Read summary

Alignment summary

Reference genome alignment statistics. These were generated using seqkit ) `seqkit bam -s`
sample_id PrimAlnPerc MultimapPerc PrimAln SecAln SupAln Unmapped TotalReads TotalRecords
sample01 100.0 0.0 218 0 0 0 218 218
sample02 100.0 0.0 229 0 0 0 229 229
sample03 100.0 0.0 206 0 0 0 206 206
sample04 100.0 0.0 193 0 0 0 193 193
sample05 100.0 0.0 168 0 0 0 168 168
sample06 100.0 0.0 195 0 0 0 195 195

Transcriptome summary

Transcriptome summary
Total genes 13
Total transcripts 15
Max trans. len 2608
Min trans. len 324
Transcriptome summary
Total genes 13
Total transcripts 15
Max trans. len 2608
Min trans. len 324
Transcriptome summary
Total genes 13
Total transcripts 15
Max trans. len 2608
Min trans. len 324
Transcriptome summary
Total genes 13
Total transcripts 14
Max trans. len 2611
Min trans. len 327
Transcriptome summary
Total genes 15
Total transcripts 17
Max trans. len 2609
Min trans. len 312
Transcriptome summary
Total genes 15
Total transcripts 16
Max trans. len 2609
Min trans. len 312

Annotation summary

The following plots summarize some of the output from gffcompare
  • Totals: Comparison of the number of stringtie-generated transcripts, multiexonic transcripts and loci between reference and query
  • Performance: How accurate are the query transcript annotations with respect to the reference at various levels
  • Missed: Features present in the reference, but absent in the query
  • Novel: Features present in the query transcripts, but absent in the reference

Query transfrag classification

Summaries of the classes assigned by gffcompare, which describe the relationship between query transfrag and the most similar reference transcript. This diagram illustrates the different classes.
Class Count Percent Description
i 4 26.67 intron
= 4 26.67 complete
x 3 20.0 exonic
k 2 13.33 containment
o 1 6.67 overlap
s 1 6.67 opposite
Class Count Percent Description
i 4 26.67 intron
= 4 26.67 complete
x 3 20.0 exonic
k 2 13.33 containment
o 1 6.67 overlap
s 1 6.67 opposite
Class Count Percent Description
i 4 26.67 intron
= 4 26.67 complete
x 3 20.0 exonic
k 2 13.33 containment
o 1 6.67 overlap
s 1 6.67 opposite
Class Count Percent Description
x 5 35.71 exonic
i 3 21.43 intron
u 2 14.29 unknown
= 2 14.29 complete
o 1 7.14 overlap
s 1 7.14 opposite
Class Count Percent Description
i 4 23.53 intron
x 3 17.65 exonic
s 3 17.65 opposite
= 2 11.76 complete
u 2 11.76 unknown
k 2 11.76 containment
o 1 5.88 overlap
Class Count Percent Description
i 4 25.0 intron
= 3 18.75 complete
s 3 18.75 opposite
u 3 18.75 unknown
x 2 12.5 exonic
k 1 6.25 containment

Isoforms

This table details each isoforms identified per sample. Table interactivity can be slow if too many isoforms are loaded. The number of isoform rows to load in this table can be set with isoform_table_nrows. It is currently set to 5000.
ref_gene_id ref_id class_code qry_id num_exons cov len sample_id parent gene iso num
TARDBPP1 ENST00000442013.1 x sample01_batch_1.3.1 2 5 2589 sample01 3.0
TARDBPP1 ENST00000442013.1 k sample01_batch_1.2.1 2 8 2610 sample01 3.0
TARDBPP1 ENST00000442013.1 = sample01_batch_1.2.2 1 0 1203 sample01 3.0
TPM3P2 ENST00000397772.2 k sample01_batch_1.9.1 3 8 2058 sample01 2.0
TPM3P2 ENST00000397772.2 s sample01_batch_1.8.1 3 12 2067 sample01 2.0
RPS4XP2 ENST00000458402.1 o sample01_batch_1.1.1 2 3 814 sample01 2.0
NCOA5 ENST00000290231.9 i sample01_batch_1.13.1 2 44 326 sample01 2.0
NCOA5 ENST00000290231.9 i sample01_batch_1.12.1 2 3 360 sample01 2.0
RPS4XP2 ENST00000458402.1 = sample01_batch_1.1.2 1 0 793 sample01 2.0
ITCH ENST00000374864.7 i sample01_batch_1.11.1 1 69 571 sample01 1.0
RP5-836E8.1 ENST00000400616.2 x sample01_batch_1.4.1 1 12 1308 sample01 1.0
RPL15P1 ENST00000439981.1 = sample01_batch_1.5.1 1 3 600 sample01 1.0
ZNF337-AS1 ENST00000428254.4 i sample01_batch_1.7.1 2 3 1457 sample01 1.0
SF3A3P1 ENST00000446317.1 x sample01_batch_1.6.1 2 3 362 sample01 1.0
RPL12P4 ENST00000432629.1 = sample01_batch_1.10.1 1 3 497 sample01 1.0
ref_gene_id ref_id class_code qry_id num_exons cov len sample_id parent gene iso num
TARDBPP1 ENST00000442013.1 x sample02_batch_1.3.1 2 6 2589 sample02 3.0
TARDBPP1 ENST00000442013.1 k sample02_batch_1.2.1 2 8 2610 sample02 3.0
TARDBPP1 ENST00000442013.1 = sample02_batch_1.2.2 1 0 1203 sample02 3.0
TPM3P2 ENST00000397772.2 k sample02_batch_1.9.1 3 8 2058 sample02 2.0
TPM3P2 ENST00000397772.2 s sample02_batch_1.8.1 3 12 2066 sample02 2.0
NCOA5 ENST00000290231.9 i sample02_batch_1.12.1 2 6 360 sample02 2.0
NCOA5 ENST00000290231.9 i sample02_batch_1.13.1 2 50 326 sample02 2.0
RPS4XP2 ENST00000458402.1 = sample02_batch_1.1.2 1 0 793 sample02 2.0
RPS4XP2 ENST00000458402.1 o sample02_batch_1.1.1 2 2 814 sample02 2.0
ITCH ENST00000374864.7 i sample02_batch_1.10.1 1 69 571 sample02 1.0
RP5-836E8.1 ENST00000400616.2 x sample02_batch_1.4.1 1 16 1308 sample02 1.0
ZNF337-AS1 ENST00000428254.4 i sample02_batch_1.7.1 2 3 1457 sample02 1.0
SF3A3P1 ENST00000446317.1 x sample02_batch_1.6.1 2 4 362 sample02 1.0
RPL12P4 ENST00000432629.1 = sample02_batch_1.11.1 1 1 497 sample02 1.0
RPL15P1 ENST00000439981.1 = sample02_batch_1.5.1 1 1 600 sample02 1.0
ref_gene_id ref_id class_code qry_id num_exons cov len sample_id parent gene iso num
TARDBPP1 ENST00000442013.1 x sample03_batch_1.3.1 2 4 2601 sample03 3.0
TARDBPP1 ENST00000442013.1 k sample03_batch_1.2.1 2 8 2610 sample03 3.0
TARDBPP1 ENST00000442013.1 = sample03_batch_1.2.2 1 0 1203 sample03 3.0
NCOA5 ENST00000290231.9 i sample03_batch_1.12.1 2 8 360 sample03 2.0
TPM3P2 ENST00000397772.2 s sample03_batch_1.8.1 3 14 2066 sample03 2.0
TPM3P2 ENST00000397772.2 k sample03_batch_1.9.1 3 3 2058 sample03 2.0
NCOA5 ENST00000290231.9 i sample03_batch_1.13.1 2 42 326 sample03 2.0
RPS4XP2 ENST00000458402.1 o sample03_batch_1.1.1 2 1 814 sample03 2.0
RPS4XP2 ENST00000458402.1 = sample03_batch_1.1.2 1 0 793 sample03 2.0
RP5-836E8.1 ENST00000400616.2 x sample03_batch_1.4.1 1 10 1308 sample03 1.0
ITCH ENST00000374864.7 i sample03_batch_1.11.1 1 62 571 sample03 1.0
SF3A3P1 ENST00000446317.1 x sample03_batch_1.6.1 2 3 362 sample03 1.0
RPL15P1 ENST00000439981.1 = sample03_batch_1.5.1 1 4 600 sample03 1.0
RPL12P4 ENST00000432629.1 = sample03_batch_1.10.1 1 4 497 sample03 1.0
ZNF337-AS1 ENST00000428254.4 i sample03_batch_1.7.1 2 3 1457 sample03 1.0
ref_gene_id ref_id class_code qry_id num_exons cov len sample_id parent gene iso num
TARDBPP1 ENST00000442013.1 x sample04_batch_1.2.2 2 3 2613 sample04 3.0
TARDBPP1 ENST00000442013.1 o sample04_batch_1.3.1 4 1 1903 sample04 3.0
TARDBPP1 ENST00000442013.1 x sample04_batch_1.2.1 2 4 2611 sample04 3.0
CDC42P1 ENST00000456658.1 x sample04_batch_1.11.1 1 32 1406 sample04 2.0
CDC42P1 ENST00000456658.1 = sample04_batch_1.12.1 1 0 548 sample04 2.0
NCOA5 ENST00000290231.9 i sample04_batch_1.10.1 2 3 329 sample04 2.0
NCOA5 ENST00000290231.9 i sample04_batch_1.9.1 2 20 357 sample04 2.0
RP5-836E8.1 ENST00000400616.2 x sample04_batch_1.4.1 1 13 1899 sample04 1.0
TPM3P2 ENST00000397772.2 s sample04_batch_1.6.1 3 7 2066 sample04 1.0
CBFA2T2 ENST00000375279.5 i sample04_batch_1.8.1 2 3 345 sample04 1.0
ADA ENST00000372874.7 x sample04_batch_1.13.1 3 2 634 sample04 1.0
FTLP3 ENST00000427242.1 = sample04_batch_1.1.1 1 2 528 sample04 1.0
- - u sample04_batch_1.5.1 4 2 2582 sample04 nan
- - u sample04_batch_1.7.1 2 2 1323 sample04 nan
ref_gene_id ref_id class_code qry_id num_exons cov len sample_id parent gene iso num
CDC42P1 ENST00000456658.1 k sample05_batch_1.11.1 1 29 1406 sample05 2.0
NCOA5 ENST00000290231.9 i sample05_batch_1.9.1 2 22 357 sample05 2.0
TARDBPP1 ENST00000442013.1 k sample05_batch_1.2.1 2 3 2611 sample05 2.0
NCOA5 ENST00000290231.9 i sample05_batch_1.10.1 2 2 329 sample05 2.0
TPM3P2 ENST00000397772.2 s sample05_batch_1.7.1 3 2 2066 sample05 2.0
TPM3P2 ENST00000397772.2 s sample05_batch_1.7.2 3 2 2067 sample05 2.0
TARDBPP1 ENST00000442013.1 o sample05_batch_1.2.2 4 2 1903 sample05 2.0
CDC42P1 ENST00000456658.1 = sample05_batch_1.12.1 1 0 548 sample05 2.0
FTLP3 ENST00000427242.1 = sample05_batch_1.1.1 1 2 528 sample05 1.0
CFAP61 ENST00000245957.8 x sample05_batch_1.6.1 3 3 852 sample05 1.0
RP5-836E8.1 ENST00000400616.2 x sample05_batch_1.4.1 1 12 1899 sample05 1.0
LINC00851 ENST00000423033.1 x sample05_batch_1.5.1 3 2 2253 sample05 1.0
PTGIS ENST00000244043.4 i sample05_batch_1.13.1 2 2 677 sample05 1.0
DDX27 ENST00000622530.3 s sample05_batch_1.14.1 3 2 315 sample05 1.0
MACROD2 ENST00000217246.7 i sample05_batch_1.15.1 2 2 1713 sample05 1.0
- - u sample05_batch_1.3.1 2 2 713 sample05 nan
- - u sample05_batch_1.8.1 2 2 1323 sample05 nan
ref_gene_id ref_id class_code qry_id num_exons cov len sample_id parent gene iso num
NCOA5 ENST00000290231.9 i sample06_batch_1.11.1 2 24 357 sample06 2.0
TARDBPP1 ENST00000442013.1 k sample06_batch_1.2.1 2 3 2611 sample06 2.0
NCOA5 ENST00000290231.9 i sample06_batch_1.12.1 2 2 329 sample06 2.0
TARDBPP1 ENST00000442013.1 = sample06_batch_1.2.2 1 0 1203 sample06 2.0
RP5-836E8.1 ENST00000400616.2 x sample06_batch_1.4.1 1 12 1899 sample06 1.0
CDC42P1 ENST00000456658.1 = sample06_batch_1.10.1 1 4 548 sample06 1.0
TPM3P2 ENST00000397772.2 s sample06_batch_1.7.1 3 5 2066 sample06 1.0
RPL21P3 ENST00000395517.2 s sample06_batch_1.5.1 2 2 543 sample06 1.0
DDX27 ENST00000622530.3 s sample06_batch_1.13.1 3 3 315 sample06 1.0
CBFA2T2 ENST00000375279.5 i sample06_batch_1.9.1 2 2 345 sample06 1.0
ADA ENST00000372874.7 x sample06_batch_1.14.1 3 2 634 sample06 1.0
MACROD2 ENST00000217246.7 i sample06_batch_1.15.1 2 2 2058 sample06 1.0
FTLP3 ENST00000427242.1 = sample06_batch_1.1.1 1 1 528 sample06 1.0
- - u sample06_batch_1.3.1 2 2 713 sample06 nan
- - u sample06_batch_1.8.1 2 2 1323 sample06 nan
- - u sample06_batch_1.6.1 4 2 2582 sample06 nan

Differential expression

This section shows differential gene expression and differential isoform usage. Salmon was used to assign reads to individual annotated isoforms defined by the GTF-format annotation. These counts were used to perform a statistical analysis to identify the genes and isoforms that show differences in abundance between the experimental conditions. Any novel genes or transcripts that do not have relevant gene or transcript IDs are prefixed with MSTRG for use in differential expression analysis. Find the full sequences of any transcripts in the final_non_redundant_transcriptome.fasta file.

Alignment summary stats
statistic sample01 sample02 sample03 sample04 sample05 sample06
Read mappings 4191 4484 4316 4266 4077 4084
Primary 1093 1157 1104 1048 1010 995
Secondary 3048 3271 3158 3151 3010 3021
Supplementary 50 56 54 67 57 68
Median Qscore 8 8 8 8 8 8
Median MAPQ 0 0 0 0 0 0
Transcripts Per Million

Table showing the annotated Transcripts Per Million identified by Minimap2 mapping and Salmon transcript detection. Displaying the top 100 transcripts with the highest number of mapped reads

Reference sample01 sample02 sample03 sample04 sample05 sample06
MSTRG.75.1 744698 722232 732968 798333 786157 775481
MSTRG.74.3 208263 230776 221012 141996 156434 156155
MSTRG.10.1 3214 3035 3080 8840 6874 7163
ENST00000372291.3 5711 6321 6056 3862 4254 4247
MSTRG.63.1 6123 6195 6287 4209 2923 3480
ENST00000290231.9 4504 4985 4776 3045 3355 3349
ENST00000427242.1 0 0 0 5243 5097 6070
ENST00000432629.1 4292 4053 4113 0 0 0
ENST00000400616.2 3855 3640 3694 0 0 0
MSTRG.12.1 0 0 0 4270 2490 3954
MSTRG.36.1 0 0 0 0 4700 5597
ENST00000439981.1 3029 2860 2902 0 0 0
MSTRG.65.1 0 0 0 2605 2532 3016
MSTRG.8.1 1752 2068 1259 1204 1171 697
ENST00000486883.4 967 854 826 1330 1378 1172
MSTRG.89.1 0 0 0 1980 1925 2292
MSTRG.64.1 1314 1241 1260 602 585 697
ENST00000458402.1 1903 1797 1824 0 0 0
ENST00000256654.8 0 0 0 2539 0 2940
ENST00000446317.1 0 0 0 1188 1154 1375
ENST00000397772.2 1256 1186 1203 0 0 0
ENST00000431775.1 1227 1158 1175 0 0 0
ENST00000543500.2 0 0 0 1130 1099 1309
ENST00000598007.2 0 0 0 1042 1013 1207
ENST00000613361.1 418 395 400 575 559 665
ENST00000535650.4 415 366 354 583 603 517
ENST00000262650.9 337 297 288 483 498 422
ENST00000374864.7 336 297 288 473 488 422
ENST00000496085.1 0 0 0 680 661 787
ENST00000457644.1 0 0 0 757 736 438
MSTRG.48.1 617 582 591 0 0 0
ENST00000376312.3 547 517 524 0 0 0
MSTRG.34.1 0 0 0 0 662 788
MSTRG.85.1 0 0 0 439 427 508
ENST00000352551.8 0 0 0 361 351 418
ENST00000243893.9 0 0 0 359 349 416
ENST00000335046.6 0 0 0 357 347 414
ENST00000405520.4 0 0 0 353 343 408
ENST00000356455.7 0 0 0 352 342 408
MSTRG.1.1 242 267 232 55 54 64
ENST00000609285.4 0 0 0 313 248 329
ENST00000466532.1 0 0 0 0 406 483
ENST00000446423.1 0 0 0 305 242 321
ENST00000609470.4 0 0 0 302 240 317
ENST00000421216.1 66 62 63 182 177 211
ENST00000324384.3 0 0 0 204 132 236
MSTRG.54.1 0 0 0 104 202 241
ENST00000381253.4 0 0 0 173 168 200
ENST00000456249.4 185 175 177 0 0 0
ENST00000481560.1 0 0 0 168 164 195
ENST00000466099.1 166 157 159 0 0 0
ENST00000446916.2 87 110 98 50 39 46
ENST00000348616.7 0 0 0 133 130 155
ENST00000202017.5 141 133 135 0 0 0
ENST00000429853.1 0 0 0 129 125 149
ENST00000468420.4 0 0 0 126 122 146
ENST00000624666.1 130 123 125 0 0 0
MSTRG.78.1 0 0 0 143 69 166
ENST00000491682.4 97 91 93 44 43 0
ENST00000493252.2 124 117 119 0 0 0
ENST00000356562.5 0 0 0 135 66 157
ENST00000262919.8 70 89 79 40 31 37
ENST00000300403.9 0 0 0 93 113 135
ENST00000278772.7 0 0 0 107 104 124
ENST00000623732.2 111 105 106 0 0 0
ENST00000344103.7 0 0 0 102 99 119
ENST00000375730.3 108 102 103 0 0 0
ENST00000462062.4 0 0 0 0 141 168
MSTRG.39.1 0 0 0 108 105 93
ENST00000413823.1 0 0 0 97 94 112
ENST00000379070.3 0 0 0 97 94 112
ENST00000484893.1 103 98 99 0 0 0
ENST00000412241.1 0 0 0 123 80 95
ENST00000377873.6 28 26 27 78 38 90
ENST00000482423.1 98 93 94 0 0 0
ENST00000371856.5 42 93 67 38 37 0
ENST00000360672.2 0 0 0 88 85 101
ENST00000449988.1 0 0 0 87 85 101
ENST00000609252.1 94 89 90 0 0 0
ENST00000262866.7 0 0 0 86 84 100
ENST00000481196.4 92 87 88 0 0 0
ENST00000435014.1 0 0 0 84 82 98
ENST00000584356.1 12 11 12 86 83 59
ENST00000372420.4 0 0 0 122 0 141
ENST00000617804.1 0 0 0 97 95 67
ENST00000618770.1 0 0 0 96 94 67
ENST00000619859.1 0 0 0 80 78 93
ENST00000621390.1 0 0 0 115 0 134
ENST00000450129.1 85 81 82 0 0 0
ENST00000618797.3 0 0 0 79 77 91
ENST00000339946.6 0 0 0 0 245 0
ENST00000457508.1 84 80 81 0 0 0
ENST00000558738.1 83 78 79 0 0 0
ENST00000344256.9 0 0 0 76 74 88
ENST00000456939.4 0 0 0 76 74 88
ENST00000372622.6 0 0 0 75 73 87
ENST00000445484.4 0 0 0 73 70 84
ENST00000449270.1 0 0 0 70 68 81
ENST00000461710.4 0 0 0 0 99 118
ENST00000217073.5 74 70 71 0 0 0
Differential gene expression

Table showing the genes from the edgeR analysis. Information shown includes the log2 fold change between experimental conditions, the log-scaled counts per million measure of abundance and the FDR-corrected p-value (False discovery rate - Benjamini-Hochberg). This table has not been filtered for genes that satisfy statistical or magnitudinal thresholds

gene_id gene_name logFC logCPM F PValue FDR
ENSG00000171984.13 C20orf196 5.94 12.26 1918191.34 6.72404669482186e-08 1.29774101210062e-05
ENSG00000124215.15 CDH26 5.53 12.0 4972599.79 1.7312632098221e-06 8.35334498739164e-05
ENSG00000175063.15 UBE2C 5.53 12.0 4972599.79 1.7312632098221e-06 8.35334498739164e-05
ENSG00000101052.11 IFT52 5.53 12.0 4972599.79 1.7312632098221e-06 8.35334498739164e-05
ENSG00000174306.20 ZHX3 5.28 11.84 9080108.16 1.26654051557923e-05 0.0004888846390135
ENSG00000204548.3 DEFB121 -5.13 11.67 6222.42 5.08874005752377e-05 0.0005604674908656
ENSG00000124226.9 RNF114 -5.44 11.84 6220.96 5.09012377632238e-05 0.0005604674908656
ENSG00000259723.1 RP5-823G15.5 -5.13 11.67 6222.42 5.08874005752377e-05 0.0005604674908656
ENSG00000182463.14 TSHZ2 -5.92 12.13 6214.33 5.09639810307549e-05 0.0005604674908656
ENSG00000101104.11 PABPC1L -6.11 12.26 6208.65 5.1017951723883e-05 0.0005604674908656
ENSG00000149646.11 CNBD2 -5.7 12.0 6218.36 5.09258428730034e-05 0.0005604674908656
ENSG00000126005.14 MMP24-AS1 -5.7 12.0 6218.36 5.09258428730034e-05 0.0005604674908656
ENSG00000131061.12 ZNF341 -6.69 12.68 6167.23 5.14143869487172e-05 0.0005604674908656
ENSG00000089123.14 TASP1 -7.19 13.07 6079.68 5.22715794589763e-05 0.0005604674908656
ENSG00000196090.11 PTPRT 2.88 14.35 391.24 2.13208938942121e-05 0.0005604674908656
ENSG00000054793.12 ATP9A 2.91 12.52 298.25 3.80491336744014e-05 0.0005604674908656
ENSG00000100991.10 TRPC4AP -5.13 11.67 6222.42 5.08874005752377e-05 0.0005604674908656
ENSG00000125850.9 OVOL2 -5.13 11.67 6222.42 5.08874005752377e-05 0.0005604674908656
ENSG00000088876.10 ZNF343 2.69 12.37 40030.67 5.74016383427703e-05 0.0005830798000081
ENSG00000101082.12 SLA2 4.96 11.67 18552551.98 9.42655997776632e-05 0.0007580525315453
ENSG00000101146.11 RAE1 4.96 11.67 18552551.98 9.42655997776632e-05 0.0007580525315453
ENSG00000124207.15 CSE1L 4.96 11.67 18552551.98 9.42655997776632e-05 0.0007580525315453
ENSG00000125851.8 PCSK2 4.96 11.67 18552551.98 9.42655997776632e-05 0.0007580525315453
ENSG00000185052.10 SLC24A3 4.96 11.67 18552551.98 9.42655997776632e-05 0.0007580525315453
MSTRG.1 MSTRG.1 -2.68 12.18 987.83 0.0001099591195694 0.000848884403076
MSTRG.74 MSTRG.74 -1.28 17.88 171.91 0.0001225187077518 0.0009094657921578
ENSG00000125821.10 DTD1 2.57 12.3 667.74 0.0001700744835538 0.0012157176046629
ENSG00000101079.19 NDRG3 -2.61 12.13 5862.34 0.0002089157912703 0.0014400267041136
ENSG00000089177.16 KIF16B -4.73 11.48 6223.01 0.0002284880676332 0.0014965383219675
MSTRG.63 MSTRG.63 -1.52 13.28 125.75 0.0002366056812451 0.0014965383219675
MSTRG.3 None -1.85 14.02 124.8 0.0002403766216631 0.0014965383219675
ENSG00000025293.14 PHF20 1.97 13.04 98.09 0.0003974686136346 0.002397232575984
MSTRG.14 None 4.56 11.48 41076307.07 0.0007202833638968 0.003475367230802
ENSG00000188559.12 RALGAPA2 4.56 11.48 41076307.07 0.0007202833638968 0.003475367230802
ENSG00000185019.15 UBOX5 4.56 11.48 41076307.07 0.0007202833638968 0.003475367230802
ENSG00000101457.11 DNTTIP1 4.56 11.48 41076307.07 0.0007202833638968 0.003475367230802
ENSG00000101144.11 BMP7 4.56 11.48 41076307.07 0.0007202833638968 0.003475367230802
ENSG00000089012.13 SIRPG 4.56 11.48 41076307.07 0.0007202833638968 0.003475367230802
ENSG00000124214.18 STAU1 -2.69 13.02 74.72 0.0006980410055575 0.003475367230802
ENSG00000234684.5 SDCBP2-AS1 7.86 13.79 646.16 0.0006969402721141 0.003475367230802
ENSG00000228340.4 MIR646HG 1.71 12.87 68.74 0.0008285759348444 0.0039003696445114
ENSG00000175170.13 FAM182B 3.77 13.13 58.15 0.0011656505994431 0.0053564420402981
MSTRG.75 MSTRG.75 -0.63 17.71 55.03 0.0013037091513181 0.0057185424137365
ENSG00000227906.6 SNAP25-AS1 2.13 12.7 55.26 0.0012923800784829 0.0057185424137365
ENSG00000100997.17 ABHD12 -3.33 12.87 49.26 0.001629709563261 0.0069896432379863
ENSG00000088325.14 TPX2 5.18 11.79 280.72 0.0018207084075641 0.0076390591882583
MSTRG.56 None 1.53 12.76 7760.26 0.0019825570340507 0.0081411384589742
MSTRG.13 MSTRG.13 2.2 12.09 326.43 0.0023934922077596 0.0096238332520333
ENSG00000170471.13 RALGAPB -4.17 11.26 6222.94 0.0026212202512577 0.0099195197743676
ENSG00000101350.7 KIF3B -4.17 11.26 6222.94 0.0026212202512577 0.0099195197743676
ENSG00000196700.6 ZNF512B -4.17 11.26 6222.94 0.0026212202512577 0.0099195197743676
MSTRG.39 MSTRG.39 4.84 11.61 171.9 0.003196151723948 0.0118626400523455
ENSG00000088826.16 SMOX 4.01 11.26 66393004.8 0.0057593115962705 0.0191646058289692
ENSG00000125772.11 GPCPD1 4.01 11.26 66393004.8 0.0057593115962705 0.0191646058289692
ENSG00000149633.10 KIAA1755 4.01 11.26 66393004.8 0.0057593115962705 0.0191646058289692
ENSG00000225458.1 RP5-1121H13.4 4.01 11.26 66393004.8 0.0057593115962705 0.0191646058289692
MSTRG.65 MSTRG.65 4.01 11.26 66393004.8 0.0057593115962705 0.0191646058289692
ENSG00000229876.1 CASC20 4.01 11.26 66393004.8 0.0057593115962705 0.0191646058289692
ENSG00000232271.1 RP4-764O22.1 4.4 11.41 89.55 0.0067227808976769 0.0205951859246292
ENSG00000118705.15 RPN2 2.03 12.0 18758.89 0.0066429165850444 0.0205951859246292
ENSG00000180083.9 WFDC11 5.37 11.9 89.56 0.0067216619651801 0.0205951859246292
ENSG00000198646.12 NCOA6 -2.54 11.79 24.27 0.0064862795316199 0.0205951859246292
ENSG00000130584.9 ZBTB46 4.4 11.41 89.55 0.0067227808976769 0.0205951859246292
ENSG00000271774.1 RP4-678D15.1 -2.03 11.84 4423.52 0.0085812530783357 0.0254797206787509
MSTRG.64 MSTRG.64 -2.03 11.84 4423.52 0.0085812530783357 0.0254797206787509
MSTRG.38 None 4.96 11.67 69.83 0.0089082866864543 0.0256611840370998
MSTRG.12 MSTRG.12 4.96 11.67 69.83 0.0089082866864543 0.0256611840370998
ENSG00000064787.11 BCAS1 5.75 12.13 68.0 0.0091792174197978 0.0260527788532497
ENSG00000274322.1 RP11-314N13.10 6.05 12.34 58.31 0.010910920422186 0.0305189513258246
ENSG00000064655.17 EYA2 1.51 12.34 261.5 0.0115603664071059 0.0318735816653062
ENSG00000124151.17 NCOA3 -2.27 12.58 15.08 0.015408374126916 0.0418847353027434
ENSG00000132669.11 RIN2 6.26 12.48 38.7 0.0172375144715199 0.0462061151806019
ENSG00000149488.12 TMC2 3.76 11.18 33.65 0.020112594879161 0.0510754054168167
ENSG00000226344.1 CST12P 3.76 11.18 33.65 0.020112594879161 0.0510754054168167
MSTRG.54 MSTRG.54 3.76 11.18 33.65 0.020112594879161 0.0510754054168167
MSTRG.78 MSTRG.78 3.76 11.18 33.65 0.020112594879161 0.0510754054168167
ENSG00000020256.18 ZFP64 -1.3 12.34 82.69 0.0221892473652013 0.0556172044348552
ENSG00000158296.12 SLC13A3 6.48 12.64 29.78 0.022991443784109 0.0568890852606799
ENSG00000101337.14 TM9SF4 -3.25 11.0 6221.87 0.0333641551596439 0.0613264947220121
ENSG00000101346.10 POFUT1 -3.25 11.0 6221.87 0.0333641551596439 0.0613264947220121
ENSG00000101363.11 MANBAL -3.25 11.0 6221.87 0.0333641551596439 0.0613264947220121
ENSG00000125885.12 MCM8 -3.25 11.0 6221.87 0.0333641551596439 0.0613264947220121
ENSG00000101003.9 GINS1 -3.25 11.0 6221.87 0.0333641551596439 0.0613264947220121
ENSG00000101181.16 MTG2 -3.25 11.0 6221.87 0.0333641551596439 0.0613264947220121
ENSG00000101191.15 DIDO1 -3.25 11.0 6221.87 0.0333641551596439 0.0613264947220121
ENSG00000101247.16 NDUFAF5 -3.25 11.0 6221.87 0.0333641551596439 0.0613264947220121
ENSG00000101134.10 DOK5 4.4 11.41 24.96 0.0278489035452151 0.0613264947220121
ENSG00000087586.16 AURKA -3.25 11.0 6221.87 0.0333641551596439 0.0613264947220121
ENSG00000088340.14 FER1L4 -3.25 11.0 6221.87 0.0333641551596439 0.0613264947220121
ENSG00000088356.5 PDRG1 -3.25 11.0 6221.87 0.0333641551596439 0.0613264947220121
ENSG00000238282.1 RP5-1164C1.2 -3.25 11.0 6221.87 0.0333641551596439 0.0613264947220121
ENSG00000235958.4 UBOX5-AS1 -3.25 11.0 6221.87 0.0333641551596439 0.0613264947220121
ENSG00000234139.2 RP4-550H1.4 -3.25 11.0 6221.87 0.0333641551596439 0.0613264947220121
ENSG00000215388.3 ACTG1P3 -3.25 11.0 6221.87 0.0333641551596439 0.0613264947220121
ENSG00000166948.8 TGM6 -3.25 11.0 6221.87 0.0333641551596439 0.0613264947220121
ENSG00000149531.13 FRG1B -3.25 11.0 6221.87 0.0333641551596439 0.0613264947220121
ENSG00000131069.18 ACSS2 -3.25 11.0 6221.87 0.0333641551596439 0.0613264947220121
ENSG00000125966.9 MMP24 -3.25 11.0 6221.87 0.0333641551596439 0.0613264947220121
MSTRG.48 MSTRG.48 -3.25 11.0 6221.87 0.0333641551596439 0.0613264947220121
MSTRG.90 None -3.25 11.0 6221.87 0.0333641551596439 0.0613264947220121
MSTRG.84 None -3.25 11.0 6221.87 0.0333641551596439 0.0613264947220121
MSTRG.7 MSTRG.7 -3.25 11.0 6221.87 0.0333641551596439 0.0613264947220121
MSTRG.24 None -3.25 11.0 6221.87 0.0333641551596439 0.0613264947220121
MSTRG.35 None -3.25 11.0 6221.87 0.0333641551596439 0.0613264947220121
MSTRG.11 None -3.25 11.0 6221.87 0.0333641551596439 0.0613264947220121
ENSG00000124191.16 TOX2 4.96 11.67 20.88 0.0337495247362604 0.0614496063594175
ENSG00000088888.16 MAVS 3.1 11.0 27711810.56 0.0508850148207671 0.068200054586167
ENSG00000080845.16 DLGAP4 3.1 11.0 27711810.56 0.0508850148207671 0.068200054586167
ENSG00000022277.11 RTFDC1 3.1 11.0 27711810.56 0.0508850148207671 0.068200054586167
ENSG00000101294.15 HM13 3.1 11.0 27711810.56 0.0508850148207671 0.068200054586167
ENSG00000101311.14 FERMT1 3.1 11.0 27711810.56 0.0508850148207671 0.068200054586167
ENSG00000101323.4 HAO1 3.1 11.0 27711810.56 0.0508850148207671 0.068200054586167
ENSG00000101353.13 MROH8 3.1 11.0 27711810.56 0.0508850148207671 0.068200054586167
ENSG00000101400.5 SNTA1 3.1 11.0 27711810.56 0.0508850148207671 0.068200054586167
ENSG00000101444.11 AHCY 3.1 11.0 27711810.56 0.0508850148207671 0.068200054586167
ENSG00000124103.8 FAM209A 3.1 11.0 27711810.56 0.0508850148207671 0.068200054586167
ENSG00000124143.9 ARHGAP40 3.1 11.0 27711810.56 0.0508850148207671 0.068200054586167
ENSG00000124177.13 CHD6 3.1 11.0 27711810.56 0.0508850148207671 0.068200054586167
ENSG00000132623.14 ANKEF1 3.1 11.0 27711810.56 0.0508850148207671 0.068200054586167
ENSG00000158445.7 KCNB1 3.1 11.0 27711810.56 0.0508850148207671 0.068200054586167
ENSG00000204663.8 CST13P 3.1 11.0 27711810.56 0.0508850148207671 0.068200054586167
ENSG00000226648.1 PLCG1-AS1 3.1 11.0 27711810.56 0.0508850148207671 0.068200054586167
ENSG00000228888.1 LINC01428 3.1 11.0 27711810.56 0.0508850148207671 0.068200054586167
ENSG00000229262.1 RP4-726N1.2 3.1 11.0 27711810.56 0.0508850148207671 0.068200054586167
ENSG00000243961.2 RP5-839B4.8 3.1 11.0 27711810.56 0.0508850148207671 0.068200054586167
ENSG00000244005.11 NFS1 3.1 11.0 27711810.56 0.0508850148207671 0.068200054586167
ENSG00000256222.2 MTRNR2L3 3.1 11.0 27711810.56 0.0508850148207671 0.068200054586167
ENSG00000260202.2 RP3-333B15.4 3.1 11.0 27711810.56 0.0508850148207671 0.068200054586167
ENSG00000268628.2 RP1-122P22.4 3.1 11.0 27711810.56 0.0508850148207671 0.068200054586167
ENSG00000274863.1 RP11-97N19.3 3.1 11.0 27711810.56 0.0508850148207671 0.068200054586167
ENSG00000279082.2 RP1-167O22.1 3.1 11.0 27711810.56 0.0508850148207671 0.068200054586167
MSTRG.4 None 3.1 11.0 27711810.56 0.0508850148207671 0.068200054586167
MSTRG.58 MSTRG.58 3.1 11.0 27711810.56 0.0508850148207671 0.068200054586167
MSTRG.6 None 3.1 11.0 27711810.56 0.0508850148207671 0.068200054586167
MSTRG.76 None 3.1 11.0 27711810.56 0.0508850148207671 0.068200054586167
MSTRG.85 MSTRG.85 3.1 11.0 27711810.56 0.0508850148207671 0.068200054586167
MSTRG.89 MSTRG.89 3.1 11.0 27711810.56 0.0508850148207671 0.068200054586167
MSTRG.8 MSTRG.8 -1.37 11.95 19.94 0.0493239329126233 0.068200054586167
ENSG00000234948.1 LINC01524 1.28 12.22 148.5 0.0391748111686984 0.068200054586167
ENSG00000101152.9 DNAJC5 3.1 11.0 27711810.56 0.0508850148207671 0.068200054586167
ENSG00000101224.16 CDC25B 3.1 11.0 27711810.56 0.0508850148207671 0.068200054586167
ENSG00000101290.12 CDS2 3.1 11.0 27711810.56 0.0508850148207671 0.068200054586167
ENSG00000101349.15 PAK7 4.22 11.34 15.58 0.0459547840143247 0.068200054586167
ENSG00000101109.10 STK4 4.22 11.34 15.58 0.0459547840143247 0.068200054586167
ENSG00000270792.4 RP11-103J8.1 1.46 11.73 70.21 0.0741562811243772 0.0987045672896883
ENSG00000125864.10 BFSP1 2.2 12.09 5.26 0.078799555277789 0.104166535401461
ENSG00000101425.11 BPI 1.32 11.67 6315.17 0.116250924863645 0.152628765297167
ENSG00000132792.17 CTNNBL1 4.22 11.34 4.86 0.140785781375367 0.183592268955715
MSTRG.16 None -0.31 15.63 3.19 0.143483028542076 0.185853855762555
ENSG00000101019.20 UQCC1 5.82 12.18 3.63 0.179668176812882 0.204915850078378
ENSG00000171456.15 ASXL1 4.4 11.41 3.63 0.179685553024743 0.204915850078378
ENSG00000172296.11 SPTLC3 4.4 11.41 3.63 0.179685553024743 0.204915850078378
MSTRG.36 MSTRG.36 3.47 11.09 3.63 0.179690575335173 0.204915850078378
ENSG00000130703.14 OSBPL2 2.59 10.9 3.63 0.179693132224104 0.204915850078378
ENSG00000125844.14 RRBP1 2.59 10.9 3.63 0.179693132224104 0.204915850078378
ENSG00000101440.8 ASIP 2.59 10.9 3.63 0.179693132224104 0.204915850078378
ENSG00000101407.11 TTI1 2.59 10.9 3.63 0.179693132224104 0.204915850078378
ENSG00000101333.15 PLCB4 2.59 10.9 3.63 0.179693132224104 0.204915850078378
ENSG00000101391.19 CDK5RAP1 4.96 11.67 3.63 0.179680552107841 0.204915850078378
ENSG00000089057.13 SLC23A2 4.01 11.26 3.63 0.179688060705615 0.204915850078378
ENSG00000225069.3 RP5-1025A1.2 2.59 10.9 3.63 0.179693132224104 0.204915850078378
MSTRG.34 MSTRG.34 2.59 10.9 3.63 0.179693132224104 0.204915850078378
ENSG00000240849.9 TMEM189 2.59 10.9 3.63 0.179693132224104 0.204915850078378
ENSG00000254995.4 STX16-NPEPL1 2.59 10.9 3.63 0.179693132224104 0.204915850078378
ENSG00000274469.1 RP11-425M5.8 2.59 10.9 3.63 0.179693132224104 0.204915850078378
ENSG00000089063.13 TMEM230 -1.58 11.41 2.55 0.180495826493908 0.204915850078378
MSTRG.47 None 2.59 10.9 3.63 0.179693132224104 0.204915850078378
ENSG00000092758.14 COL9A3 2.59 10.9 3.63 0.179693132224104 0.204915850078378
ENSG00000042062.10 FAM65C 2.59 10.9 3.63 0.179693132224104 0.204915850078378
ENSG00000100979.13 PLTP 2.59 10.9 3.63 0.179693132224104 0.204915850078378
ENSG00000215529.11 EFCAB8 -0.97 11.79 16.45 0.194231020448404 0.219219806704924
ENSG00000101443.16 WFDC2 3.47 11.09 2.74 0.22256174640256 0.249734982881943
MSTRG.10 MSTRG.10 0.55 12.79 11.36 0.224237169833576 0.250160542068671
ENSG00000280350.1 RP5-1065O2.4 -1.07 11.48 1805.01 0.235257013827678 0.260945998096217
ENSG00000179242.14 CDH4 -0.68 12.18 4.04 0.256785343225795 0.283197549957591
ENSG00000101236.15 RNF24 0.97 11.55 3.93 0.272423102001176 0.298736697080835
ENSG00000088970.14 KIZ 1.15 11.61 1.2 0.331125622074974 0.36105788169757
ENSG00000080839.10 RBL1 -0.57 12.13 550.63 0.353177109933633 0.382939225939276
MSTRG.66 None -0.14 17.16 0.94 0.38319406571591 0.41316455130263
ENSG00000124198.8 ARFGEF2 0.76 11.48 1777.48 0.404857548665543 0.429326960947526
ENSG00000088854.12 C20orf194 0.76 11.48 1777.48 0.404857548665543 0.429326960947526
ENSG00000130699.15 TAF4 0.76 11.48 1777.48 0.404857548665543 0.429326960947526
MSTRG.53 None 0.4 12.48 2.4 0.438725142041501 0.462699193519179
ENSG00000087495.15 PHACTR3 0.76 11.48 0.61 0.473780535252441 0.496954583172397
ENSG00000149636.14 DSN1 -0.92 11.0 0.53 0.504887515875499 0.52672048953498
ENSG00000226995.6 LINC00658 -0.66 11.18 0.9 0.56084144313865 0.581948379170749
ENSG00000182621.15 PLCB1 0.09 14.88 2.29 0.649045726907353 0.669870723492615
ENSG00000132670.19 PTPRA -0.15 11.26 54.54 0.88400539809773 0.88400539809773
ENSG00000277938.1 RP5-965G21.3 -0.15 11.26 54.54 0.88400539809773 0.88400539809773
ENSG00000227195.7 MIR663AHG -0.15 11.26 54.54 0.88400539809773 0.88400539809773
ENSG00000154930.13 ACSS1 -0.15 11.26 54.54 0.88400539809773 0.88400539809773
ENSG00000062598.16 ELMO2 -0.15 11.26 54.54 0.88400539809773 0.88400539809773
ENSG00000101463.5 SYNDIG1 -0.15 11.26 54.54 0.88400539809773 0.88400539809773
Results of the edgeR Analysis.

This plot visualises differences in measurements between the two experimental conditions. M is the log2 ratio of gene expression calculated between the conditions. A is a log2 transformed mean expression value. The figure below presents the MA figure from this edgeR analysis. Genes that satisfy the logFC and FDR-corrected (False discovery rate - Benjamini-Hochberg) p-value thresholds defined are shaded as 'Up-' or 'Down-' regulated.

Differential Isoform usage

Table showing gene isoforms, ranked by adjusted p-value, from the DEXSeq analysis. Information shown includes the log2 fold change between experimental conditions, the log-scaled transcript abundance and the false discovery corrected p-value (FDR - Benjamini-Hochberg) . This table has not been filtered for genes that satisfy statistical or magnitudinal thresholds

gene_id:transcript_id gene_name Log2MeanExon Log2FC pvalue padj
ENSG00000182621.15: ENST00000626161.1 None 0.86301871511606 13.018997656315 0.0001607653374057 0.0085205628825067
ENSG00000182621.15: ENST00000626114.1 None 2.12253236422214 -1.82746788214343 0.0004892701563061 0.0129656591421118
ENSG00000196090.11: ENST00000373198.7 None 1.35165233466146 -1.29962534449639 0.0017755178339823 0.0313674817336882
ENSG00000175170.13: ENST00000584356.1 None 1.31045176000795 -0.553281837352508 0.0100173078806734 0.132729329418923
ENSG00000182621.15: ENST00000338037.9 None 3.03326457550731 -0.675450969358931 0.0183318540217669 0.194317652630729
ENSG00000172264.15: ENST00000402914.4 None 3.38248110988961 -0.756556282722864 0.0262932783638605 0.232257292214101
ENSG00000196090.11: ENST00000617474.1 None 1.73893897556517 13.7950317104374 0.0390308815752158 0.268950692562207
ENSG00000196090.11: ENST00000373190.4 None 1.67095694704978 13.7279180151573 0.0456708723218842 0.268950692562207
ENSG00000196090.11: ENST00000373201.4 None 1.67095694704978 13.7279180151425 0.0456708723218842 0.268950692562207
ENSG00000182621.15: ENST00000378637.5 None 1.7908451363128 1.32453969163109 0.059034775095954 0.292311007245988
ENSG00000172264.15: ENST00000490428.4 None 3.00453515524464 0.709115610057716 0.0606683222586012 0.292311007245988
ENSG00000025293.14: ENST00000374000.7 None 0.734581161693187 10.7212380727543 0.103346877864387 0.456448710567708
ENSG00000182621.15: ENST00000629992.1 None 0.911210965284336 1.49446268363441 0.125947238908852 0.504909371596392
ENSG00000196090.11: ENST00000618610.1 None 0.911210965284336 -0.45163142175832 0.133372286836783 0.504909371596392
ENSG00000025293.14: ENST00000374012.6 None 0.787179701404464 -0.50030011401628 0.151904937243826 0.512179624558081
ENSG00000124214.18: ENST00000371856.5 None 1.66959139200807 0.252207542014709 0.154620264017534 0.512179624558081
ENSG00000025293.14: ENST00000461122.4 None 0.274058029720744 10.2618111973886 0.219550924187988 0.684482293056669
ENSG00000182621.15: ENST00000378641.6 None 1.51188632876353 0.909500148687464 0.261252686709089 0.769244021976763
ENSG00000124214.18: ENST00000371828.6 None 0.631784081954606 -11.3209131601713 0.292467782075688 0.775039622500573
ENSG00000124214.18: ENST00000340954.10 None 0.631784081954606 -11.3208856025567 0.292467782075688 0.775039622500573
ENSG00000025293.14: ENST00000339089.9 None 1.12459788864558 -0.0408678222063266 0.317968262901375 0.80249133017966
ENSG00000172264.15: ENST00000477147.4 None 2.83101942561577 0.374696450498133 0.355189440649822 0.839188663977647
ENSG00000182621.15: ENST00000630495.1 None 1.934716546709 0.646465758458278 0.382869952220888 0.839188663977647
ENSG00000196090.11: ENST00000612229.3 None 0.275592961083685 12.3356274161776 0.388434393391929 0.839188663977647
ENSG00000196090.11: ENST00000373193.6 None 1.48095302267268 0.285335702350409 0.395843709423418 0.839188663977647
ENSG00000124214.18: ENST00000437404.2 None 0.886951360599911 -0.0108253743408251 0.486310916235341 0.92201417009856
ENSG00000089123.14: ENST00000480436.4 None 0.631784081954606 0.5312091425192 0.512844174765167 0.92201417009856
ENSG00000131061.12: ENST00000375200.4 None 0.631784081954606 -6.56212907301779e-06 0.550855241472327 0.92201417009856
ENSG00000131061.12: ENST00000483118.4 None 0.631784081954606 -6.56212907212961e-06 0.550855241472327 0.92201417009856
ENSG00000131061.12: ENST00000497876.4 None 0.631784081954606 -6.56212907301779e-06 0.550855241472327 0.92201417009856
ENSG00000131061.12: ENST00000342427.5 None 0.631784081954606 1.96862081347504e-05 0.550855241472327 0.92201417009856
ENSG00000172264.15: ENST00000217246.7 None 4.38631034136321 -0.119132678258971 0.556687800814225 0.92201417009856
ENSG00000175170.13: ENST00000376403.4 None 0.593581884432014 11.2994242120958 0.633617214751554 0.938088343557889
ENSG00000175170.13: ENST00000478164.1 None 0.593581884432014 11.2995037714981 0.633617214751554 0.938088343557889
ENSG00000175170.13: ENST00000582267.4 None 0.593581884432014 11.2995037714986 0.633617214751554 0.938088343557889
ENSG00000172264.15: ENST00000494602.4 None 2.93211052213426 0.182051093632322 0.640553819222887 0.938088343557889
ENSG00000182621.15: ENST00000625874.1 None 1.95784528734983 -0.0905002253525198 0.654891862483809 0.938088343557889
ENSG00000234684.5: ENST00000609470.4 None 2.18732217421356 1.09831255299397e-05 0.711458153396513 0.94268205325038
ENSG00000234684.5: ENST00000609285.4 None 2.18732217421356 1.09831253896076e-05 0.711458153396513 0.94268205325038
ENSG00000234684.5: ENST00000446423.1 None 2.18732217421356 -2.19660000837507e-05 0.711458153396513 0.94268205325038
ENSG00000196090.11: ENST00000356100.5 None 1.88731605952733 0.77076177435454 0.740066080202463 0.956670786603183
ENSG00000089123.14: ENST00000465381.4 None 1.36874967612081 -0.205749451423837 0.800544724492443 0.986717916234872
ENSG00000089123.14: ENST00000337743.7 None 1.36874967612081 -0.205720205388313 0.800544724492443 0.986717916234872
ENSG00000078747.11: ENST00000486883.4 None 5.39285533814094 -0.0298500942790563 0.848564435075665 1.0
ENSG00000078747.11: ENST00000262650.9 None 5.45092618645698 0.0233792040746517 0.877925303709236 1.0
ENSG00000175170.13: ENST00000584071.1 None 0.274058029720744 10.9775840206814 0.931540886174586 1.0
MSTRG.74: MSTRG.74.3 None 6.59012926626195 0.0072496745242292 0.945426665581222 1.0
ENSG00000124160.10: ENST00000372291.3 None 6.59784276025107 -0.0036114024764097 0.972726657088861 1.0
ENSG00000124160.10: ENST00000290231.9 None 6.59784276025107 -0.0036114024761051 0.972726657088861 1.0
ENSG00000078747.11: ENST00000535650.4 None 5.40838486859287 0.0030587545896532 0.984278747936438 1.0
ENSG00000078747.11: ENST00000374864.7 None 5.44100454370989 0.0023196034926593 0.987841282374554 1.0
ENSG00000088812.16: ENST00000446916.2 None 3.20204070116592 -1.4161116723698798e-11 1.0 1.0
ENSG00000088812.16: ENST00000262919.8 None 3.20204070116592 1.4161116723698798e-11 1.0 1.0

The figure below presents the MA plot from the DEXSeq analysis. M is the log2 ratio of isoform transcript abundance between conditions. A is the log2 transformed mean abundance value. Transcripts that satisfy the logFC and FDR-corrected (False discovery rate - Benjamini-Hochberg) p-value thresholds defined are shaded as 'Up-' or 'Down-' regulated.

Table showing gene and transcript identifiers and their FDR-corrected (False discovery rate - Benjamini-Hochberg) probabilities for the genes and their isoforms that have been identified as showing DTU using the R packages DEXSeq and StageR. This list has been shortened requiring that both gene and transcript must satisfy the p-value threshold
geneID txID gene transcript gene_name
ENSG00000182621.15 ENST00000626114.1 0.008517720505512 0.0176137256270198 PLCB1
ENSG00000182621.15 ENST00000338037.9 0.008517720505512 0.659946744783607 PLCB1
ENSG00000182621.15 ENST00000626161.1 0.008517720505512 0.0057875521466083 PLCB1
ENSG00000182621.15 ENST00000629992.1 0.008517720505512 1.0 PLCB1
ENSG00000182621.15 ENST00000378637.5 0.008517720505512 1.0 PLCB1
ENSG00000182621.15 ENST00000378641.6 0.008517720505512 1.0 PLCB1
ENSG00000182621.15 ENST00000630495.1 0.008517720505512 1.0 PLCB1
ENSG00000182621.15 ENST00000625874.1 0.008517720505512 1.0 PLCB1
ENSG00000196090.11 ENST00000612229.3 0.0468782589322508 1.0 PTPRT
ENSG00000196090.11 ENST00000373201.4 0.0468782589322508 1.0 PTPRT
ENSG00000196090.11 ENST00000617474.1 0.0468782589322508 1.0 PTPRT
ENSG00000196090.11 ENST00000373190.4 0.0468782589322508 1.0 PTPRT
ENSG00000196090.11 ENST00000356100.5 0.0468782589322508 1.0 PTPRT
ENSG00000196090.11 ENST00000373193.6 0.0468782589322508 1.0 PTPRT
ENSG00000196090.11 ENST00000618610.1 0.0468782589322508 1.0 PTPRT
ENSG00000196090.11 ENST00000373198.7 0.0468782589322508 0.0639186420233646 PTPRT
ENSG00000175170.13 ENST00000376403.4 0.173343151181439 nan FAM182B
ENSG00000175170.13 ENST00000478164.1 0.173343151181439 nan FAM182B
ENSG00000175170.13 ENST00000584356.1 0.173343151181439 nan FAM182B
ENSG00000175170.13 ENST00000584071.1 0.173343151181439 nan FAM182B
ENSG00000175170.13 ENST00000582267.4 0.173343151181439 nan FAM182B
MSTRG.16 ENST00000494602.4 0.330042338287625 nan MACROD2
MSTRG.16 ENST00000217246.7 0.330042338287625 nan MACROD2
MSTRG.16 ENST00000477147.4 0.330042338287625 nan MACROD2
MSTRG.16 ENST00000490428.4 0.330042338287625 nan MACROD2
MSTRG.16 ENST00000402914.4 0.330042338287625 nan MACROD2
ENSG00000025293.14 ENST00000339089.9 0.890581143195122 nan PHF20
ENSG00000025293.14 ENST00000374012.6 0.890581143195122 nan PHF20
ENSG00000025293.14 ENST00000374000.7 0.890581143195122 nan PHF20
ENSG00000025293.14 ENST00000461122.4 0.890581143195122 nan PHF20
MSTRG.66 ENST00000486883.4 1.0 nan ITCH
MSTRG.66 ENST00000535650.4 1.0 nan ITCH
ENSG00000131061.12 ENST00000483118.4 1.0 nan ZNF341
ENSG00000131061.12 ENST00000497876.4 1.0 nan ZNF341
ENSG00000131061.12 ENST00000375200.4 1.0 nan ZNF341
ENSG00000124214.18 ENST00000340954.10 1.0 nan STAU1
ENSG00000124214.18 ENST00000371828.6 1.0 nan STAU1
ENSG00000124214.18 ENST00000437404.2 1.0 nan STAU1
ENSG00000124214.18 ENST00000371856.5 1.0 nan STAU1
ENSG00000089123.14 ENST00000480436.4 1.0 nan TASP1
ENSG00000089123.14 ENST00000337743.7 1.0 nan TASP1
ENSG00000089123.14 ENST00000465381.4 1.0 nan TASP1
MSTRG.66 ENST00000262650.9 1.0 nan ITCH
MSTRG.66 ENST00000374864.7 1.0 nan ITCH
MSTRG.74 ENST00000290231.9 1.0 nan NCOA5
MSTRG.74 MSTRG.74.3 1.0 nan MSTRG.74
MSTRG.3 ENST00000262919.8 1.0 nan ATRN
MSTRG.3 ENST00000446916.2 1.0 nan ATRN
MSTRG.74 ENST00000372291.3 1.0 nan NCOA5
ENSG00000131061.12 ENST00000342427.5 1.0 nan ZNF341
ENSG00000234684.5 ENST00000609470.4 1.0 nan SDCBP2-AS1
ENSG00000234684.5 ENST00000609285.4 1.0 nan SDCBP2-AS1
ENSG00000234684.5 ENST00000446423.1 1.0 nan SDCBP2-AS1
View dtu_plots.pdf file to see plots of differential isoform usage

Software versions

Name Version
pysam 0.21.0
aplanat 0.6.20
pandas 1.3.5
scikit-learn 1.0.2
fastcat 0.10.2
minimap2 2.24-r1122
samtools 1.17
bedtools v2.30.0
pychopper 2.7.10
gffread 0.12.7
seqkit v2.2.0
stringtie 2.1.1

Workflow parameters

Key Value
fastq wf-transcriptomes/data/differential_expression/differential_expression_fastq
bam None
ref_genome wf-transcriptomes/data/differential_expression/hg38_chr20.fa
ref_annotation wf-transcriptomes/data/differential_expression/gencode.v22.annotation.chr20.gtf
transcriptome_source reference-guided
threads 4
isoform_table_nrows 5000
out_dir wf-transcriptomes
sample None
sample_sheet wf-transcriptomes/data/differential_expression/sample_sheet.csv
analyse_unclassified False
igv False
direct_rna True
pychopper_opts None
pychopper_backend edlib
cdna_kit SQK-PCS109
minimap2_index_opts -k 15
minimap2_opts -uf
minimum_mapping_quality 40
poly_context 24
max_poly_run 8
bundle_min_reads 50000
stringtie_opts --conservative
gffcompare_opts -R
plot_gffcmp_stats True
de_analysis True
ref_transcriptome None
min_samps_gene_expr 3
min_samps_feature_expr 1
min_gene_expr 10
min_feature_expr 3
store_dir wf-transcriptomes/store_dir