h_5.tsv = c(7.867480669, 
361.1331651, 14.63979526, 218.9941277, 330.2108122, 147.5707818
), aox3_0h_1.tsv = c(14.15880435, 381.2255777, 40.53415811, 456.0047815, 
317.8303883, 159.6022776), aox3_0h_2.tsv = c(16.7311523, 291.2105347, 
27.30607326, 339.5042008, 179.0730805, 61.18757328), aox3_0h_3.tsv = c(19.09795927, 
293.2638492, 25.89886385, 398.8993785, 185.8289419, 70.22345994
), aox3_12h_1.tsv = c(81.20410372, 541.3370048, 85.56280843, 
974.0674911, 836.3820935, 353.6488805), aox3_12h_2.tsv = c(29.20942766, 
248.4582068, 51.52438237, 486.5817019, 390.8069314, 151.3860219
), aox3_12h_3.tsv = c(46.13590166, 273.2940355, 63.7297075, 503.9319503, 
395.8325311, 157.8115329), aox3_24h_1.tsv = c(34.29811675, 386.5204438, 
72.86154515, 693.3497618, 570.2158898, 194.3375745), aox3_24h_2.tsv = c(6.882795111, 
92.6003284, 26.22967721, 228.5226723, 120.5788092, 49.8811201
), aox3_24h_3.tsv = c(18.1408733, 196.4513931, 40.71817893, 375.4835311, 
334.5830825, 97.88584005), WT_0h_1.tsv = c(18.68220076, 114.5750048, 
9.829645971, 220.5843393, 174.4842611, 94.2738265), WT_0h_2.tsv = c(13.60937828, 
73.97033656, 17.038227, 214.8653415, 155.5073735, 100.5135226
), WT_0h_3.tsv = c(16.96217952, 76.57929551, 16.07674964, 141.6508369, 
145.1300591, 73.15117509), WT_12h_2.tsv = c(5.05511416, 11.33088644, 
4.189101647, 44.84100697, 44.55982506, 18.2843175), WT_12h_3.tsv = c(0.990461611, 
0.949660867, 1.699219964, 15.91825777, 15.35309945, 9.38446604
), WT_12h_5.tsv = c(5.933614952, 46.86761146, 10.29591467, 122.7757985, 
69.69893277, 56.94217399), WT_24h_1.tsv = c(4.029020182, 31.21885208, 
10.11987433, 100.5907921, 76.64674385, 37.26256017), WT_24h_4.tsv = c(3.054100241, 
102.1107272, 18.4440106, 121.8360378, 154.6688737, 44.27986257
), WT_24h_5.tsv = c(8.133354312, 97.5821868, 10.70295122, 176.7748047, 
164.02099, 24.53833578)), class = c("spec_tbl_df", "tbl_df", 
"tbl", "data.frame"), row.names = c(NA, -6L), spec = structure(list(
    cols = list(AGI = structure(list(), class = c("collector_character", 
    "collector")), aox1_0h_1.tsv = structure(list(), class = c("collector_double", 
    "collector")), aox1_0h_4.tsv = structure(list(), class = c("collector_double", 
    "collector")), aox1_0h_5.tsv = structure(list(), class = c("collector_double", 
    "collector")), aox1_12h_4.tsv = structure(list(), class = c("collector_double", 
    "collector")), aox1_12h_5.tsv = structure(list(), class = c("collector_double", 
    "collector")), aox1_12h_6.tsv = structure(list(), class = c("collector_double", 
    "collector")), aox1_24h_4.tsv = structure(list(), class = c("collector_double", 
    "collector")), aox1_24h_6.tsv = structure(list(), class = c("collector_double", 
    "collector")), aox2_0h_3.tsv = structure(list(), class = c("collector_double", 
    "collector")), aox2_0h_4.tsv = structure(list(), class = c("collector_double", 
    "collector")), aox2_0h_5.tsv = structure(list(), class = c("collector_double", 
    "collector")), aox2_12h_1.tsv = structure(list(), class = c("collector_double", 
    "collector")), aox2_12h_2.tsv = structure(list(), class = c("collector_double", 
    "collector")), aox2_12h_3.tsv = structure(list(), class = c("collector_double", 
    "collector")), aox2_24h_1.tsv = structure(list(), class = c("collector_double", 
    "collector")), aox2_24h_4.tsv = structure(list(), class = c("collector_double", 
    "collector")), aox2_24h_5.tsv = structure(list(), class = c("collector_double", 
    "collector")), aox3_0h_1.tsv = structure(list(), class = c("collector_double", 
    "collector")), aox3_0h_2.tsv = structure(list(), class = c("collector_double", 
    "collector")), aox3_0h_3.tsv = structure(list(), class = c("collector_double", 
    "collector")), aox3_12h_1.tsv = structure(list(), class = c("collector_double", 
    "collector")), aox3_12h_2.tsv = structure(list(), class = c("collector_double", 
    "collector")), aox3_12h_3.tsv = structure(list(), class = c("collector_double", 
    "collector")), aox3_24h_1.tsv = structure(list(), class = c("collector_double", 
    "collector")), aox3_24h_2.tsv = structure(list(), class = c("collector_double", 
    "collector")), aox3_24h_3.tsv = structure(list(), class = c("collector_double", 
    "collector")), WT_0h_1.tsv = structure(list(), class = c("collector_double", 
    "collector")), WT_0h_2.tsv = structure(list(), class = c("collector_double", 
    "collector")), WT_0h_3.tsv = structure(list(), class = c("collector_double", 
    "collector")), WT_12h_2.tsv = structure(list(), class = c("collector_double", 
    "collector")), WT_12h_3.tsv = structure(list(), class = c("collector_double", 
    "collector")), WT_12h_5.tsv = structure(list(), class = c("collector_double", 
    "collector")), WT_24h_1.tsv = structure(list(), class = c("collector_double", 
    "collector")), WT_24h_4.tsv = structure(list(), class = c("collector_double", 
    "collector")), WT_24h_5.tsv = structure(list(), class = c("collector_double", 
    "collector"))), default = structure(list(), class = c("collector_guess", 
    "collector")), skip = 1), class = "col_spec"))

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