Summary of minimap2 mapping from
seqkit
seqkit bam -s
| PrimAlnPerc | MultimapPerc | PrimAln | SecAln | SupAln | Unmapped | TotalReads | TotalRecords | File | sample_id |
|---|---|---|---|---|---|---|---|---|---|
| 100.0 | 0.0 | 218 | 0 | 0 | 0 | 218 | 218 | - | sample01 |
| 100.0 | 0.0 | 229 | 0 | 0 | 0 | 229 | 229 | - | sample02 |
| 100.0 | 0.0 | 206 | 0 | 0 | 0 | 206 | 206 | - | sample03 |
| 100.0 | 0.0 | 193 | 0 | 0 | 0 | 193 | 193 | - | sample04 |
| 100.0 | 0.0 | 168 | 0 | 0 | 0 | 168 | 168 | - | sample05 |
| 100.0 | 0.0 | 195 | 0 | 0 | 0 | 195 | 195 | - | sample06 |
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
The classes that are assigned by gffcompare, which describe the relationship between query transfrag and the most similar reference transcript.
This diagram illustrates the different classes.
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 | sample04_batch_1.2.1 | 2 | 4 | 2611 | sample04 | 3.0 |
| TARDBPP1 | ENST00000442013.1 | = | sample01_batch_1.2.2 | 1 | 0 | 1203 | sample01 | 3.0 |
| TARDBPP1 | ENST00000442013.1 | x | sample01_batch_1.3.1 | 2 | 5 | 2589 | sample01 | 3.0 |
| TARDBPP1 | ENST00000442013.1 | k | sample02_batch_1.2.1 | 2 | 8 | 2610 | sample02 | 3.0 |
| TARDBPP1 | ENST00000442013.1 | o | sample04_batch_1.3.1 | 4 | 1 | 1903 | sample04 | 3.0 |
| TARDBPP1 | ENST00000442013.1 | k | sample01_batch_1.2.1 | 2 | 8 | 2610 | sample01 | 3.0 |
| TARDBPP1 | ENST00000442013.1 | x | sample04_batch_1.2.2 | 2 | 3 | 2613 | sample04 | 3.0 |
| TARDBPP1 | ENST00000442013.1 | k | sample03_batch_1.2.1 | 2 | 8 | 2610 | sample03 | 3.0 |
| TARDBPP1 | ENST00000442013.1 | = | sample02_batch_1.2.2 | 1 | 0 | 1203 | sample02 | 3.0 |
| TARDBPP1 | ENST00000442013.1 | x | sample03_batch_1.3.1 | 2 | 4 | 2601 | sample03 | 3.0 |
| TARDBPP1 | ENST00000442013.1 | = | sample03_batch_1.2.2 | 1 | 0 | 1203 | sample03 | 3.0 |
| TARDBPP1 | ENST00000442013.1 | x | sample02_batch_1.3.1 | 2 | 6 | 2589 | sample02 | 3.0 |
| TARDBPP1 | ENST00000442013.1 | k | sample05_batch_1.2.1 | 2 | 3 | 2611 | sample05 | 2.0 |
| TPM3P2 | ENST00000397772.2 | k | sample03_batch_1.9.1 | 3 | 3 | 2058 | sample03 | 2.0 |
| TARDBPP1 | ENST00000442013.1 | k | sample06_batch_1.2.1 | 2 | 3 | 2611 | sample06 | 2.0 |
| NCOA5 | ENST00000290231.9 | i | sample01_batch_1.12.1 | 2 | 3 | 360 | sample01 | 2.0 |
| NCOA5 | ENST00000290231.9 | i | sample04_batch_1.12.1 | 2 | 3 | 329 | sample04 | 2.0 |
| RPS4XP2 | ENST00000458402.1 | o | sample01_batch_1.1.1 | 2 | 3 | 814 | sample01 | 2.0 |
| NCOA5 | ENST00000290231.9 | i | sample06_batch_1.12.1 | 2 | 2 | 329 | sample06 | 2.0 |
| RPS4XP2 | ENST00000458402.1 | o | sample02_batch_1.1.1 | 2 | 2 | 814 | sample02 | 2.0 |
| TARDBPP1 | ENST00000442013.1 | o | sample05_batch_1.2.2 | 4 | 2 | 1903 | 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 |
| RPS4XP2 | ENST00000458402.1 | o | sample03_batch_1.1.1 | 2 | 1 | 814 | sample03 | 2.0 |
| CDC42P1 | ENST00000456658.1 | = | sample04_batch_1.10.1 | 1 | 0 | 548 | sample04 | 2.0 |
| TARDBPP1 | ENST00000442013.1 | = | sample06_batch_1.2.2 | 1 | 0 | 1203 | sample06 | 2.0 |
| CDC42P1 | ENST00000456658.1 | = | sample05_batch_1.12.1 | 1 | 0 | 548 | sample05 | 2.0 |
| RPS4XP2 | ENST00000458402.1 | = | sample01_batch_1.1.2 | 1 | 0 | 793 | sample01 | 2.0 |
| RPS4XP2 | ENST00000458402.1 | = | sample03_batch_1.1.2 | 1 | 0 | 793 | sample03 | 2.0 |
| NCOA5 | ENST00000290231.9 | i | sample05_batch_1.10.1 | 2 | 2 | 329 | sample05 | 2.0 |
| RPS4XP2 | ENST00000458402.1 | = | sample02_batch_1.1.2 | 1 | 0 | 793 | sample02 | 2.0 |
| TPM3P2 | ENST00000397772.2 | s | sample02_batch_1.8.1 | 3 | 12 | 2066 | sample02 | 2.0 |
| NCOA5 | ENST00000290231.9 | i | sample06_batch_1.11.1 | 2 | 24 | 357 | sample06 | 2.0 |
| TPM3P2 | ENST00000397772.2 | s | sample03_batch_1.8.1 | 3 | 14 | 2066 | sample03 | 2.0 |
| TPM3P2 | ENST00000397772.2 | s | sample01_batch_1.8.1 | 3 | 12 | 2067 | sample01 | 2.0 |
| TPM3P2 | ENST00000397772.2 | k | sample02_batch_1.9.1 | 3 | 8 | 2058 | sample02 | 2.0 |
| NCOA5 | ENST00000290231.9 | i | sample03_batch_1.12.1 | 2 | 8 | 360 | sample03 | 2.0 |
| NCOA5 | ENST00000290231.9 | i | sample04_batch_1.11.1 | 2 | 20 | 357 | sample04 | 2.0 |
| NCOA5 | ENST00000290231.9 | i | sample05_batch_1.9.1 | 2 | 22 | 357 | sample05 | 2.0 |
| TPM3P2 | ENST00000397772.2 | k | sample01_batch_1.9.1 | 3 | 8 | 2058 | sample01 | 2.0 |
| CDC42P1 | ENST00000456658.1 | k | sample05_batch_1.11.1 | 1 | 29 | 1406 | sample05 | 2.0 |
| CDC42P1 | ENST00000456658.1 | x | sample04_batch_1.9.1 | 1 | 32 | 1406 | sample04 | 2.0 |
| NCOA5 | ENST00000290231.9 | i | sample03_batch_1.13.1 | 2 | 42 | 326 | sample03 | 2.0 |
| NCOA5 | ENST00000290231.9 | i | sample02_batch_1.12.1 | 2 | 6 | 360 | sample02 | 2.0 |
| NCOA5 | ENST00000290231.9 | i | sample01_batch_1.13.1 | 2 | 44 | 326 | sample01 | 2.0 |
| NCOA5 | ENST00000290231.9 | i | sample02_batch_1.13.1 | 2 | 50 | 326 | sample02 | 2.0 |
| LINC00851 | ENST00000423033.1 | x | sample05_batch_1.5.1 | 3 | 2 | 2253 | sample05 | 1.0 |
| MACROD2 | ENST00000217246.7 | i | sample06_batch_1.15.1 | 2 | 2 | 2058 | sample06 | 1.0 |
| RP5-836E8.1 | ENST00000400616.2 | x | sample01_batch_1.4.1 | 1 | 12 | 1308 | sample01 | 1.0 |
| RPL21P3 | ENST00000395517.2 | s | sample06_batch_1.5.1 | 2 | 2 | 543 | sample06 | 1.0 |
| ADA | ENST00000372874.7 | x | sample06_batch_1.14.1 | 3 | 2 | 634 | sample06 | 1.0 |
| RP5-836E8.1 | ENST00000400616.2 | x | sample05_batch_1.4.1 | 1 | 12 | 1899 | sample05 | 1.0 |
| CDC42P1 | ENST00000456658.1 | = | sample06_batch_1.10.1 | 1 | 4 | 548 | sample06 | 1.0 |
| RP5-836E8.1 | ENST00000400616.2 | x | sample04_batch_1.4.1 | 1 | 13 | 1899 | sample04 | 1.0 |
| RPL15P1 | ENST00000439981.1 | = | sample02_batch_1.5.1 | 1 | 1 | 600 | sample02 | 1.0 |
| FTLP3 | ENST00000427242.1 | = | sample06_batch_1.1.1 | 1 | 1 | 528 | sample06 | 1.0 |
| CBFA2T2 | ENST00000375279.5 | i | sample06_batch_1.9.1 | 2 | 2 | 345 | sample06 | 1.0 |
| RPL12P4 | ENST00000432629.1 | = | sample02_batch_1.11.1 | 1 | 1 | 497 | sample02 | 1.0 |
| ITCH | ENST00000374864.7 | i | sample03_batch_1.10.1 | 1 | 62 | 571 | sample03 | 1.0 |
| RP5-836E8.1 | ENST00000400616.2 | x | sample02_batch_1.4.1 | 1 | 16 | 1308 | sample02 | 1.0 |
| FTLP3 | ENST00000427242.1 | = | sample05_batch_1.1.1 | 1 | 2 | 528 | sample05 | 1.0 |
| ADA | ENST00000372874.7 | x | sample04_batch_1.13.1 | 3 | 2 | 634 | sample04 | 1.0 |
| TPM3P2 | ENST00000397772.2 | s | sample06_batch_1.7.1 | 3 | 5 | 2066 | sample06 | 1.0 |
| RPL12P4 | ENST00000432629.1 | = | sample03_batch_1.11.1 | 1 | 4 | 497 | sample03 | 1.0 |
| RPL15P1 | ENST00000439981.1 | = | sample03_batch_1.5.1 | 1 | 4 | 600 | sample03 | 1.0 |
| SF3A3P1 | ENST00000446317.1 | x | sample02_batch_1.6.1 | 2 | 4 | 362 | sample02 | 1.0 |
| TPM3P2 | ENST00000397772.2 | s | sample04_batch_1.6.1 | 3 | 7 | 2066 | sample04 | 1.0 |
| ZNF337-AS1 | ENST00000428254.4 | i | sample03_batch_1.7.1 | 2 | 3 | 1457 | sample03 | 1.0 |
| SF3A3P1 | ENST00000446317.1 | x | sample03_batch_1.6.1 | 2 | 3 | 362 | sample03 | 1.0 |
| CFAP61 | ENST00000245957.8 | x | sample05_batch_1.6.1 | 3 | 3 | 852 | sample05 | 1.0 |
| ITCH | ENST00000374864.7 | i | sample01_batch_1.11.1 | 1 | 69 | 571 | sample01 | 1.0 |
| ZNF337-AS1 | ENST00000428254.4 | i | sample02_batch_1.7.1 | 2 | 3 | 1457 | sample02 | 1.0 |
| DDX27 | ENST00000622530.3 | s | sample06_batch_1.13.1 | 3 | 3 | 315 | sample06 | 1.0 |
| CBFA2T2 | ENST00000375279.5 | i | sample04_batch_1.8.1 | 2 | 3 | 345 | sample04 | 1.0 |
| RPL12P4 | ENST00000432629.1 | = | sample01_batch_1.10.1 | 1 | 3 | 497 | 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 |
| RPL15P1 | ENST00000439981.1 | = | sample01_batch_1.5.1 | 1 | 3 | 600 | sample01 | 1.0 |
| RP5-836E8.1 | ENST00000400616.2 | x | sample03_batch_1.4.1 | 1 | 10 | 1308 | sample03 | 1.0 |
| RP5-836E8.1 | ENST00000400616.2 | x | sample06_batch_1.4.1 | 1 | 12 | 1899 | sample06 | 1.0 |
| MACROD2 | ENST00000217246.7 | i | sample05_batch_1.15.1 | 2 | 2 | 1713 | sample05 | 1.0 |
| FTLP3 | ENST00000427242.1 | = | sample04_batch_1.1.1 | 1 | 2 | 528 | sample04 | 1.0 |
| DDX27 | ENST00000622530.3 | s | sample05_batch_1.13.1 | 3 | 2 | 315 | sample05 | 1.0 |
| PTGIS | ENST00000244043.4 | i | sample05_batch_1.14.1 | 2 | 2 | 677 | sample05 | 1.0 |
| ITCH | ENST00000374864.7 | i | sample02_batch_1.10.1 | 1 | 69 | 571 | sample02 | 1.0 |
| - | - | u | sample04_batch_1.5.1 | 4 | 2 | 2582 | sample04 | NaN |
| - | - | u | sample04_batch_1.7.1 | 2 | 2 | 1323 | sample04 | NaN |
| - | - | 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_1.8.1 | 2 | 2 | 1323 | sample06 | NaN |
| - | - | u | sample05_batch_1.3.1 | 2 | 2 | 713 | sample05 | NaN |
| - | - | u | sample05_batch_1.8.1 | 2 | 2 | 1323 | sample05 | NaN |
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.
| fname | sample01 | sample02 | sample03 | sample04 | sample05 | sample06 |
|---|---|---|---|---|---|---|
| Read mappings | 4193 | 4487 | 4319 | 4266 | 4077 | 4084 |
| Primary | 1093 | 1157 | 1104 | 1048 | 1010 | 995 |
| Secondary | 3050 | 3275 | 3161 | 3151 | 3010 | 3021 |
| Supplementary | 50 | 55 | 54 | 67 | 57 | 68 |
| Median Qscore | 8 | 8 | 8 | 8 | 8 | 8 |
| Median MAPQ | 0 | 0 | 0 | 0 | 0 | 0 |
Table showing the annotated Transcripts Per Million identified by Minimap2 mapping and Salmon transcript detection with the highest number of mapped reads
| sample05 | sample03 | sample01 | sample04 | sample02 | sample06 | |
|---|---|---|---|---|---|---|
| Reference | ||||||
| MSTRG.83.1 | 786039 | 732982 | 744714 | 798213 | 722246 | 775346 |
| MSTRG.82.3 | 156410 | 221016 | 208267 | 141974 | 230780 | 156128 |
| MSTRG.10.1 | 6873 | 3080 | 3214 | 8839 | 3035 | 7162 |
| ENST00000372291.3 | 4254 | 6056 | 5711 | 3861 | 6321 | 4246 |
| MSTRG.63.1 | 2922 | 6287 | 6123 | 4209 | 6195 | 3480 |
| ENST00000290231.9 | 3355 | 4776 | 4504 | 3045 | 4985 | 3348 |
| ENST00000427242.1 | 5096 | 0 | 0 | 5243 | 0 | 6069 |
| ENST00000432629.1 | 0 | 4113 | 4292 | 0 | 4053 | 0 |
| ENST00000400616.2 | 0 | 3694 | 3855 | 0 | 3640 | 0 |
| MSTRG.12.1 | 2490 | 0 | 0 | 4269 | 0 | 3953 |
| MSTRG.44.1 | 4699 | 0 | 0 | 0 | 0 | 5596 |
| ENST00000439981.1 | 0 | 2902 | 3029 | 0 | 2860 | 0 |
| MSTRG.65.1 | 2532 | 0 | 0 | 2605 | 0 | 3015 |
| MSTRG.8.1 | 1170 | 1259 | 1752 | 1204 | 2068 | 697 |
| ENST00000486883.4 | 1377 | 826 | 967 | 1330 | 854 | 1171 |
| MSTRG.89.1 | 1925 | 0 | 0 | 1980 | 0 | 2292 |
| MSTRG.64.1 | 585 | 1260 | 1314 | 602 | 1241 | 697 |
| ENST00000458402.1 | 0 | 1824 | 1903 | 0 | 1797 | 0 |
| ENST00000256654.8 | 0 | 0 | 0 | 2539 | 0 | 2939 |
| ENST00000446317.1 | 1154 | 0 | 0 | 1187 | 0 | 1375 |
| ENST00000397772.2 | 0 | 1203 | 1256 | 0 | 1186 | 0 |
| ENST00000431775.1 | 0 | 1175 | 1227 | 0 | 1158 | 0 |
| ENST00000543500.2 | 1099 | 0 | 0 | 1130 | 0 | 1308 |
| ENST00000598007.2 | 1013 | 0 | 0 | 1042 | 0 | 1206 |
| ENST00000613361.1 | 559 | 400 | 418 | 575 | 395 | 665 |
| ENST00000535650.4 | 603 | 354 | 415 | 583 | 366 | 517 |
| ENST00000262650.9 | 498 | 288 | 337 | 483 | 297 | 422 |
| ENST00000374864.7 | 488 | 288 | 336 | 473 | 297 | 422 |
| ENST00000496085.1 | 661 | 0 | 0 | 680 | 0 | 787 |
| ENST00000457644.1 | 736 | 0 | 0 | 757 | 0 | 438 |
| MSTRG.48.1 | 0 | 591 | 617 | 0 | 582 | 0 |
| ENST00000376312.3 | 0 | 524 | 547 | 0 | 517 | 0 |
| MSTRG.43.1 | 662 | 0 | 0 | 0 | 0 | 788 |
| MSTRG.85.1 | 427 | 0 | 0 | 439 | 0 | 508 |
| ENST00000352551.8 | 351 | 0 | 0 | 361 | 0 | 418 |
| ENST00000243893.9 | 349 | 0 | 0 | 359 | 0 | 416 |
| ENST00000335046.6 | 347 | 0 | 0 | 357 | 0 | 414 |
| ENST00000405520.4 | 343 | 0 | 0 | 353 | 0 | 408 |
| ENST00000356455.7 | 342 | 0 | 0 | 352 | 0 | 408 |
| MSTRG.1.1 | 54 | 232 | 242 | 55 | 267 | 64 |
| ENST00000609285.4 | 248 | 0 | 0 | 313 | 0 | 329 |
| ENST00000466532.1 | 406 | 0 | 0 | 0 | 0 | 483 |
| ENST00000446423.1 | 242 | 0 | 0 | 305 | 0 | 321 |
| ENST00000609470.4 | 240 | 0 | 0 | 302 | 0 | 317 |
| ENST00000421216.1 | 177 | 63 | 66 | 182 | 62 | 211 |
| ENST00000324384.3 | 132 | 0 | 0 | 204 | 0 | 236 |
| MSTRG.62.1 | 202 | 0 | 0 | 104 | 0 | 241 |
| ENST00000381253.4 | 168 | 0 | 0 | 173 | 0 | 200 |
| ENST00000456249.4 | 0 | 177 | 185 | 0 | 175 | 0 |
| ENST00000481560.1 | 164 | 0 | 0 | 168 | 0 | 195 |
| ENST00000466099.1 | 0 | 159 | 166 | 0 | 157 | 0 |
| ENST00000446916.2 | 39 | 98 | 87 | 50 | 110 | 46 |
| ENST00000348616.7 | 130 | 0 | 0 | 133 | 0 | 154 |
| ENST00000202017.5 | 0 | 135 | 141 | 0 | 133 | 0 |
| ENST00000429853.1 | 125 | 0 | 0 | 129 | 0 | 149 |
| ENST00000468420.4 | 122 | 0 | 0 | 126 | 0 | 146 |
| MSTRG.68.1 | 69 | 0 | 0 | 143 | 0 | 166 |
| ENST00000624666.1 | 0 | 125 | 130 | 0 | 123 | 0 |
| ENST00000491682.4 | 43 | 93 | 97 | 44 | 91 | 0 |
| ENST00000493252.2 | 0 | 119 | 124 | 0 | 117 | 0 |
| ENST00000356562.5 | 66 | 0 | 0 | 135 | 0 | 157 |
| ENST00000262919.8 | 31 | 79 | 70 | 40 | 89 | 37 |
| ENST00000300403.9 | 113 | 0 | 0 | 93 | 0 | 135 |
| ENST00000278772.7 | 104 | 0 | 0 | 107 | 0 | 124 |
| ENST00000482133.1 | 104 | 0 | 0 | 107 | 0 | 123 |
| ENST00000623732.2 | 0 | 106 | 111 | 0 | 105 | 0 |
| ENST00000344103.7 | 99 | 0 | 0 | 102 | 0 | 119 |
| ENST00000375730.3 | 0 | 103 | 108 | 0 | 102 | 0 |
| ENST00000462062.4 | 141 | 0 | 0 | 0 | 0 | 168 |
| MSTRG.16.1 | 105 | 0 | 0 | 108 | 0 | 93 |
| ENST00000379070.3 | 94 | 0 | 0 | 97 | 0 | 112 |
| ENST00000413823.1 | 94 | 0 | 0 | 97 | 0 | 112 |
| ENST00000484893.1 | 0 | 99 | 103 | 0 | 98 | 0 |
| ENST00000412241.1 | 80 | 0 | 0 | 123 | 0 | 95 |
| ENST00000377873.6 | 38 | 27 | 28 | 78 | 26 | 90 |
| ENST00000482423.1 | 0 | 94 | 98 | 0 | 93 | 0 |
| ENST00000371856.5 | 37 | 67 | 42 | 38 | 93 | 0 |
| ENST00000360672.2 | 85 | 0 | 0 | 88 | 0 | 101 |
| ENST00000609252.1 | 0 | 90 | 94 | 0 | 89 | 0 |
| ENST00000449988.1 | 85 | 0 | 0 | 87 | 0 | 101 |
| ENST00000262866.7 | 84 | 0 | 0 | 86 | 0 | 100 |
| ENST00000481196.4 | 0 | 88 | 92 | 0 | 87 | 0 |
| ENST00000435014.1 | 82 | 0 | 0 | 84 | 0 | 98 |
| ENST00000372420.4 | 0 | 0 | 0 | 122 | 0 | 141 |
| ENST00000584356.1 | 83 | 12 | 12 | 86 | 11 | 59 |
| ENST00000617804.1 | 95 | 0 | 0 | 97 | 0 | 67 |
| ENST00000618770.1 | 94 | 0 | 0 | 96 | 0 | 67 |
| ENST00000619859.1 | 78 | 0 | 0 | 80 | 0 | 93 |
| ENST00000621390.1 | 0 | 0 | 0 | 115 | 0 | 134 |
| ENST00000450129.1 | 0 | 82 | 85 | 0 | 81 | 0 |
| ENST00000618797.3 | 77 | 0 | 0 | 79 | 0 | 91 |
| ENST00000339946.6 | 245 | 0 | 0 | 0 | 0 | 0 |
| ENST00000457508.1 | 0 | 81 | 84 | 0 | 80 | 0 |
| ENST00000558738.1 | 0 | 79 | 83 | 0 | 78 | 0 |
| ENST00000344256.9 | 74 | 0 | 0 | 76 | 0 | 88 |
| ENST00000456939.4 | 74 | 0 | 0 | 76 | 0 | 88 |
| ENST00000372622.6 | 73 | 0 | 0 | 75 | 0 | 87 |
| ENST00000445484.4 | 70 | 0 | 0 | 73 | 0 | 84 |
| ENST00000449270.1 | 68 | 0 | 0 | 70 | 0 | 81 |
| ENST00000461710.4 | 99 | 0 | 0 | 0 | 0 | 118 |
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 false discovery corrected p-value (FDR). This table has not been filtered for genes that satisfy statistical or magnitudinal thresholds
| logFC | logCPM | F | PValue | FDR | |
|---|---|---|---|---|---|
| ENSG00000171984.13 | 5.95 | 12.26 | 2049028.00 | 6.308693e-08 | 0.000012 |
| ENSG00000101052.11 | 5.54 | 12.00 | 5325262.84 | 1.529904e-06 | 0.000074 |
| ENSG00000124215.15 | 5.54 | 12.00 | 5325262.84 | 1.529904e-06 | 0.000074 |
| ENSG00000175063.15 | 5.54 | 12.00 | 5325262.84 | 1.529904e-06 | 0.000074 |
| ENSG00000174306.20 | 5.29 | 11.84 | 9739431.02 | 1.141694e-05 | 0.000441 |
| ENSG00000089123.14 | -7.18 | 13.07 | 6279.71 | 5.070401e-05 | 0.000515 |
| ENSG00000131061.12 | -6.68 | 12.67 | 6369.57 | 4.987841e-05 | 0.000515 |
| ENSG00000088876.10 | 2.71 | 12.37 | 42486.47 | 4.971045e-05 | 0.000515 |
| ENSG00000101104.11 | -6.10 | 12.26 | 6411.92 | 4.949789e-05 | 0.000515 |
| ENSG00000182463.14 | -5.91 | 12.13 | 6417.72 | 4.944625e-05 | 0.000515 |
| ENSG00000149646.11 | -5.69 | 12.00 | 6421.81 | 4.940983e-05 | 0.000515 |
| ENSG00000126005.14 | -5.69 | 12.00 | 6421.81 | 4.940983e-05 | 0.000515 |
| ENSG00000259723.1 | -5.12 | 11.67 | 6425.93 | 4.937325e-05 | 0.000515 |
| ENSG00000204548.3 | -5.12 | 11.67 | 6425.93 | 4.937325e-05 | 0.000515 |
| ENSG00000125850.9 | -5.12 | 11.67 | 6425.93 | 4.937325e-05 | 0.000515 |
| ENSG00000100991.10 | -5.12 | 11.67 | 6425.93 | 4.937325e-05 | 0.000515 |
| ENSG00000054793.12 | 2.93 | 12.52 | 302.95 | 3.692540e-05 | 0.000515 |
| ENSG00000196090.11 | 2.90 | 14.35 | 397.79 | 2.065170e-05 | 0.000515 |
| ENSG00000124226.9 | -5.43 | 11.84 | 6424.45 | 4.938638e-05 | 0.000515 |
| ENSG00000185052.10 | 4.97 | 11.67 | 19936803.01 | 8.668099e-05 | 0.000697 |
| ENSG00000125851.8 | 4.97 | 11.67 | 19936803.01 | 8.668099e-05 | 0.000697 |
| ENSG00000124207.15 | 4.97 | 11.67 | 19936803.01 | 8.668099e-05 | 0.000697 |
| ENSG00000101146.11 | 4.97 | 11.67 | 19936803.01 | 8.668099e-05 | 0.000697 |
| ENSG00000101082.12 | 4.97 | 11.67 | 19936803.01 | 8.668099e-05 | 0.000697 |
| MSTRG.1 | -2.66 | 12.18 | 961.56 | 1.249517e-04 | 0.000965 |
| MSTRG.82 | -1.26 | 17.88 | 166.60 | 1.312772e-04 | 0.000974 |
| ENSG00000125821.10 | 2.59 | 12.30 | 679.61 | 1.492201e-04 | 0.001067 |
| ENSG00000101079.19 | -2.59 | 12.13 | 6015.78 | 2.356767e-04 | 0.001579 |
| ENSG00000089177.16 | -4.72 | 11.48 | 6426.52 | 2.452637e-04 | 0.001579 |
| MSTRG.63 | -1.50 | 13.28 | 122.60 | 2.501341e-04 | 0.001579 |
| ENSG00000088812.16 | -1.83 | 14.02 | 121.78 | 2.536764e-04 | 0.001579 |
| ENSG00000025293.14 | 1.99 | 13.04 | 100.24 | 3.808528e-04 | 0.002297 |
| ENSG00000234684.5 | 7.87 | 13.79 | 652.58 | 6.923554e-04 | 0.003426 |
| ENSG00000221328.1 | 4.57 | 11.48 | 44380338.87 | 6.756675e-04 | 0.003426 |
| ENSG00000188559.12 | 4.57 | 11.48 | 44380338.87 | 6.756675e-04 | 0.003426 |
| ENSG00000089012.13 | 4.57 | 11.48 | 44380338.87 | 6.756675e-04 | 0.003426 |
| ENSG00000101457.11 | 4.57 | 11.48 | 44380338.87 | 6.756675e-04 | 0.003426 |
| ENSG00000101144.11 | 4.57 | 11.48 | 44380338.87 | 6.756675e-04 | 0.003426 |
| ENSG00000185019.15 | 4.57 | 11.48 | 44380338.87 | 6.756675e-04 | 0.003426 |
| ENSG00000124214.18 | -2.67 | 13.02 | 73.43 | 7.250872e-04 | 0.003499 |
| ENSG00000228340.4 | 1.73 | 12.87 | 70.44 | 7.895885e-04 | 0.003717 |
| ENSG00000175170.13 | 3.79 | 13.13 | 58.92 | 1.137112e-03 | 0.005225 |
| ENSG00000227906.6 | 2.15 | 12.70 | 56.38 | 1.243413e-03 | 0.005581 |
| MSTRG.83 | -0.61 | 17.71 | 51.75 | 1.478171e-03 | 0.006484 |
| ENSG00000089101.16 | 1.55 | 12.76 | 8323.14 | 1.717977e-03 | 0.007368 |
| ENSG00000088325.14 | 5.19 | 11.79 | 283.40 | 1.808167e-03 | 0.007586 |
| ENSG00000100997.17 | -3.20 | 12.79 | 43.47 | 2.096273e-03 | 0.008608 |
| ENSG00000101350.7 | -4.16 | 11.26 | 6426.45 | 2.751477e-03 | 0.010621 |
| ENSG00000170471.13 | -4.16 | 11.26 | 6426.45 | 2.751477e-03 | 0.010621 |
| ENSG00000196700.6 | -4.16 | 11.26 | 6426.45 | 2.751477e-03 | 0.010621 |
| MSTRG.16 | 4.85 | 11.61 | 173.54 | 3.172802e-03 | 0.012007 |
| MSTRG.65 | 4.02 | 11.26 | 74008418.38 | 5.511864e-03 | 0.018663 |
| ENSG00000229876.1 | 4.02 | 11.26 | 74008418.38 | 5.511864e-03 | 0.018663 |
| ENSG00000225458.1 | 4.02 | 11.26 | 74008418.38 | 5.511864e-03 | 0.018663 |
| ENSG00000125772.11 | 4.02 | 11.26 | 74008418.38 | 5.511864e-03 | 0.018663 |
| ENSG00000088826.16 | 4.02 | 11.26 | 74008418.38 | 5.511864e-03 | 0.018663 |
| ENSG00000149633.10 | 4.02 | 11.26 | 74008418.38 | 5.511864e-03 | 0.018663 |
| ENSG00000118705.15 | 2.05 | 12.00 | 19981.91 | 6.098944e-03 | 0.020295 |
| ENSG00000180083.9 | 5.38 | 11.90 | 90.42 | 6.669161e-03 | 0.020866 |
| ENSG00000130584.9 | 4.41 | 11.41 | 90.41 | 6.670272e-03 | 0.020866 |
| ENSG00000232271.1 | 4.41 | 11.41 | 90.41 | 6.670272e-03 | 0.020866 |
| ENSG00000198646.12 | -2.52 | 11.79 | 23.87 | 6.702959e-03 | 0.020866 |
| ENSG00000230010.1 | 4.97 | 11.67 | 70.49 | 8.837202e-03 | 0.026650 |
| MSTRG.12 | 4.97 | 11.67 | 70.49 | 8.837202e-03 | 0.026650 |
| ENSG00000271774.1 | -2.02 | 11.84 | 4523.21 | 9.268694e-03 | 0.026699 |
| ENSG00000214200.2 | -2.02 | 11.84 | 4523.21 | 9.268694e-03 | 0.026699 |
| ENSG00000064787.11 | 5.76 | 12.13 | 68.64 | 9.105808e-03 | 0.026699 |
| ENSG00000064655.17 | 1.53 | 12.34 | 268.94 | 1.047338e-02 | 0.029726 |
| ENSG00000274322.1 | 6.06 | 12.34 | 58.87 | 1.082263e-02 | 0.030272 |
| ENSG00000124151.17 | -2.25 | 12.58 | 14.80 | 1.594747e-02 | 0.043969 |
| ENSG00000132669.11 | 6.27 | 12.48 | 39.07 | 1.709442e-02 | 0.046468 |
| ENSG00000226344.1 | 3.77 | 11.18 | 33.97 | 1.994457e-02 | 0.051324 |
| ENSG00000149488.12 | 3.77 | 11.18 | 33.97 | 1.994457e-02 | 0.051324 |
| MSTRG.62 | 3.77 | 11.18 | 33.97 | 1.994457e-02 | 0.051324 |
| MSTRG.68 | 3.77 | 11.18 | 33.97 | 1.994457e-02 | 0.051324 |
| ENSG00000158296.12 | 6.49 | 12.64 | 30.06 | 2.279846e-02 | 0.057896 |
| ENSG00000020256.18 | -1.28 | 12.34 | 80.25 | 2.433477e-02 | 0.060995 |
| ENSG00000149531.13 | -3.24 | 11.00 | 6425.51 | 3.424008e-02 | 0.064159 |
| ENSG00000166948.8 | -3.24 | 11.00 | 6425.51 | 3.424008e-02 | 0.064159 |
| ENSG00000215388.3 | -3.24 | 11.00 | 6425.51 | 3.424008e-02 | 0.064159 |
| ENSG00000234139.2 | -3.24 | 11.00 | 6425.51 | 3.424008e-02 | 0.064159 |
| ENSG00000235958.4 | -3.24 | 11.00 | 6425.51 | 3.424008e-02 | 0.064159 |
| ENSG00000185834.10 | -3.24 | 11.00 | 6425.51 | 3.424008e-02 | 0.064159 |
| ENSG00000227343.1 | -3.24 | 11.00 | 6425.51 | 3.424008e-02 | 0.064159 |
| MSTRG.48 | -3.24 | 11.00 | 6425.51 | 3.424008e-02 | 0.064159 |
| ENSG00000226948.1 | -3.24 | 11.00 | 6425.51 | 3.424008e-02 | 0.064159 |
| ENSG00000124228.13 | -3.24 | 11.00 | 6425.51 | 3.424008e-02 | 0.064159 |
| ENSG00000215586.2 | -3.24 | 11.00 | 6425.51 | 3.424008e-02 | 0.064159 |
| ENSG00000131069.18 | -3.24 | 11.00 | 6425.51 | 3.424008e-02 | 0.064159 |
| ENSG00000238282.1 | -3.24 | 11.00 | 6425.51 | 3.424008e-02 | 0.064159 |
| ENSG00000101363.11 | -3.24 | 11.00 | 6425.51 | 3.424008e-02 | 0.064159 |
| ENSG00000101134.10 | 4.41 | 11.41 | 25.20 | 2.761407e-02 | 0.064159 |
| ENSG00000124191.16 | 4.97 | 11.67 | 21.07 | 3.346428e-02 | 0.064159 |
| ENSG00000088340.14 | -3.24 | 11.00 | 6425.51 | 3.424008e-02 | 0.064159 |
| ENSG00000088356.5 | -3.24 | 11.00 | 6425.51 | 3.424008e-02 | 0.064159 |
| ENSG00000101003.9 | -3.24 | 11.00 | 6425.51 | 3.424008e-02 | 0.064159 |
| ENSG00000087586.16 | -3.24 | 11.00 | 6425.51 | 3.424008e-02 | 0.064159 |
| ENSG00000101181.16 | -3.24 | 11.00 | 6425.51 | 3.424008e-02 | 0.064159 |
| ENSG00000101191.15 | -3.24 | 11.00 | 6425.51 | 3.424008e-02 | 0.064159 |
| ENSG00000101247.16 | -3.24 | 11.00 | 6425.51 | 3.424008e-02 | 0.064159 |
| ENSG00000101337.14 | -3.24 | 11.00 | 6425.51 | 3.424008e-02 | 0.064159 |
| ENSG00000101346.10 | -3.24 | 11.00 | 6425.51 | 3.424008e-02 | 0.064159 |
| ENSG00000125966.9 | -3.24 | 11.00 | 6425.51 | 3.424008e-02 | 0.064159 |
| MSTRG.13 | 1.30 | 12.22 | 153.35 | 3.616879e-02 | 0.067121 |
| ENSG00000244005.11 | 3.10 | 11.00 | 34475670.24 | 4.969645e-02 | 0.068024 |
| ENSG00000204663.8 | 3.10 | 11.00 | 34475670.24 | 4.969645e-02 | 0.068024 |
| ENSG00000226648.1 | 3.10 | 11.00 | 34475670.24 | 4.969645e-02 | 0.068024 |
| ENSG00000228888.1 | 3.10 | 11.00 | 34475670.24 | 4.969645e-02 | 0.068024 |
| ENSG00000229262.1 | 3.10 | 11.00 | 34475670.24 | 4.969645e-02 | 0.068024 |
| ENSG00000243961.2 | 3.10 | 11.00 | 34475670.24 | 4.969645e-02 | 0.068024 |
| ENSG00000256222.2 | 3.10 | 11.00 | 34475670.24 | 4.969645e-02 | 0.068024 |
| ENSG00000226608.3 | 3.10 | 11.00 | 34475670.24 | 4.969645e-02 | 0.068024 |
| ENSG00000268628.2 | 3.10 | 11.00 | 34475670.24 | 4.969645e-02 | 0.068024 |
| ENSG00000274863.1 | 3.10 | 11.00 | 34475670.24 | 4.969645e-02 | 0.068024 |
| ENSG00000279082.2 | 3.10 | 11.00 | 34475670.24 | 4.969645e-02 | 0.068024 |
| ENSG00000230568.1 | 3.10 | 11.00 | 34475670.24 | 4.969645e-02 | 0.068024 |
| MSTRG.56 | 3.10 | 11.00 | 34475670.24 | 4.969645e-02 | 0.068024 |
| ENSG00000158445.7 | 3.10 | 11.00 | 34475670.24 | 4.969645e-02 | 0.068024 |
| ENSG00000168734.12 | 3.10 | 11.00 | 34475670.24 | 4.969645e-02 | 0.068024 |
| ENSG00000260202.2 | 3.10 | 11.00 | 34475670.24 | 4.969645e-02 | 0.068024 |
| ENSG00000132623.14 | 3.10 | 11.00 | 34475670.24 | 4.969645e-02 | 0.068024 |
| ENSG00000101353.13 | 3.10 | 11.00 | 34475670.24 | 4.969645e-02 | 0.068024 |
| ENSG00000124177.13 | 3.10 | 11.00 | 34475670.24 | 4.969645e-02 | 0.068024 |
| ENSG00000101109.10 | 4.23 | 11.34 | 15.73 | 4.556737e-02 | 0.068024 |
| ENSG00000101349.15 | 4.23 | 11.34 | 15.73 | 4.556737e-02 | 0.068024 |
| ENSG00000022277.11 | 3.10 | 11.00 | 34475670.24 | 4.969645e-02 | 0.068024 |
| ENSG00000080845.16 | 3.10 | 11.00 | 34475670.24 | 4.969645e-02 | 0.068024 |
| ENSG00000088888.16 | 3.10 | 11.00 | 34475670.24 | 4.969645e-02 | 0.068024 |
| ENSG00000101152.9 | 3.10 | 11.00 | 34475670.24 | 4.969645e-02 | 0.068024 |
| ENSG00000101224.16 | 3.10 | 11.00 | 34475670.24 | 4.969645e-02 | 0.068024 |
| ENSG00000125804.12 | 3.10 | 11.00 | 34475670.24 | 4.969645e-02 | 0.068024 |
| ENSG00000101290.12 | 3.10 | 11.00 | 34475670.24 | 4.969645e-02 | 0.068024 |
| ENSG00000101311.14 | 3.10 | 11.00 | 34475670.24 | 4.969645e-02 | 0.068024 |
| ENSG00000101323.4 | 3.10 | 11.00 | 34475670.24 | 4.969645e-02 | 0.068024 |
| MSTRG.85 | 3.10 | 11.00 | 34475670.24 | 4.969645e-02 | 0.068024 |
| ENSG00000101400.5 | 3.10 | 11.00 | 34475670.24 | 4.969645e-02 | 0.068024 |
| ENSG00000101444.11 | 3.10 | 11.00 | 34475670.24 | 4.969645e-02 | 0.068024 |
| ENSG00000124103.8 | 3.10 | 11.00 | 34475670.24 | 4.969645e-02 | 0.068024 |
| ENSG00000124143.9 | 3.10 | 11.00 | 34475670.24 | 4.969645e-02 | 0.068024 |
| ENSG00000101294.15 | 3.10 | 11.00 | 34475670.24 | 4.969645e-02 | 0.068024 |
| MSTRG.89 | 3.10 | 11.00 | 34475670.24 | 4.969645e-02 | 0.068024 |
| ENSG00000233402.1 | -1.35 | 11.95 | 19.31 | 5.271140e-02 | 0.071643 |
| ENSG00000270792.4 | 1.48 | 11.73 | 72.13 | 7.028824e-02 | 0.094865 |
| ENSG00000125864.10 | 2.22 | 12.09 | 5.36 | 7.687824e-02 | 0.103038 |
| ENSG00000172264.15 | -0.37 | 15.64 | 5.06 | 8.283462e-02 | 0.110256 |
| ENSG00000101425.11 | 1.33 | 11.67 | 6787.89 | 1.108789e-01 | 0.146573 |
| ENSG00000234948.1 | 1.03 | 12.09 | 72.07 | 1.134674e-01 | 0.148974 |
| ENSG00000132792.17 | 4.23 | 11.34 | 4.91 | 1.397293e-01 | 0.182215 |
| MSTRG.43 | 2.60 | 10.90 | 3.66 | 1.784281e-01 | 0.204980 |
| ENSG00000274469.1 | 2.60 | 10.90 | 3.66 | 1.784281e-01 | 0.204980 |
| ENSG00000254995.4 | 2.60 | 10.90 | 3.66 | 1.784281e-01 | 0.204980 |
| ENSG00000240849.9 | 2.60 | 10.90 | 3.66 | 1.784281e-01 | 0.204980 |
| ENSG00000225069.3 | 2.60 | 10.90 | 3.66 | 1.784281e-01 | 0.204980 |
| ENSG00000130703.14 | 2.60 | 10.90 | 3.66 | 1.784281e-01 | 0.204980 |
| ENSG00000125844.14 | 2.60 | 10.90 | 3.66 | 1.784281e-01 | 0.204980 |
| ENSG00000101440.8 | 2.60 | 10.90 | 3.66 | 1.784281e-01 | 0.204980 |
| ENSG00000101407.11 | 2.60 | 10.90 | 3.66 | 1.784281e-01 | 0.204980 |
| ENSG00000213742.5 | 2.60 | 10.90 | 3.66 | 1.784281e-01 | 0.204980 |
| ENSG00000100979.13 | 2.60 | 10.90 | 3.66 | 1.784281e-01 | 0.204980 |
| ENSG00000101333.15 | 2.60 | 10.90 | 3.66 | 1.784281e-01 | 0.204980 |
| ENSG00000101391.19 | 4.97 | 11.67 | 3.66 | 1.784157e-01 | 0.204980 |
| ENSG00000171456.15 | 4.41 | 11.41 | 3.66 | 1.784206e-01 | 0.204980 |
| ENSG00000172296.11 | 4.41 | 11.41 | 3.66 | 1.784206e-01 | 0.204980 |
| ENSG00000101019.20 | 5.83 | 12.18 | 3.66 | 1.784034e-01 | 0.204980 |
| MSTRG.44 | 3.48 | 11.09 | 3.66 | 1.784256e-01 | 0.204980 |
| ENSG00000042062.10 | 2.60 | 10.90 | 3.66 | 1.784281e-01 | 0.204980 |
| ENSG00000092758.14 | 2.60 | 10.90 | 3.66 | 1.784281e-01 | 0.204980 |
| ENSG00000089057.13 | 4.02 | 11.26 | 3.66 | 1.784231e-01 | 0.204980 |
| ENSG00000089063.13 | -1.56 | 11.41 | 2.49 | 1.848706e-01 | 0.211124 |
| ENSG00000215529.11 | -0.95 | 11.79 | 15.79 | 2.033290e-01 | 0.230838 |
| MSTRG.10 | 0.57 | 12.79 | 12.20 | 2.079570e-01 | 0.234712 |
| ENSG00000101443.16 | 3.48 | 11.09 | 2.77 | 2.211093e-01 | 0.248105 |
| ENSG00000280350.1 | -1.06 | 11.48 | 1817.67 | 2.435773e-01 | 0.271736 |
| ENSG00000101236.15 | 0.99 | 11.55 | 4.08 | 2.630516e-01 | 0.291776 |
| ENSG00000179242.14 | -0.66 | 12.18 | 3.81 | 2.707770e-01 | 0.298628 |
| ENSG00000088970.14 | 1.17 | 11.61 | 1.24 | 3.240567e-01 | 0.355358 |
| ENSG00000080839.10 | -0.55 | 12.13 | 535.56 | 3.700244e-01 | 0.403473 |
| ENSG00000088854.12 | 0.78 | 11.48 | 1947.80 | 3.932835e-01 | 0.421687 |
| ENSG00000124198.8 | 0.78 | 11.48 | 1947.80 | 3.932835e-01 | 0.421687 |
| ENSG00000130699.15 | 0.78 | 11.48 | 1947.80 | 3.932835e-01 | 0.421687 |
| ENSG00000078747.11 | -0.12 | 17.16 | 0.68 | 4.517540e-01 | 0.481705 |
| ENSG00000087495.15 | 0.78 | 11.48 | 0.65 | 4.636703e-01 | 0.491694 |
| ENSG00000149636.14 | -0.91 | 11.00 | 0.51 | 5.120851e-01 | 0.540068 |
| ENSG00000226995.6 | -0.64 | 11.18 | 0.85 | 5.714025e-01 | 0.599352 |
| ENSG00000182621.15 | 0.07 | 14.86 | 1.43 | 7.177802e-01 | 0.748819 |
| ENSG00000078699.20 | -0.15 | 12.67 | 0.40 | 7.524355e-01 | 0.780753 |
| ENSG00000062598.16 | -0.13 | 11.26 | 44.33 | 8.975368e-01 | 0.897537 |
| ENSG00000101463.5 | -0.13 | 11.26 | 44.33 | 8.975368e-01 | 0.897537 |
| ENSG00000125885.12 | -0.13 | 11.26 | 44.33 | 8.975368e-01 | 0.897537 |
| ENSG00000132670.19 | -0.13 | 11.26 | 44.33 | 8.975368e-01 | 0.897537 |
| ENSG00000154930.13 | -0.13 | 11.26 | 44.33 | 8.975368e-01 | 0.897537 |
| ENSG00000227195.7 | -0.13 | 11.26 | 44.33 | 8.975368e-01 | 0.897537 |
| ENSG00000277938.1 | -0.13 | 11.26 | 44.33 | 8.975368e-01 | 0.897537 |
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 p-value thresholds defined are shaded as 'Up-' or 'Down-' regulated.
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). This table has not been filtered for genes that satisfy statistical or magnitudinal thresholds
| Log2MeanExon | Log2FC | pvalue | padj | |
|---|---|---|---|---|
| gene_id:trancript_id | ||||
| ENSG00000182621.15:ENST00000626161.1 | 0.864615 | 1.163817e+01 | 0.000133 | 0.007045 |
| ENSG00000182621.15:ENST00000626114.1 | 2.119933 | -1.786014e+00 | 0.000652 | 0.017265 |
| ENSG00000196090.11:ENST00000373198.7 | 1.351070 | -1.299798e+00 | 0.001777 | 0.031402 |
| ENSG00000172264.15:ENST00000402914.4 | 3.388680 | -9.686638e-01 | 0.005670 | 0.075124 |
| ENSG00000175170.13:ENST00000584356.1 | 1.310923 | -5.537456e-01 | 0.010020 | 0.106216 |
| ENSG00000182621.15:ENST00000338037.9 | 3.031855 | -6.339971e-01 | 0.024995 | 0.220793 |
| ENSG00000196090.11:ENST00000617474.1 | 1.740537 | 1.379207e+01 | 0.039040 | 0.263659 |
| ENSG00000196090.11:ENST00000373201.4 | 1.672484 | 1.372496e+01 | 0.045681 | 0.263659 |
| ENSG00000196090.11:ENST00000373190.4 | 1.672484 | 1.372496e+01 | 0.045681 | 0.263659 |
| ENSG00000182621.15:ENST00000378637.5 | 1.790900 | 1.365995e+00 | 0.049747 | 0.263659 |
| ENSG00000025293.14:ENST00000374000.7 | 0.736175 | 1.071824e+01 | 0.103373 | 0.498071 |
| ENSG00000182621.15:ENST00000629992.1 | 0.911328 | 1.535917e+00 | 0.113531 | 0.501426 |
| ENSG00000196090.11:ENST00000618610.1 | 0.911328 | -4.518046e-01 | 0.133416 | 0.543927 |
| ENSG00000025293.14:ENST00000374012.6 | 0.787161 | -5.005226e-01 | 0.151945 | 0.546403 |
| ENSG00000124214.18:ENST00000371856.5 | 1.667107 | 2.521320e-01 | 0.154642 | 0.546403 |
| ENSG00000172264.15:ENST00000490428.4 | 3.014501 | 4.687502e-01 | 0.210065 | 0.653209 |
| ENSG00000025293.14:ENST00000461122.4 | 0.275651 | 1.025882e+01 | 0.219600 | 0.653209 |
| ENSG00000172264.15:ENST00000494602.4 | 2.829944 | 4.845179e-01 | 0.229344 | 0.653209 |
| ENSG00000182621.15:ENST00000378641.6 | 1.511531 | 9.509549e-01 | 0.234169 | 0.653209 |
| ENSG00000124214.18:ENST00000340954.10 | 0.627986 | -1.132337e+01 | 0.292516 | 0.738255 |
| ENSG00000124214.18:ENST00000371828.6 | 0.627986 | -1.132340e+01 | 0.292516 | 0.738255 |
| ENSG00000025293.14:ENST00000339089.9 | 1.124916 | -4.108992e-02 | 0.318009 | 0.766112 |
| ENSG00000196090.11:ENST00000612229.3 | 0.277001 | 1.233267e+01 | 0.388490 | 0.874231 |
| ENSG00000196090.11:ENST00000373193.6 | 1.481473 | 2.851627e-01 | 0.395878 | 0.874231 |
| ENSG00000124214.18:ENST00000437404.2 | 0.884027 | -1.090062e-02 | 0.486360 | 0.941801 |
| ENSG00000172264.15:ENST00000477147.4 | 2.734494 | 2.828842e-01 | 0.499391 | 0.941801 |
| ENSG00000089123.14:ENST00000480436.4 | 0.627986 | 5.312093e-01 | 0.512854 | 0.941801 |
| ENSG00000131061.12:ENST00000483118.4 | 0.627986 | -6.563246e-06 | 0.550865 | 0.941801 |
| ENSG00000131061.12:ENST00000497876.4 | 0.627986 | -6.563246e-06 | 0.550865 | 0.941801 |
| ENSG00000131061.12:ENST00000375200.4 | 0.627986 | -6.563246e-06 | 0.550865 | 0.941801 |
| ENSG00000131061.12:ENST00000342427.5 | 0.627986 | 1.968956e-05 | 0.550865 | 0.941801 |
| ENSG00000175170.13:ENST00000582267.4 | 0.595172 | 1.129626e+01 | 0.633647 | 0.980614 |
| ENSG00000175170.13:ENST00000478164.1 | 0.595172 | 1.129626e+01 | 0.633647 | 0.980614 |
| ENSG00000175170.13:ENST00000376403.4 | 0.595172 | 1.129619e+01 | 0.633647 | 0.980614 |
| ENSG00000234684.5:ENST00000446423.1 | 2.189020 | -2.194078e-05 | 0.711459 | 0.980614 |
| ENSG00000234684.5:ENST00000609285.4 | 2.189020 | 1.097051e-05 | 0.711459 | 0.980614 |
| ENSG00000234684.5:ENST00000609470.4 | 2.189020 | 1.097052e-05 | 0.711459 | 0.980614 |
| ENSG00000182621.15:ENST00000625874.1 | 1.956576 | -4.904556e-02 | 0.711974 | 0.980614 |
| ENSG00000182621.15:ENST00000630495.1 | 1.751147 | 3.659921e-01 | 0.722990 | 0.980614 |
| ENSG00000196090.11:ENST00000356100.5 | 1.888161 | 7.705886e-01 | 0.740086 | 0.980614 |
| ENSG00000089123.14:ENST00000465381.4 | 1.364952 | -2.057492e-01 | 0.800547 | 1.000000 |
| ENSG00000089123.14:ENST00000337743.7 | 1.364952 | -2.057200e-01 | 0.800547 | 1.000000 |
| ENSG00000078747.11:ENST00000486883.4 | 5.391616 | -2.985110e-02 | 0.848443 | 1.000000 |
| ENSG00000078747.11:ENST00000262650.9 | 5.449735 | 2.337941e-02 | 0.877814 | 1.000000 |
| ENSG00000175170.13:ENST00000584071.1 | 0.275651 | 1.097435e+01 | 0.931487 | 1.000000 |
| MSTRG.82:MSTRG.82.3 | 6.587912 | 7.249677e-03 | 0.945340 | 1.000000 |
| MSTRG.82:ENST00000372291.3 | 6.595617 | -3.611366e-03 | 0.972683 | 1.000000 |
| MSTRG.82:ENST00000290231.9 | 6.595617 | -3.611366e-03 | 0.972683 | 1.000000 |
| ENSG00000172264.15:ENST00000217246.7 | 4.384766 | -9.318355e-03 | 0.973355 | 1.000000 |
| ENSG00000078747.11:ENST00000535650.4 | 5.407176 | 3.058134e-03 | 0.984268 | 1.000000 |
| ENSG00000078747.11:ENST00000374864.7 | 5.439794 | 2.319498e-03 | 0.987838 | 1.000000 |
| ENSG00000088812.16:ENST00000262919.8 | 3.199529 | 1.384537e-11 | 1.000000 | 1.000000 |
| ENSG00000088812.16:ENST00000446916.2 | 3.199529 | -1.384537e-11 | 1.000000 | 1.000000 |
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 p-value thresholds defined are shaded as 'Up-' or 'Down-' regulated.
Table showing gene and transcript identifiers and their FDR corrected 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 | ENST00000630495.1 | 0.007043 | 1.000000 | PLCB1 |
| ENSG00000182621.15 | ENST00000626114.1 | 0.007043 | 0.015636 | PLCB1 |
| ENSG00000182621.15 | ENST00000629992.1 | 0.007043 | 1.000000 | PLCB1 |
| ENSG00000182621.15 | ENST00000378641.6 | 0.007043 | 1.000000 | PLCB1 |
| ENSG00000182621.15 | ENST00000626161.1 | 0.007043 | 0.003190 | PLCB1 |
| ENSG00000182621.15 | ENST00000625874.1 | 0.007043 | 1.000000 | PLCB1 |
| ENSG00000182621.15 | ENST00000378637.5 | 0.007043 | 0.994940 | PLCB1 |
| ENSG00000182621.15 | ENST00000338037.9 | 0.007043 | 0.599889 | PLCB1 |
| ENSG00000196090.11 | ENST00000618610.1 | 0.046929 | 1.000000 | PTPRT |
| ENSG00000196090.11 | ENST00000612229.3 | 0.046929 | 1.000000 | PTPRT |
| ENSG00000196090.11 | ENST00000373198.7 | 0.046929 | 0.042659 | PTPRT |
| ENSG00000196090.11 | ENST00000356100.5 | 0.046929 | 1.000000 | PTPRT |
| ENSG00000196090.11 | ENST00000373190.4 | 0.046929 | 1.000000 | PTPRT |
| ENSG00000196090.11 | ENST00000373201.4 | 0.046929 | 1.000000 | PTPRT |
| ENSG00000196090.11 | ENST00000617474.1 | 0.046929 | 0.936949 | PTPRT |
| ENSG00000196090.11 | ENST00000373193.6 | 0.046929 | 1.000000 | PTPRT |
| ENSG00000172264.15 | ENST00000477147.4 | 0.098996 | 1.000000 | MACROD2 |
| ENSG00000172264.15 | ENST00000402914.4 | 0.098996 | 0.068037 | MACROD2 |
| ENSG00000172264.15 | ENST00000494602.4 | 0.098996 | 1.000000 | MACROD2 |
| ENSG00000172264.15 | ENST00000490428.4 | 0.098996 | 1.000000 | MACROD2 |
| ENSG00000172264.15 | ENST00000217246.7 | 0.098996 | 1.000000 | MACROD2 |
| ENSG00000175170.13 | ENST00000584071.1 | 0.130046 | NaN | FAM182B |
| ENSG00000175170.13 | ENST00000376403.4 | 0.130046 | NaN | FAM182B |
| ENSG00000175170.13 | ENST00000582267.4 | 0.130046 | NaN | FAM182B |
| ENSG00000175170.13 | ENST00000478164.1 | 0.130046 | NaN | FAM182B |
| ENSG00000175170.13 | ENST00000584356.1 | 0.130046 | NaN | FAM182B |
| ENSG00000025293.14 | ENST00000461122.4 | 0.890763 | NaN | PHF20 |
| ENSG00000025293.14 | ENST00000339089.9 | 0.890763 | NaN | PHF20 |
| ENSG00000025293.14 | ENST00000374012.6 | 0.890763 | NaN | PHF20 |
| ENSG00000025293.14 | ENST00000374000.7 | 0.890763 | NaN | PHF20 |
| ENSG00000124214.18 | ENST00000437404.2 | 1.000000 | NaN | STAU1 |
| ENSG00000131061.12 | ENST00000483118.4 | 1.000000 | NaN | ZNF341 |
| ENSG00000089123.14 | ENST00000480436.4 | 1.000000 | NaN | TASP1 |
| ENSG00000124214.18 | ENST00000371856.5 | 1.000000 | NaN | STAU1 |
| ENSG00000088812.16 | ENST00000446916.2 | 1.000000 | NaN | ATRN |
| ENSG00000089123.14 | ENST00000337743.7 | 1.000000 | NaN | TASP1 |
| ENSG00000124214.18 | ENST00000371828.6 | 1.000000 | NaN | STAU1 |
| ENSG00000124214.18 | ENST00000340954.10 | 1.000000 | NaN | STAU1 |
| ENSG00000131061.12 | ENST00000497876.4 | 1.000000 | NaN | ZNF341 |
| ENSG00000089123.14 | ENST00000465381.4 | 1.000000 | NaN | TASP1 |
| MSTRG.82 | ENST00000290231.9 | 1.000000 | NaN | NCOA5 |
| ENSG00000131061.12 | ENST00000375200.4 | 1.000000 | NaN | ZNF341 |
| ENSG00000234684.5 | ENST00000609470.4 | 1.000000 | NaN | SDCBP2-AS1 |
| ENSG00000234684.5 | ENST00000446423.1 | 1.000000 | NaN | SDCBP2-AS1 |
| ENSG00000234684.5 | ENST00000609285.4 | 1.000000 | NaN | SDCBP2-AS1 |
| ENSG00000078747.11 | ENST00000486883.4 | 1.000000 | NaN | ITCH |
| ENSG00000078747.11 | ENST00000535650.4 | 1.000000 | NaN | ITCH |
| ENSG00000078747.11 | ENST00000374864.7 | 1.000000 | NaN | ITCH |
| ENSG00000078747.11 | ENST00000262650.9 | 1.000000 | NaN | ITCH |
| MSTRG.82 | MSTRG.82.3 | 1.000000 | NaN | MSTRG.82 |
| MSTRG.82 | ENST00000372291.3 | 1.000000 | NaN | NCOA5 |
| ENSG00000088812.16 | ENST00000262919.8 | 1.000000 | NaN | ATRN |
| ENSG00000131061.12 | ENST00000342427.5 | 1.000000 | NaN | ZNF341 |
The table below highlights versions of key software used within the analysis.
| 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 |
The table below highlights values of the main parameters used in this analysis.
| 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 |
| transcriptome-source | wf-transcriptomes/data/reference-guided |
| transcriptomeSource | wf-transcriptomes/data/reference-guided |
This report was produced using the
epi2me-labs/wf-transcriptomes. The
workflow can be run using nextflow epi2me-labs/wf-transcriptomes --help
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