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_1.12.1 2 44 326 sample01 2.0
NCOA5 ENST00000290231.9 i sample01_batch_1.11.1 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_1.13.1 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_1.11.1 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_1.12.1 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_1.13.1 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_1.9.1 1 32 1406 sample04 2.0
CDC42P1 ENST00000456658.1 = sample04_batch_1.10.1 1 0 548 sample04 2.0
NCOA5 ENST00000290231.9 i sample04_batch_1.12.1 2 3 329 sample04 2.0
NCOA5 ENST00000290231.9 i sample04_batch_1.11.1 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_1.7.1 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_1.8.1 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_1.9.1 1 29 1406 sample05 2.0
NCOA5 ENST00000290231.9 i sample05_batch_1.11.1 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_1.12.1 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_1.10.1 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
DDX27 ENST00000622530.3 s sample05_batch_1.14.1 3 2 315 sample05 1.0
PTGIS ENST00000244043.4 i sample05_batch_1.13.1 2 2 677 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_1.8.1 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_1.6.1 4 2 2582 sample06 nan
- - u sample06_batch_1.9.1 2 2 1323 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 3050 3275 3161 3151 3010 3021
Supplementary 48 52 51 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 744716 722248 732985 798286 786108 775426
MSTRG.74.3 208268 230781 221017 141987 156424 156144
MSTRG.10.1 3214 3035 3080 8840 6874 7163
ENST00000372291.3 5711 6321 6056 3861 4254 4246
MSTRG.63.1 6123 6195 6287 4209 2922 3480
ENST00000290231.9 4504 4985 4776 3045 3355 3349
ENST00000427242.1 0 0 0 5243 5097 6069
ENST00000432629.1 4292 4053 4113 0 0 0
ENST00000400616.2 3855 3640 3694 0 0 0
MSTRG.12.1 0 0 0 4269 2490 3954
MSTRG.23.1 0 0 0 0 4699 5596
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 1377 1172
MSTRG.85.1 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 2939
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.45.1 0 0 0 0 662 788
MSTRG.88.1 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.3.1 242 267 232 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.62.1 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 0 133 130 154
ENST00000202017.5 141 133 135 0 0 0
ENST00000429853.1 0 0 0 129 125 149
ENST00000468420.4 0 0 0 126 122 146
MSTRG.78.1 0 0 0 143 69 166
ENST00000624666.1 130 123 125 0 0 0
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.16.1 0 0 0 108 105 93
ENST00000379070.3 0 0 0 97 94 112
ENST00000413823.1 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
ENST00000494921.1 24 22 23 66 64 76
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
ENST00000372420.4 0 0 0 122 0 141
ENST00000584356.1 12 11 12 86 83 59
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
ENST00000457508.1 84 80 81 0 0 0
ENST00000339946.6 0 0 0 0 245 0
ENST00000558738.1 83 78 79 0 0 0
ENST00000456939.4 0 0 0 76 74 88
ENST00000344256.9 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
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 5.95 12.26 2017419.31 6.38652093515644e-08 1.22621201955004e-05
ENSG00000101052.11 IFT52 5.54 12.0 5191583.37 1.53822752438223e-06 7.38349211703469e-05
ENSG00000124215.15 CDH26 5.54 12.0 5191583.37 1.53822752438223e-06 7.38349211703469e-05
ENSG00000175063.15 UBE2C 5.54 12.0 5191583.37 1.53822752438223e-06 7.38349211703469e-05
ENSG00000174306.20 ZHX3 5.29 11.84 9434494.43 1.14690447391131e-05 0.0004404113179819
ENSG00000182463.14 TSHZ2 -5.91 12.13 6274.22 5.05942679353844e-05 0.0004976677062984
ENSG00000131061.12 ZNF341 -6.68 12.67 6228.32 5.10254716315212e-05 0.0004976677062984
ENSG00000101104.11 PABPC1L -6.1 12.26 6268.65 5.06462187720521e-05 0.0004976677062984
ENSG00000125850.9 OVOL2 -5.12 11.67 6282.18 5.05201562658581e-05 0.0004976677062984
ENSG00000100991.10 TRPC4AP -5.12 11.67 6282.18 5.05201562658581e-05 0.0004976677062984
ENSG00000204548.3 DEFB121 -5.12 11.67 6282.18 5.05201562658581e-05 0.0004976677062984
ENSG00000089123.14 TASP1 -7.18 13.07 6143.53 5.18403860727572e-05 0.0004976677062984
ENSG00000259723.1 RP5-823G15.5 -5.12 11.67 6282.18 5.05201562658581e-05 0.0004976677062984
ENSG00000124226.9 RNF114 -5.43 11.84 6280.73 5.05336114435612e-05 0.0004976677062984
ENSG00000126005.14 MMP24-AS1 -5.69 12.0 6278.17 5.05574473163824e-05 0.0004976677062984
ENSG00000149646.11 CNBD2 -5.69 12.0 6278.17 5.05574473163824e-05 0.0004976677062984
ENSG00000088876.10 ZNF343 2.71 12.37 41497.58 5.00255195525205e-05 0.0004976677062984
ENSG00000196090.11 PTPRT 2.9 14.35 397.57 2.06431546758685e-05 0.0004976677062984
ENSG00000125821.10 DTD1 2.77 12.41 935.38 2.87398428897705e-05 0.0004976677062984
ENSG00000054793.12 ATP9A 2.93 12.52 302.76 3.6917749866262e-05 0.0004976677062984
ENSG00000101082.12 SLA2 4.97 11.67 19163530.69 8.70006091137423e-05 0.0006681646779935
ENSG00000101146.11 RAE1 4.97 11.67 19163530.69 8.70006091137423e-05 0.0006681646779935
ENSG00000124207.15 CSE1L 4.97 11.67 19163530.69 8.70006091137423e-05 0.0006681646779935
ENSG00000125851.8 PCSK2 4.97 11.67 19163530.69 8.70006091137423e-05 0.0006681646779935
ENSG00000185052.10 SLC24A3 4.97 11.67 19163530.69 8.70006091137423e-05 0.0006681646779935
MSTRG.3 MSTRG.3 -2.66 12.18 971.06 0.0001242578682727 0.0009175965657063
MSTRG.74 MSTRG.74 -1.26 17.88 167.07 0.0001303255160172 0.0009267592250115
ENSG00000101079.19 NDRG3 -2.59 12.13 5881.99 0.0002344424188558 0.0015578963939948
ENSG00000089177.16 KIF16B -4.72 11.48 6282.77 0.0002445071451376 0.0015578963939948
MSTRG.63 MSTRG.63 -1.5 13.28 122.69 0.0002494507118322 0.0015578963939948
MSTRG.5 None -1.83 14.02 122.21 0.0002515353552804 0.0015578963939948
ENSG00000025293.14 PHF20 1.99 13.04 100.15 0.0003811468607071 0.0022868811642431
ENSG00000185019.15 UBOX5 4.57 11.48 42204411.72 0.0006775657779318 0.0034008414908533
ENSG00000234684.5 SDCBP2-AS1 7.87 13.79 652.62 0.0006907959278295 0.0034008414908533
MSTRG.25 None 4.57 11.48 42204411.72 0.0006775657779318 0.0034008414908533
ENSG00000188559.12 RALGAPA2 4.57 11.48 42204411.72 0.0006775657779318 0.0034008414908533
ENSG00000101144.11 BMP7 4.57 11.48 42204411.72 0.0006775657779318 0.0034008414908533
ENSG00000101457.11 DNTTIP1 4.57 11.48 42204411.72 0.0006775657779318 0.0034008414908533
ENSG00000089012.13 SIRPG 4.57 11.48 42204411.72 0.0006775657779318 0.0034008414908533
ENSG00000124214.18 STAU1 -2.67 13.02 73.56 0.0007218007840081 0.003464643763239
ENSG00000228340.4 MIR646HG 1.73 12.87 70.37 0.000790500684445 0.0037018568637426
ENSG00000175170.13 FAM182B 3.78 13.13 58.89 0.0011370599905064 0.0051979885280296
ENSG00000227906.6 SNAP25-AS1 2.15 12.7 56.34 0.0012442481389752 0.0055557126205407
MSTRG.75 MSTRG.75 -0.61 17.71 51.84 0.0014722331931586 0.0064242902974195
ENSG00000100997.17 ABHD12 -3.32 12.87 48.6 0.0016764567643175 0.0071528821944217
MSTRG.54 None 1.55 12.76 8131.59 0.0017288382780347 0.0072160206387539
ENSG00000088325.14 TPX2 5.19 11.79 283.38 0.0018050194476564 0.007373696467022
MSTRG.13 MSTRG.13 2.22 12.09 332.53 0.0021787078718655 0.0087148314874621
ENSG00000101350.7 KIF3B -4.16 11.26 6282.7 0.0027456631715123 0.0103366142927522
ENSG00000170471.13 RALGAPB -4.16 11.26 6282.7 0.0027456631715123 0.0103366142927522
ENSG00000196700.6 ZNF512B -4.16 11.26 6282.7 0.0027456631715123 0.0103366142927522
MSTRG.16 MSTRG.16 4.85 11.61 173.53 0.0031679448807239 0.0116970272519039
ENSG00000229876.1 CASC20 4.02 11.26 68826140.11 0.0055224934026599 0.0182813574708742
MSTRG.65 MSTRG.65 4.02 11.26 68826140.11 0.0055224934026599 0.0182813574708742
ENSG00000149633.10 KIAA1755 4.02 11.26 68826140.11 0.0055224934026599 0.0182813574708742
ENSG00000225458.1 RP5-1121H13.4 4.02 11.26 68826140.11 0.0055224934026599 0.0182813574708742
ENSG00000088826.16 SMOX 4.02 11.26 68826140.11 0.0055224934026599 0.0182813574708742
ENSG00000125772.11 GPCPD1 4.02 11.26 68826140.11 0.0055224934026599 0.0182813574708742
ENSG00000118705.15 RPN2 2.05 12.0 19505.36 0.0061218806028376 0.0199220521312681
ENSG00000180083.9 WFDC11 5.38 11.9 90.41 0.0066607926836627 0.0203852128741415
ENSG00000130584.9 ZBTB46 4.41 11.41 90.4 0.0066619008203576 0.0203852128741415
ENSG00000232271.1 RP4-764O22.1 4.41 11.41 90.4 0.0066619008203576 0.0203852128741415
ENSG00000198646.12 NCOA6 -2.52 11.79 23.89 0.0066888979743276 0.0203852128741415
MSTRG.12 MSTRG.12 4.97 11.67 70.49 0.0088270255796861 0.0260736755584576
MSTRG.15 None 4.97 11.67 70.49 0.0088270255796861 0.0260736755584576
ENSG00000064787.11 BCAS1 5.76 12.13 68.64 0.0090954250028346 0.026082747180801
ENSG00000271774.1 RP4-678D15.1 -2.02 11.84 4423.25 0.0092376396265337 0.026082747180801
MSTRG.64 MSTRG.64 -2.02 11.84 4423.25 0.0092376396265337 0.026082747180801
ENSG00000064655.17 EYA2 1.53 12.34 268.48 0.0105189677793998 0.0292701712122428
ENSG00000274322.1 RP11-314N13.10 6.06 12.34 58.87 0.0108109676184177 0.0296529397533742
ENSG00000124151.17 NCOA3 -2.25 12.58 14.81 0.0159146485738293 0.0430367961433131
ENSG00000132669.11 RIN2 6.27 12.48 39.06 0.0170788236590836 0.0455435297575562
ENSG00000149488.12 TMC2 3.77 11.18 33.96 0.0199274577118083 0.0503430510614105
ENSG00000226344.1 CST12P 3.77 11.18 33.96 0.0199274577118083 0.0503430510614105
MSTRG.62 MSTRG.62 3.77 11.18 33.96 0.0199274577118083 0.0503430510614105
MSTRG.78 MSTRG.78 3.77 11.18 33.96 0.0199274577118083 0.0503430510614105
ENSG00000158296.12 SLC13A3 6.49 12.64 30.06 0.0227799703831292 0.0568020040722181
ENSG00000020256.18 ZFP64 -1.28 12.34 80.31 0.0242373179421148 0.0596610903190517
ENSG00000088356.5 PDRG1 -3.24 11.0 6281.69 0.0342013947972946 0.0631410365488515
ENSG00000101003.9 GINS1 -3.24 11.0 6281.69 0.0342013947972946 0.0631410365488515
ENSG00000087586.16 AURKA -3.24 11.0 6281.69 0.0342013947972946 0.0631410365488515
ENSG00000088340.14 FER1L4 -3.24 11.0 6281.69 0.0342013947972946 0.0631410365488515
ENSG00000101134.10 DOK5 4.41 11.41 25.2 0.0275935159976789 0.0631410365488515
ENSG00000124191.16 TOX2 4.97 11.67 21.07 0.0334415855260532 0.0631410365488515
ENSG00000101337.14 TM9SF4 -3.24 11.0 6281.69 0.0342013947972946 0.0631410365488515
ENSG00000101247.16 NDUFAF5 -3.24 11.0 6281.69 0.0342013947972946 0.0631410365488515
ENSG00000101191.15 DIDO1 -3.24 11.0 6281.69 0.0342013947972946 0.0631410365488515
ENSG00000101181.16 MTG2 -3.24 11.0 6281.69 0.0342013947972946 0.0631410365488515
ENSG00000101346.10 POFUT1 -3.24 11.0 6281.69 0.0342013947972946 0.0631410365488515
ENSG00000101363.11 MANBAL -3.24 11.0 6281.69 0.0342013947972946 0.0631410365488515
ENSG00000125966.9 MMP24 -3.24 11.0 6281.69 0.0342013947972946 0.0631410365488515
ENSG00000131069.18 ACSS2 -3.24 11.0 6281.69 0.0342013947972946 0.0631410365488515
ENSG00000235958.4 UBOX5-AS1 -3.24 11.0 6281.69 0.0342013947972946 0.0631410365488515
ENSG00000238282.1 RP5-1164C1.2 -3.24 11.0 6281.69 0.0342013947972946 0.0631410365488515
MSTRG.11 None -3.24 11.0 6281.69 0.0342013947972946 0.0631410365488515
MSTRG.14 None -3.24 11.0 6281.69 0.0342013947972946 0.0631410365488515
ENSG00000149531.13 FRG1B -3.24 11.0 6281.69 0.0342013947972946 0.0631410365488515
ENSG00000166948.8 TGM6 -3.24 11.0 6281.69 0.0342013947972946 0.0631410365488515
ENSG00000215388.3 ACTG1P3 -3.24 11.0 6281.69 0.0342013947972946 0.0631410365488515
ENSG00000234139.2 RP4-550H1.4 -3.24 11.0 6281.69 0.0342013947972946 0.0631410365488515
MSTRG.87 None -3.24 11.0 6281.69 0.0342013947972946 0.0631410365488515
MSTRG.86 None -3.24 11.0 6281.69 0.0342013947972946 0.0631410365488515
MSTRG.48 MSTRG.48 -3.24 11.0 6281.69 0.0342013947972946 0.0631410365488515
MSTRG.2 MSTRG.2 -3.24 11.0 6281.69 0.0342013947972946 0.0631410365488515
ENSG00000101294.15 HM13 3.1 11.0 30378687.44 0.0497479975782754 0.0682258252502062
ENSG00000101311.14 FERMT1 3.1 11.0 30378687.44 0.0497479975782754 0.0682258252502062
ENSG00000101323.4 HAO1 3.1 11.0 30378687.44 0.0497479975782754 0.0682258252502062
ENSG00000101353.13 MROH8 3.1 11.0 30378687.44 0.0497479975782754 0.0682258252502062
ENSG00000101400.5 SNTA1 3.1 11.0 30378687.44 0.0497479975782754 0.0682258252502062
ENSG00000101444.11 AHCY 3.1 11.0 30378687.44 0.0497479975782754 0.0682258252502062
ENSG00000124103.8 FAM209A 3.1 11.0 30378687.44 0.0497479975782754 0.0682258252502062
ENSG00000124143.9 ARHGAP40 3.1 11.0 30378687.44 0.0497479975782754 0.0682258252502062
ENSG00000124177.13 CHD6 3.1 11.0 30378687.44 0.0497479975782754 0.0682258252502062
ENSG00000132623.14 ANKEF1 3.1 11.0 30378687.44 0.0497479975782754 0.0682258252502062
ENSG00000158445.7 KCNB1 3.1 11.0 30378687.44 0.0497479975782754 0.0682258252502062
ENSG00000204663.8 CST13P 3.1 11.0 30378687.44 0.0497479975782754 0.0682258252502062
ENSG00000226648.1 PLCG1-AS1 3.1 11.0 30378687.44 0.0497479975782754 0.0682258252502062
ENSG00000228888.1 LINC01428 3.1 11.0 30378687.44 0.0497479975782754 0.0682258252502062
ENSG00000229262.1 RP4-726N1.2 3.1 11.0 30378687.44 0.0497479975782754 0.0682258252502062
ENSG00000243961.2 RP5-839B4.8 3.1 11.0 30378687.44 0.0497479975782754 0.0682258252502062
ENSG00000244005.11 NFS1 3.1 11.0 30378687.44 0.0497479975782754 0.0682258252502062
ENSG00000256222.2 MTRNR2L3 3.1 11.0 30378687.44 0.0497479975782754 0.0682258252502062
ENSG00000260202.2 RP3-333B15.4 3.1 11.0 30378687.44 0.0497479975782754 0.0682258252502062
ENSG00000268628.2 RP1-122P22.4 3.1 11.0 30378687.44 0.0497479975782754 0.0682258252502062
ENSG00000274863.1 RP11-97N19.3 3.1 11.0 30378687.44 0.0497479975782754 0.0682258252502062
ENSG00000279082.2 RP1-167O22.1 3.1 11.0 30378687.44 0.0497479975782754 0.0682258252502062
MSTRG.1 None 3.1 11.0 30378687.44 0.0497479975782754 0.0682258252502062
MSTRG.56 MSTRG.56 3.1 11.0 30378687.44 0.0497479975782754 0.0682258252502062
MSTRG.6 None 3.1 11.0 30378687.44 0.0497479975782754 0.0682258252502062
MSTRG.76 None 3.1 11.0 30378687.44 0.0497479975782754 0.0682258252502062
MSTRG.85 MSTRG.85 3.1 11.0 30378687.44 0.0497479975782754 0.0682258252502062
MSTRG.88 MSTRG.88 3.1 11.0 30378687.44 0.0497479975782754 0.0682258252502062
ENSG00000080845.16 DLGAP4 3.1 11.0 30378687.44 0.0497479975782754 0.0682258252502062
ENSG00000022277.11 RTFDC1 3.1 11.0 30378687.44 0.0497479975782754 0.0682258252502062
ENSG00000101349.15 PAK7 4.23 11.34 15.73 0.0455411649125762 0.0682258252502062
ENSG00000101109.10 STK4 4.23 11.34 15.73 0.0455411649125762 0.0682258252502062
ENSG00000088888.16 MAVS 3.1 11.0 30378687.44 0.0497479975782754 0.0682258252502062
ENSG00000101152.9 DNAJC5 3.1 11.0 30378687.44 0.0497479975782754 0.0682258252502062
ENSG00000101224.16 CDC25B 3.1 11.0 30378687.44 0.0497479975782754 0.0682258252502062
ENSG00000101290.12 CDS2 3.1 11.0 30378687.44 0.0497479975782754 0.0682258252502062
MSTRG.8 MSTRG.8 -1.35 11.95 19.37 0.0525593065382243 0.0715701195414119
ENSG00000270792.4 RP11-103J8.1 1.48 11.73 72.05 0.0704539464038235 0.0952616740108036
ENSG00000125864.10 BFSP1 2.22 12.09 5.35 0.0769317034554607 0.103292916527612
ENSG00000101425.11 BPI 1.33 11.67 6623.36 0.111109748805578 0.14814633174077
ENSG00000234948.1 LINC01524 1.03 12.09 71.93 0.113773929875941 0.150652376111591
ENSG00000132792.17 CTNNBL1 4.23 11.34 4.91 0.139695376284058 0.183708987989995
ENSG00000125844.14 RRBP1 2.6 10.9 3.66 0.178395332670899 0.206336770318148
ENSG00000101440.8 ASIP 2.6 10.9 3.66 0.178395332670899 0.206336770318148
ENSG00000092758.14 COL9A3 2.6 10.9 3.66 0.178395332670899 0.206336770318148
ENSG00000042062.10 FAM65C 2.6 10.9 3.66 0.178395332670899 0.206336770318148
ENSG00000101333.15 PLCB4 2.6 10.9 3.66 0.178395332670899 0.206336770318148
ENSG00000100979.13 PLTP 2.6 10.9 3.66 0.178395332670899 0.206336770318148
ENSG00000274469.1 RP11-425M5.8 2.6 10.9 3.66 0.178395332670899 0.206336770318148
ENSG00000240849.9 TMEM189 2.6 10.9 3.66 0.178395332670899 0.206336770318148
MSTRG.47 None 2.6 10.9 3.66 0.178395332670899 0.206336770318148
MSTRG.45 MSTRG.45 2.6 10.9 3.66 0.178395332670899 0.206336770318148
ENSG00000225069.3 RP5-1025A1.2 2.6 10.9 3.66 0.178395332670899 0.206336770318148
ENSG00000130703.14 OSBPL2 2.6 10.9 3.66 0.178395332670899 0.206336770318148
ENSG00000254995.4 STX16-NPEPL1 2.6 10.9 3.66 0.178395332670899 0.206336770318148
ENSG00000101407.11 TTI1 2.6 10.9 3.66 0.178395332670899 0.206336770318148
ENSG00000171456.15 ASXL1 4.41 11.41 3.66 0.178387836950907 0.206336770318148
ENSG00000172296.11 SPTLC3 4.41 11.41 3.66 0.178387836950907 0.206336770318148
ENSG00000101019.20 UQCC1 5.83 12.18 3.66 0.178370633515943 0.206336770318148
ENSG00000101391.19 CDK5RAP1 4.97 11.67 3.66 0.17838288729052 0.206336770318148
ENSG00000089057.13 SLC23A2 4.02 11.26 3.66 0.178390318693869 0.206336770318148
MSTRG.23 MSTRG.23 3.48 11.09 3.66 0.178392806963385 0.206336770318148
ENSG00000089063.13 TMEM230 -1.56 11.41 2.49 0.184635340764995 0.2122753618376
MSTRG.27 None -0.25 15.65 2.44 0.188397088558098 0.215310958352112
ENSG00000215529.11 EFCAB8 -0.95 11.79 15.82 0.202924771949307 0.230541752747142
MSTRG.10 MSTRG.10 0.57 12.79 12.16 0.208650765267475 0.235652629007972
ENSG00000101443.16 WFDC2 3.48 11.09 2.77 0.221078828224324 0.248228859760644
ENSG00000280350.1 RP5-1065O2.4 -1.06 11.48 1778.7 0.243209161836266 0.271489296933506
ENSG00000101236.15 RNF24 0.99 11.55 4.08 0.263456864211932 0.292391433113821
ENSG00000179242.14 CDH4 -0.66 12.18 3.82 0.270154414288767 0.298101422663467
ENSG00000088970.14 KIZ 1.17 11.61 1.24 0.324314822433736 0.355819690898728
ENSG00000080839.10 RBL1 -0.55 12.13 524.91 0.369277274220926 0.402847935513737
ENSG00000124198.8 ARFGEF2 0.78 11.48 1899.03 0.393785587754286 0.422384541054877
ENSG00000130699.15 TAF4 0.78 11.48 1899.03 0.393785587754286 0.422384541054877
ENSG00000088854.12 C20orf194 0.78 11.48 1899.03 0.393785587754286 0.422384541054877
MSTRG.66 None -0.12 17.16 0.69 0.448575086029039 0.478480091764309
ENSG00000087495.15 PHACTR3 0.78 11.48 0.64 0.464064858676774 0.492267695391937
ENSG00000149636.14 DSN1 -0.91 11.0 0.51 0.511716102434247 0.539832371798766
ENSG00000226995.6 LINC00658 -0.64 11.18 0.85 0.570938697233772 0.599017649556744
MSTRG.61 None -0.15 12.67 0.4 0.751043468671984 0.783697532527287
ENSG00000101463.5 SYNDIG1 -0.14 11.26 43.82 0.89694430983841 0.901640353345417
ENSG00000132670.19 PTPRA -0.14 11.26 43.82 0.89694430983841 0.901640353345417
ENSG00000227195.7 MIR663AHG -0.14 11.26 43.82 0.89694430983841 0.901640353345417
ENSG00000277938.1 RP5-965G21.3 -0.14 11.26 43.82 0.89694430983841 0.901640353345417
ENSG00000062598.16 ELMO2 -0.14 11.26 43.82 0.89694430983841 0.901640353345417
ENSG00000125885.12 MCM8 -0.14 11.26 43.82 0.89694430983841 0.901640353345417
ENSG00000154930.13 ACSS1 -0.14 11.26 43.82 0.89694430983841 0.901640353345417
ENSG00000182621.15 PLCB1 0.02 14.83 0.11 0.925541119391658 0.925541119391658
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 0.861646903905838 11.7428340868924 0.0001018571933963 0.0055002884434041
ENSG00000172264.15: ENST00000464883.4 None 0.446609404626995 11.6656771984353 0.0003459409176426 0.009340404776351
ENSG00000182621.15: ENST00000626114.1 None 2.12778597579922 -1.7193559749469 0.0009594810364333 0.0172706586558008
ENSG00000196090.11: ENST00000373198.7 None 1.35332861821605 -1.29962783478175 0.0017813105567072 0.0240476925155477
ENSG00000172264.15: ENST00000402914.4 None 3.32299547589353 -0.968098308096154 0.0036500504451027 0.0394205448071093
ENSG00000175170.13: ENST00000584356.1 None 1.31018025575088 -0.553035698938975 0.0100264662455822 0.0902381962102398
ENSG00000182621.15: ENST00000338037.9 None 3.03674914925231 -0.567336733345337 0.0376579457303479 0.246792219567768
ENSG00000196090.11: ENST00000617474.1 None 1.73770659059886 13.7987355617265 0.0390566926083214 0.246792219567768
ENSG00000196090.11: ENST00000373201.4 None 1.66994040420797 13.7316215111496 0.04570226288292 0.246792219567768
ENSG00000196090.11: ENST00000373190.4 None 1.66994040420797 13.7316215111467 0.04570226288292 0.246792219567768
ENSG00000172264.15: ENST00000494602.4 None 3.00636098459055 0.719970520364929 0.0866786606918726 0.425513425214647
ENSG00000182621.15: ENST00000629992.1 None 0.91178445124431 1.60257910287577 0.0979834162238591 0.42962031673495
ENSG00000025293.14: ENST00000374000.7 None 0.732929613783818 10.7250688509546 0.103427113288044 0.42962031673495
ENSG00000196090.11: ENST00000618610.1 None 0.91178445124431 -0.451636691578632 0.133504622822546 0.491351460860549
ENSG00000172264.15: ENST00000217246.7 None 4.4593183696854 -0.223746497125817 0.136811738609109 0.491351460860549
ENSG00000025293.14: ENST00000374012.6 None 0.787658374996643 -0.500221631163261 0.152026436862276 0.491351460860549
ENSG00000124214.18: ENST00000371856.5 None 1.67557860304886 0.25240901160909 0.154684719159803 0.491351460860549
ENSG00000182621.15: ENST00000378637.5 None 1.51307960005081 1.01761627699056 0.200051148323407 0.553114550885575
ENSG00000182621.15: ENST00000378641.6 None 1.51307960005081 1.01761627699056 0.200051148323407 0.553114550885575
ENSG00000172264.15: ENST00000477147.4 None 2.72426988713007 0.607945275701407 0.204857241068732 0.553114550885575
ENSG00000025293.14: ENST00000461122.4 None 0.272301275395016 10.2656396508171 0.219699642548623 0.564941937982175
ENSG00000124214.18: ENST00000371828.6 None 0.637482789177349 -11.3173155907525 0.292612457205256 0.687003160394949
ENSG00000124214.18: ENST00000340954.10 None 0.637482789177349 -11.3172881127491 0.292612457205256 0.687003160394949
ENSG00000025293.14: ENST00000339089.9 None 1.12469085133781 -0.0407879707640484 0.318089747089553 0.715701930951495
ENSG00000196090.11: ENST00000612229.3 None 0.274771228477747 12.3393269161045 0.388605385304567 0.822350467469746
ENSG00000196090.11: ENST00000373193.6 None 1.48129702215581 0.285332509679594 0.395946521374322 0.822350467469746
ENSG00000172264.15: ENST00000490428.4 None 3.01785250065712 0.369783790886365 0.426858256478385 0.853716512956769
ENSG00000124214.18: ENST00000437404.2 None 0.891255552136099 -0.0106192332227943 0.486457996043105 0.901446121021347
ENSG00000089123.14: ENST00000480436.4 None 0.637482789177349 0.531209721481527 0.512874759704675 0.901446121021347
ENSG00000131061.12: ENST00000342427.5 None 0.637482789177349 1.96805512118203e-05 0.550883740624156 0.901446121021347
ENSG00000131061.12: ENST00000483118.4 None 0.637482789177349 -6.56024339651395e-06 0.550883740624156 0.901446121021347
ENSG00000131061.12: ENST00000497876.4 None 0.637482789177349 -6.56024339651395e-06 0.550883740624156 0.901446121021347
ENSG00000131061.12: ENST00000375200.4 None 0.637482789177349 -6.5602433947376e-06 0.550883740624156 0.901446121021347
ENSG00000175170.13: ENST00000478164.1 None 0.59159308736061 11.3034957249541 0.633707257382528 0.94757854233939
ENSG00000175170.13: ENST00000376403.4 None 0.59159308736061 11.3034159668804 0.633707257382528 0.94757854233939
ENSG00000175170.13: ENST00000582267.4 None 0.59159308736061 11.3034957249515 0.633707257382528 0.94757854233939
ENSG00000182621.15: ENST00000630495.1 None 1.7539142656938 0.432653359298262 0.649266779010322 0.94757854233939
ENSG00000234684.5: ENST00000446423.1 None 2.18576008711634 -2.19975958479779e-05 0.711459967957612 0.960470956742777
ENSG00000234684.5: ENST00000609285.4 None 2.18576008711634 1.09989237069286e-05 0.711459967957612 0.960470956742777
ENSG00000234684.5: ENST00000609470.4 None 2.18576008711634 1.0998923698935e-05 0.711459967957612 0.960470956742777
ENSG00000196090.11: ENST00000356100.5 None 1.88693346850556 0.770756470252939 0.740125558826847 0.974799516503652
ENSG00000182621.15: ENST00000625874.1 None 1.96023794507771 0.0176155457853577 0.793748396505192 0.982493187218395
ENSG00000089123.14: ENST00000337743.7 None 1.37444838334356 -0.205719508619193 0.800550004400173 0.982493187218395
ENSG00000089123.14: ENST00000465381.4 None 1.37444838334356 -0.205748746579884 0.800550004400173 0.982493187218395
ENSG00000078747.11: ENST00000486883.4 None 5.39504861358411 -0.029850636530897 0.848160506023122 1.0
ENSG00000078747.11: ENST00000262650.9 None 5.45305185549683 0.0233780020634597 0.87755512016615 1.0
ENSG00000175170.13: ENST00000584071.1 None 0.272301275395016 10.9815803246586 0.931376053462039 1.0
MSTRG.74: MSTRG.74.3 None 6.59410708391664 0.0072497148159511 0.945140772430271 1.0
ENSG00000124160.10: ENST00000290231.9 None 6.60182975968386 -0.0036112969189492 0.972583243540354 1.0
ENSG00000124160.10: ENST00000372291.3 None 6.60182975968386 -0.0036112969192965 0.972583243540354 1.0
ENSG00000078747.11: ENST00000535650.4 None 5.41054002097232 0.0030575728924882 0.98424338282025 1.0
ENSG00000078747.11: ENST00000374864.7 None 5.4431650063145 0.0023177037356578 0.98783085741646 1.0
ENSG00000088812.16: ENST00000446916.2 None 3.2068152418461 -1.46056500227587e-11 1.0 1.0
ENSG00000088812.16: ENST00000262919.8 None 3.2068152418461 1.46056500227587e-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 ENST00000338037.9 0.0054990955014229 0.903790697528349 PLCB1
ENSG00000182621.15 ENST00000378637.5 0.0054990955014229 1.0 PLCB1
ENSG00000182621.15 ENST00000378641.6 0.0054990955014229 1.0 PLCB1
ENSG00000182621.15 ENST00000630495.1 0.0054990955014229 1.0 PLCB1
ENSG00000182621.15 ENST00000625874.1 0.0054990955014229 1.0 PLCB1
ENSG00000182621.15 ENST00000626161.1 0.0054990955014229 0.0024445726415129 PLCB1
ENSG00000182621.15 ENST00000629992.1 0.0054990955014229 1.0 PLCB1
ENSG00000182621.15 ENST00000626114.1 0.0054990955014229 0.0230275448744011 PLCB1
MSTRG.27 ENST00000217246.7 0.0093335267886047 1.0 MACROD2
MSTRG.27 ENST00000477147.4 0.0093335267886047 1.0 MACROD2
MSTRG.27 ENST00000490428.4 0.0093335267886047 1.0 MACROD2
MSTRG.27 ENST00000464883.4 0.0093335267886047 0.005535054682282 MACROD2
MSTRG.27 ENST00000402914.4 0.0093335267886047 0.0584008071216434 MACROD2
MSTRG.27 ENST00000494602.4 0.0093335267886047 1.0 MACROD2
ENSG00000196090.11 ENST00000612229.3 0.031942258560274 1.0 PTPRT
ENSG00000196090.11 ENST00000618610.1 0.031942258560274 1.0 PTPRT
ENSG00000196090.11 ENST00000356100.5 0.031942258560274 1.0 PTPRT
ENSG00000196090.11 ENST00000373190.4 0.031942258560274 1.0 PTPRT
ENSG00000196090.11 ENST00000373198.7 0.031942258560274 0.0427514533609736 PTPRT
ENSG00000196090.11 ENST00000373193.6 0.031942258560274 1.0 PTPRT
ENSG00000196090.11 ENST00000617474.1 0.031942258560274 0.937360622599713 PTPRT
ENSG00000196090.11 ENST00000373201.4 0.031942258560274 1.0 PTPRT
ENSG00000175170.13 ENST00000478164.1 0.132507215154747 nan FAM182B
ENSG00000175170.13 ENST00000584356.1 0.132507215154747 nan FAM182B
ENSG00000175170.13 ENST00000376403.4 0.132507215154747 nan FAM182B
ENSG00000175170.13 ENST00000584071.1 0.132507215154747 nan FAM182B
ENSG00000175170.13 ENST00000582267.4 0.132507215154747 nan FAM182B
ENSG00000025293.14 ENST00000374012.6 0.903118146884724 nan PHF20
ENSG00000025293.14 ENST00000339089.9 0.903118146884724 nan PHF20
ENSG00000025293.14 ENST00000374000.7 0.903118146884724 nan PHF20
ENSG00000025293.14 ENST00000461122.4 0.903118146884724 nan PHF20
ENSG00000234684.5 ENST00000609470.4 1.0 nan SDCBP2-AS1
MSTRG.66 ENST00000486883.4 1.0 nan ITCH
MSTRG.66 ENST00000535650.4 1.0 nan ITCH
MSTRG.66 ENST00000374864.7 1.0 nan ITCH
MSTRG.66 ENST00000262650.9 1.0 nan ITCH
MSTRG.74 ENST00000372291.3 1.0 nan NCOA5
ENSG00000234684.5 ENST00000446423.1 1.0 nan SDCBP2-AS1
MSTRG.74 MSTRG.74.3 1.0 nan MSTRG.74
MSTRG.74 ENST00000290231.9 1.0 nan NCOA5
ENSG00000234684.5 ENST00000609285.4 1.0 nan SDCBP2-AS1
MSTRG.5 ENST00000446916.2 1.0 nan ATRN
MSTRG.5 ENST00000262919.8 1.0 nan ATRN
ENSG00000124214.18 ENST00000437404.2 1.0 nan STAU1
ENSG00000124214.18 ENST00000371856.5 1.0 nan STAU1
ENSG00000124214.18 ENST00000371828.6 1.0 nan STAU1
ENSG00000124214.18 ENST00000340954.10 1.0 nan STAU1
ENSG00000089123.14 ENST00000337743.7 1.0 nan TASP1
ENSG00000089123.14 ENST00000465381.4 1.0 nan TASP1
ENSG00000089123.14 ENST00000480436.4 1.0 nan TASP1
ENSG00000131061.12 ENST00000342427.5 1.0 nan ZNF341
ENSG00000131061.12 ENST00000483118.4 1.0 nan ZNF341
ENSG00000131061.12 ENST00000497876.4 1.0 nan ZNF341
ENSG00000131061.12 ENST00000375200.4 1.0 nan ZNF341
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