Mitch Report
Antony Kaspi & Mark Ziemann
date generated: 2025-05-15
Background
Mitch performs unidimensional and multidimensional gene set enrichment analysis. The concept behind this dates to work by Cox and Mann (https://doi.org/10.1186/1471-2105-13-S16-S12). This implementation is suited to R based workflows of multi-omics datasets. This software was developed by Antony Kaspi and Mark Ziemann. Learn more about Mitch at the website: https://github.com/markziemann/Mitch
Input profiles
Here is the first few lines of the input profile.
| score | |
|---|---|
| Q5FLS4 | -3.603801 |
| Q5FMB3 | 3.974694 |
| P02769 | 3.659556 |
| Q5FMB2 | 3.380907 |
| Q5FIJ4 | -3.389340 |
| Q5FHZ6 | 2.823909 |
Here are some metrics about the input data profile:
| Profile metrics | |
|---|---|
| num_genesets | 427 |
| num_genes_in_profile | 844 |
| duplicated_genes_present | 0 |
| num_profile_genes_in_sets | 542 |
| num_profile_genes_not_in_sets | 302 |
Here is a plot of the input profiles. Note the dynamic ranges.
Here is the contour plot of the profile including all detected genes.
Input genesets
Here are some metrics about the gene sets used:
GMT file of genesets:| Gene sets metrics | |
|---|---|
| num_genesets | 427 |
| num_genesets_excluded | 413 |
| num_genesets_included | 14 |
Differential pathway expression
Interactive enrichment scatterplot
Significance is calculated by -log10(p-value). All points shown are FDR<0.05.
Significance is calculated by -log10(p-value). Top N sets shown irrespective of FDR.
Results table
Top N= 50 gene sets| set | setSize | pANOVA | s.dist | p.adjustANOVA |
|---|---|---|---|---|
| translation | 58 | 7.69e-10 | -0.479 | 5.77e-08 |
| ‘de novo’ UMP biosynthetic process | 6 | 1.41e-03 | 0.754 | 5.28e-02 |
| SOS response | 8 | 1.56e-02 | -0.496 | 3.10e-01 |
| ribosomal small subunit assembly | 3 | 2.20e-02 | -0.765 | 3.10e-01 |
| division septum assembly | 5 | 2.42e-02 | -0.584 | 3.10e-01 |
| protein refolding | 3 | 2.48e-02 | 0.750 | 3.10e-01 |
| DNA topological change | 5 | 4.55e-02 | -0.518 | 3.71e-01 |
| ribosome disassembly | 3 | 4.94e-02 | -0.656 | 3.71e-01 |
| lipoteichoic acid biosynthetic process | 4 | 5.52e-02 | 0.555 | 3.71e-01 |
| DNA-templated DNA replication | 8 | 5.67e-02 | -0.391 | 3.71e-01 |
| chromosome segregation | 8 | 6.13e-02 | -0.384 | 3.71e-01 |
| amino acid metabolic process | 5 | 6.53e-02 | 0.477 | 3.71e-01 |
| acetate metabolic process | 3 | 6.93e-02 | -0.607 | 3.71e-01 |
| acetyl-CoA biosynthetic process | 3 | 6.93e-02 | -0.607 | 3.71e-01 |
| nucleotide-excision repair | 3 | 9.23e-02 | -0.562 | 4.28e-01 |
| proteolysis | 33 | 9.42e-02 | 0.172 | 4.28e-01 |
| cell division | 18 | 9.69e-02 | -0.228 | 4.28e-01 |
| intermediate filament organization | 5 | 1.03e-01 | 0.422 | 4.30e-01 |
| threonine biosynthetic process | 6 | 1.15e-01 | -0.373 | 4.54e-01 |
| FtsZ-dependent cytokinesis | 4 | 1.25e-01 | -0.444 | 4.63e-01 |
| protein transport | 7 | 1.30e-01 | -0.332 | 4.63e-01 |
| peptide transport | 10 | 1.37e-01 | -0.273 | 4.67e-01 |
| rRNA processing | 5 | 1.54e-01 | -0.370 | 4.90e-01 |
| epithelial cell differentiation | 3 | 1.57e-01 | 0.473 | 4.90e-01 |
| cellular response to heat | 3 | 1.66e-01 | 0.463 | 4.97e-01 |
| tRNA threonylcarbamoyladenosine modification | 3 | 1.78e-01 | 0.450 | 5.14e-01 |
| glutamine metabolic process | 5 | 2.19e-01 | 0.319 | 6.00e-01 |
| purine nucleotide biosynthetic process | 3 | 2.28e-01 | 0.403 | 6.00e-01 |
| negative regulation of DNA-templated transcription | 8 | 2.32e-01 | -0.245 | 6.00e-01 |
| amino acid transport | 6 | 2.65e-01 | -0.264 | 6.31e-01 |
| methylation | 9 | 2.66e-01 | 0.216 | 6.31e-01 |
| peptidoglycan biosynthetic process | 18 | 2.75e-01 | 0.150 | 6.31e-01 |
| carbohydrate metabolic process | 17 | 2.78e-01 | 0.154 | 6.31e-01 |
| phospholipid biosynthetic process | 4 | 2.91e-01 | -0.306 | 6.43e-01 |
| proteolysis involved in protein catabolic process | 3 | 3.27e-01 | 0.327 | 7.02e-01 |
| L-arginine biosynthetic process | 4 | 3.40e-01 | 0.276 | 7.06e-01 |
| gluconeogenesis | 6 | 3.63e-01 | 0.216 | 7.06e-01 |
| peptide cross-linking | 3 | 3.70e-01 | 0.300 | 7.06e-01 |
| DNA repair | 12 | 3.83e-01 | -0.147 | 7.06e-01 |
| regulation of DNA-templated transcription elongation | 3 | 3.95e-01 | 0.284 | 7.06e-01 |
| epidermis development | 3 | 3.97e-01 | 0.283 | 7.06e-01 |
| DNA-templated transcription termination | 4 | 3.97e-01 | -0.245 | 7.06e-01 |
| tRNA methylation | 3 | 4.17e-01 | 0.271 | 7.06e-01 |
| tRNA wobble uridine modification | 3 | 4.17e-01 | 0.271 | 7.06e-01 |
| purine ribonucleoside salvage | 3 | 4.33e-01 | 0.262 | 7.06e-01 |
| biosynthetic process | 4 | 4.33e-01 | 0.227 | 7.06e-01 |
| methionine biosynthetic process | 3 | 4.47e-01 | -0.254 | 7.14e-01 |
| transmembrane transport | 13 | 4.73e-01 | 0.116 | 7.38e-01 |
| DNA recombination | 13 | 4.87e-01 | -0.112 | 7.44e-01 |
| carbohydrate catabolic process | 7 | 5.09e-01 | -0.145 | 7.44e-01 |
Results (complete table)
Click HERE to show results for all gene sets
| set | setSize | pANOVA | s.dist | p.adjustANOVA |
|---|---|---|---|---|
| translation | 58 | 7.69e-10 | -0.47900 | 5.77e-08 |
| ‘de novo’ UMP biosynthetic process | 6 | 1.41e-03 | 0.75400 | 5.28e-02 |
| SOS response | 8 | 1.56e-02 | -0.49600 | 3.10e-01 |
| ribosomal small subunit assembly | 3 | 2.20e-02 | -0.76500 | 3.10e-01 |
| division septum assembly | 5 | 2.42e-02 | -0.58400 | 3.10e-01 |
| protein refolding | 3 | 2.48e-02 | 0.75000 | 3.10e-01 |
| DNA topological change | 5 | 4.55e-02 | -0.51800 | 3.71e-01 |
| ribosome disassembly | 3 | 4.94e-02 | -0.65600 | 3.71e-01 |
| lipoteichoic acid biosynthetic process | 4 | 5.52e-02 | 0.55500 | 3.71e-01 |
| DNA-templated DNA replication | 8 | 5.67e-02 | -0.39100 | 3.71e-01 |
| chromosome segregation | 8 | 6.13e-02 | -0.38400 | 3.71e-01 |
| amino acid metabolic process | 5 | 6.53e-02 | 0.47700 | 3.71e-01 |
| acetate metabolic process | 3 | 6.93e-02 | -0.60700 | 3.71e-01 |
| acetyl-CoA biosynthetic process | 3 | 6.93e-02 | -0.60700 | 3.71e-01 |
| nucleotide-excision repair | 3 | 9.23e-02 | -0.56200 | 4.28e-01 |
| proteolysis | 33 | 9.42e-02 | 0.17200 | 4.28e-01 |
| cell division | 18 | 9.69e-02 | -0.22800 | 4.28e-01 |
| intermediate filament organization | 5 | 1.03e-01 | 0.42200 | 4.30e-01 |
| threonine biosynthetic process | 6 | 1.15e-01 | -0.37300 | 4.54e-01 |
| FtsZ-dependent cytokinesis | 4 | 1.25e-01 | -0.44400 | 4.63e-01 |
| protein transport | 7 | 1.30e-01 | -0.33200 | 4.63e-01 |
| peptide transport | 10 | 1.37e-01 | -0.27300 | 4.67e-01 |
| rRNA processing | 5 | 1.54e-01 | -0.37000 | 4.90e-01 |
| epithelial cell differentiation | 3 | 1.57e-01 | 0.47300 | 4.90e-01 |
| cellular response to heat | 3 | 1.66e-01 | 0.46300 | 4.97e-01 |
| tRNA threonylcarbamoyladenosine modification | 3 | 1.78e-01 | 0.45000 | 5.14e-01 |
| glutamine metabolic process | 5 | 2.19e-01 | 0.31900 | 6.00e-01 |
| purine nucleotide biosynthetic process | 3 | 2.28e-01 | 0.40300 | 6.00e-01 |
| negative regulation of DNA-templated transcription | 8 | 2.32e-01 | -0.24500 | 6.00e-01 |
| amino acid transport | 6 | 2.65e-01 | -0.26400 | 6.31e-01 |
| methylation | 9 | 2.66e-01 | 0.21600 | 6.31e-01 |
| peptidoglycan biosynthetic process | 18 | 2.75e-01 | 0.15000 | 6.31e-01 |
| carbohydrate metabolic process | 17 | 2.78e-01 | 0.15400 | 6.31e-01 |
| phospholipid biosynthetic process | 4 | 2.91e-01 | -0.30600 | 6.43e-01 |
| proteolysis involved in protein catabolic process | 3 | 3.27e-01 | 0.32700 | 7.02e-01 |
| L-arginine biosynthetic process | 4 | 3.40e-01 | 0.27600 | 7.06e-01 |
| gluconeogenesis | 6 | 3.63e-01 | 0.21600 | 7.06e-01 |
| peptide cross-linking | 3 | 3.70e-01 | 0.30000 | 7.06e-01 |
| DNA repair | 12 | 3.83e-01 | -0.14700 | 7.06e-01 |
| regulation of DNA-templated transcription elongation | 3 | 3.95e-01 | 0.28400 | 7.06e-01 |
| epidermis development | 3 | 3.97e-01 | 0.28300 | 7.06e-01 |
| DNA-templated transcription termination | 4 | 3.97e-01 | -0.24500 | 7.06e-01 |
| tRNA methylation | 3 | 4.17e-01 | 0.27100 | 7.06e-01 |
| tRNA wobble uridine modification | 3 | 4.17e-01 | 0.27100 | 7.06e-01 |
| purine ribonucleoside salvage | 3 | 4.33e-01 | 0.26200 | 7.06e-01 |
| biosynthetic process | 4 | 4.33e-01 | 0.22700 | 7.06e-01 |
| methionine biosynthetic process | 3 | 4.47e-01 | -0.25400 | 7.14e-01 |
| transmembrane transport | 13 | 4.73e-01 | 0.11600 | 7.38e-01 |
| DNA recombination | 13 | 4.87e-01 | -0.11200 | 7.44e-01 |
| carbohydrate catabolic process | 7 | 5.09e-01 | -0.14500 | 7.44e-01 |
| homocysteine catabolic process | 4 | 5.16e-01 | 0.18800 | 7.44e-01 |
| response to toxic substance | 4 | 5.16e-01 | 0.18800 | 7.44e-01 |
| maltodextrin transmembrane transport | 3 | 5.39e-01 | -0.20500 | 7.56e-01 |
| recombinational repair | 3 | 5.54e-01 | -0.19800 | 7.56e-01 |
| acetyl-CoA metabolic process | 3 | 5.61e-01 | 0.19500 | 7.56e-01 |
| glycerol catabolic process | 4 | 5.64e-01 | 0.16700 | 7.56e-01 |
| regulation of DNA-templated transcription | 10 | 6.02e-01 | -0.09580 | 7.66e-01 |
| diaminopimelate biosynthetic process | 5 | 6.05e-01 | 0.13400 | 7.66e-01 |
| lysine biosynthetic process via diaminopimelate | 5 | 6.05e-01 | 0.13400 | 7.66e-01 |
| phosphoenolpyruvate-dependent sugar phosphotransferase system | 10 | 6.17e-01 | -0.09210 | 7.66e-01 |
| DNA replication | 10 | 6.23e-01 | -0.09040 | 7.66e-01 |
| cell wall macromolecule catabolic process | 3 | 6.99e-01 | -0.12900 | 8.32e-01 |
| peptidoglycan catabolic process | 3 | 6.99e-01 | -0.12900 | 8.32e-01 |
| glycolytic process | 9 | 7.19e-01 | 0.06960 | 8.43e-01 |
| mismatch repair | 4 | 7.41e-01 | 0.09580 | 8.55e-01 |
| enzyme-directed rRNA pseudouridine synthesis | 4 | 7.71e-01 | -0.08420 | 8.62e-01 |
| tetrahydrofolate interconversion | 4 | 7.71e-01 | 0.08420 | 8.62e-01 |
| rRNA base methylation | 3 | 7.82e-01 | -0.09270 | 8.62e-01 |
| thiamine biosynthetic process | 3 | 8.12e-01 | 0.07970 | 8.82e-01 |
| protein folding | 4 | 8.26e-01 | -0.06370 | 8.85e-01 |
| double-strand break repair | 4 | 8.74e-01 | 0.04610 | 9.14e-01 |
| cell morphogenesis | 3 | 8.78e-01 | -0.05150 | 9.14e-01 |
| guanosine tetraphosphate biosynthetic process | 3 | 9.24e-01 | -0.03170 | 9.50e-01 |
| cell wall organization | 21 | 9.57e-01 | -0.00683 | 9.70e-01 |
| regulation of cell shape | 23 | 9.75e-01 | 0.00381 | 9.75e-01 |
Detailed Gene set reports
translation
| set | translation |
| setSize | 58 |
| pANOVA | 7.69e-10 |
| s.dist | -0.479 |
| p.adjustANOVA | 5.77e-08 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q5FJK5 | -406.0 |
| Q5FJN2 | -402.0 |
| Q5FM66 | -392.0 |
| Q5FM77 | -381.0 |
| Q5FMB6 | -378.0 |
| Q5FM79 | -376.0 |
| Q5FM74 | -375.0 |
| Q5FM12 | -374.0 |
| Q5FN09 | -371.0 |
| Q5FJM3 | -370.0 |
| Q5FM82 | -368.0 |
| Q5FM91 | -360.0 |
| Q5FM73 | -358.0 |
| Q5FM89 | -355.0 |
| Q5FM86 | -351.5 |
| Q5FM90 | -339.0 |
| Q5FM94 | -338.0 |
| Q5FIW9 | -337.0 |
| Q5FKF5 | -335.5 |
| Q5FJI3 | -333.0 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q5FJK5 | -406.0 |
| Q5FJN2 | -402.0 |
| Q5FM66 | -392.0 |
| Q5FM77 | -381.0 |
| Q5FMB6 | -378.0 |
| Q5FM79 | -376.0 |
| Q5FM74 | -375.0 |
| Q5FM12 | -374.0 |
| Q5FN09 | -371.0 |
| Q5FJM3 | -370.0 |
| Q5FM82 | -368.0 |
| Q5FM91 | -360.0 |
| Q5FM73 | -358.0 |
| Q5FM89 | -355.0 |
| Q5FM86 | -351.5 |
| Q5FM90 | -339.0 |
| Q5FM94 | -338.0 |
| Q5FIW9 | -337.0 |
| Q5FKF5 | -335.5 |
| Q5FJI3 | -333.0 |
| Q5FM22 | -323.0 |
| Q5FJT3 | -318.0 |
| Q5FJK8 | -313.0 |
| Q5FM80 | -310.0 |
| Q5FM78 | -307.0 |
| Q5FM93 | -305.0 |
| Q5FM68 | -297.5 |
| Q5FLL2 | -296.0 |
| Q5FM59 | -294.0 |
| Q5FM84 | -287.0 |
| Q5FKT1 | -284.0 |
| Q5FM81 | -279.0 |
| Q5FM64 | -271.0 |
| Q5FM58 | -270.0 |
| Q5FKX2 | -265.0 |
| Q5FKH0 | -238.5 |
| Q5FL79 | -155.0 |
| Q5FM13 | -152.0 |
| Q5FM67 | -148.0 |
| Q5FM85 | -140.0 |
| Q5FIZ7 | -113.0 |
| Q5FKT2 | -105.0 |
| Q5FJG0 | -53.0 |
| Q5FN07 | -47.0 |
| Q5FM23 | -18.0 |
| Q5FM88 | 2.0 |
| Q5FM75 | 46.0 |
| Q5FMA5 | 50.0 |
| Q5FJF9 | 99.0 |
| Q5FKE5 | 103.5 |
| Q5FLL1 | 136.0 |
| Q5FLL0 | 169.0 |
| Q5FM72 | 230.0 |
| Q5FN05 | 267.5 |
| Q5FJM6 | 281.0 |
| Q5FM83 | 326.0 |
| Q5FMA9 | 337.0 |
| Q5FKI9 | 369.0 |
‘de novo’ UMP biosynthetic process
| set | ‘de novo’ UMP biosynthetic process |
| setSize | 6 |
| pANOVA | 0.00141 |
| s.dist | 0.754 |
| p.adjustANOVA | 0.0528 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q5FJC0 | 391 |
| Q5FJB2 | 385 |
| Q5FJB8 | 379 |
| Q5FJB7 | 366 |
| Q5FJB9 | 322 |
| Q5FJY6 | 98 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q5FJC0 | 391 |
| Q5FJB2 | 385 |
| Q5FJB8 | 379 |
| Q5FJB7 | 366 |
| Q5FJB9 | 322 |
| Q5FJY6 | 98 |
SOS response
| set | SOS response |
| setSize | 8 |
| pANOVA | 0.0156 |
| s.dist | -0.496 |
| p.adjustANOVA | 0.31 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q5FL60 | -414.0 |
| Q5FL82 | -405.0 |
| Q5FL61 | -382.0 |
| Q5FLW9 | -364.0 |
| Q5FKC4 | -176.0 |
| Q5FN12 | -69.0 |
| Q5FJH0 | 103.5 |
| Q5FKH6 | 109.0 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q5FL60 | -414.0 |
| Q5FL82 | -405.0 |
| Q5FL61 | -382.0 |
| Q5FLW9 | -364.0 |
| Q5FKC4 | -176.0 |
| Q5FN12 | -69.0 |
| Q5FJH0 | 103.5 |
| Q5FKH6 | 109.0 |
ribosomal small subunit assembly
| set | ribosomal small subunit assembly |
| setSize | 3 |
| pANOVA | 0.022 |
| s.dist | -0.765 |
| p.adjustANOVA | 0.31 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q5FJN2 | -402.0 |
| Q5FM86 | -351.5 |
| Q5FJT7 | -188.5 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q5FJN2 | -402.0 |
| Q5FM86 | -351.5 |
| Q5FJT7 | -188.5 |
division septum assembly
| set | division septum assembly |
| setSize | 5 |
| pANOVA | 0.0242 |
| s.dist | -0.584 |
| p.adjustANOVA | 0.31 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q5FKR5 | -351.5 |
| Q5FKX1 | -329.5 |
| Q5FKU8 | -219.0 |
| Q5FKU9 | -168.5 |
| Q5FI44 | -118.0 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q5FKR5 | -351.5 |
| Q5FKX1 | -329.5 |
| Q5FKU8 | -219.0 |
| Q5FKU9 | -168.5 |
| Q5FI44 | -118.0 |
protein refolding
| set | protein refolding |
| setSize | 3 |
| pANOVA | 0.0248 |
| s.dist | 0.75 |
| p.adjustANOVA | 0.31 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q93G07 | 413 |
| Q5FMA2 | 283 |
| Q84BU3 | 272 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q93G07 | 413 |
| Q5FMA2 | 283 |
| Q84BU3 | 272 |
DNA topological change
| set | DNA topological change |
| setSize | 5 |
| pANOVA | 0.0455 |
| s.dist | -0.518 |
| p.adjustANOVA | 0.371 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q5FK08 | -350 |
| Q5FN11 | -314 |
| Q5FK07 | -295 |
| Q5FN10 | -248 |
| Q5FKE2 | 158 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q5FK08 | -350 |
| Q5FN11 | -314 |
| Q5FK07 | -295 |
| Q5FN10 | -248 |
| Q5FKE2 | 158 |
ribosome disassembly
| set | ribosome disassembly |
| setSize | 3 |
| pANOVA | 0.0494 |
| s.dist | -0.656 |
| p.adjustANOVA | 0.371 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q5FM92 | -395.0 |
| Q5FIW7 | -325.0 |
| Q5FMW9 | -85.5 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q5FM92 | -395.0 |
| Q5FIW7 | -325.0 |
| Q5FMW9 | -85.5 |
lipoteichoic acid biosynthetic process
| set | lipoteichoic acid biosynthetic process |
| setSize | 4 |
| pANOVA | 0.0552 |
| s.dist | 0.555 |
| p.adjustANOVA | 0.371 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q5FHV1 | 309.0 |
| Q5FHV3 | 295.5 |
| Q5FHV4 | 216.0 |
| Q5FHV2 | 142.0 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q5FHV1 | 309.0 |
| Q5FHV3 | 295.5 |
| Q5FHV4 | 216.0 |
| Q5FHV2 | 142.0 |
DNA-templated DNA replication
| set | DNA-templated DNA replication |
| setSize | 8 |
| pANOVA | 0.0567 |
| s.dist | -0.391 |
| p.adjustANOVA | 0.371 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q5FLW9 | -364.0 |
| Q5FN11 | -314.0 |
| Q5FN10 | -248.0 |
| Q5FKX4 | -218.0 |
| Q5FIV7 | -145.0 |
| Q5FKS3 | -66.0 |
| Q5FJN1 | 24.0 |
| Q5FM07 | 83.5 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q5FLW9 | -364.0 |
| Q5FN11 | -314.0 |
| Q5FN10 | -248.0 |
| Q5FKX4 | -218.0 |
| Q5FIV7 | -145.0 |
| Q5FKS3 | -66.0 |
| Q5FJN1 | 24.0 |
| Q5FM07 | 83.5 |
chromosome segregation
| set | chromosome segregation |
| setSize | 8 |
| pANOVA | 0.0613 |
| s.dist | -0.384 |
| p.adjustANOVA | 0.371 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q5FK08 | -350 |
| Q5FK07 | -295 |
| Q5FJJ8 | -281 |
| Q5FKE0 | -214 |
| Q5FI46 | -207 |
| Q5FKG3 | -175 |
| Q5FI44 | -118 |
| Q5FJX7 | 416 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q5FK08 | -350 |
| Q5FK07 | -295 |
| Q5FJJ8 | -281 |
| Q5FKE0 | -214 |
| Q5FI46 | -207 |
| Q5FKG3 | -175 |
| Q5FI44 | -118 |
| Q5FJX7 | 416 |
amino acid metabolic process
| set | amino acid metabolic process |
| setSize | 5 |
| pANOVA | 0.0653 |
| s.dist | 0.477 |
| p.adjustANOVA | 0.371 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| G1UB50 | 399 |
| Q5FJB7 | 366 |
| Q5FIH5 | 317 |
| Q5FKQ7 | 144 |
| Q5FKI3 | -187 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| G1UB50 | 399 |
| Q5FJB7 | 366 |
| Q5FIH5 | 317 |
| Q5FKQ7 | 144 |
| Q5FKI3 | -187 |
acetate metabolic process
| set | acetate metabolic process |
| setSize | 3 |
| pANOVA | 0.0693 |
| s.dist | -0.607 |
| p.adjustANOVA | 0.371 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q5FLS4 | -411 |
| Q5FL15 | -361 |
| Q5FI01 | 29 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q5FLS4 | -411 |
| Q5FL15 | -361 |
| Q5FI01 | 29 |
acetyl-CoA biosynthetic process
| set | acetyl-CoA biosynthetic process |
| setSize | 3 |
| pANOVA | 0.0693 |
| s.dist | -0.607 |
| p.adjustANOVA | 0.371 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q5FLS4 | -411 |
| Q5FL15 | -361 |
| Q5FI01 | 29 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q5FLS4 | -411 |
| Q5FL15 | -361 |
| Q5FI01 | 29 |
nucleotide-excision repair
| set | nucleotide-excision repair |
| setSize | 3 |
| pANOVA | 0.0923 |
| s.dist | -0.562 |
| p.adjustANOVA | 0.428 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q5FL60 | -414 |
| Q5FL61 | -382 |
| Q5FKH6 | 109 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q5FL60 | -414 |
| Q5FL61 | -382 |
| Q5FKH6 | 109 |
proteolysis
| set | proteolysis |
| setSize | 33 |
| pANOVA | 0.0942 |
| s.dist | 0.172 |
| p.adjustANOVA | 0.428 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q5FLA7 | 395.0 |
| Q5FJU8 | 392.0 |
| Q5FI23 | 387.0 |
| Q5FHW6 | 349.0 |
| Q5FMP9 | 348.0 |
| Q5FJX6 | 343.0 |
| Q5FME4 | 335.5 |
| Q5FIA0 | 300.0 |
| Q5FIK4 | 288.0 |
| Q5FMI4 | 241.0 |
| Q5FLH4 | 235.0 |
| Q5FKS6 | 227.0 |
| Q5FIL6 | 211.0 |
| Q5FJK0 | 161.5 |
| Q5FME3 | 137.0 |
| Q5FKK6 | 106.5 |
| P00761 | 94.0 |
| Q5FJC6 | 92.0 |
| Q5FMH5 | 88.0 |
| Q5FK68 | 81.0 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q5FLA7 | 395.0 |
| Q5FJU8 | 392.0 |
| Q5FI23 | 387.0 |
| Q5FHW6 | 349.0 |
| Q5FMP9 | 348.0 |
| Q5FJX6 | 343.0 |
| Q5FME4 | 335.5 |
| Q5FIA0 | 300.0 |
| Q5FIK4 | 288.0 |
| Q5FMI4 | 241.0 |
| Q5FLH4 | 235.0 |
| Q5FKS6 | 227.0 |
| Q5FIL6 | 211.0 |
| Q5FJK0 | 161.5 |
| Q5FME3 | 137.0 |
| Q5FKK6 | 106.5 |
| P00761 | 94.0 |
| Q5FJC6 | 92.0 |
| Q5FMH5 | 88.0 |
| Q5FK68 | 81.0 |
| Q5FM39 | -89.0 |
| Q5FI74 | -101.0 |
| Q5FLC2 | -102.0 |
| Q5FMT9 | -104.0 |
| Q5FI35 | -120.0 |
| Q5FMS7 | -133.0 |
| Q5FIQ6 | -138.0 |
| Q5FJM9 | -164.0 |
| Q5FIR5 | -182.5 |
| Q5FL86 | -223.0 |
| Q5FJP7 | -251.0 |
| Q5FMJ2 | -258.0 |
| Q5FMA3 | -401.0 |
cell division
| set | cell division |
| setSize | 18 |
| pANOVA | 0.0969 |
| s.dist | -0.228 |
| p.adjustANOVA | 0.428 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q5FMA3 | -401.0 |
| Q5FKV2 | -264.0 |
| Q5FME5 | -255.0 |
| Q5FL56 | -249.0 |
| Q5FMB5 | -241.0 |
| Q5FKR7 | -240.0 |
| Q5FKE0 | -214.0 |
| Q5FKG3 | -175.0 |
| Q5FL88 | -173.0 |
| Q5FKR6 | -159.0 |
| Q5FKX6 | -131.0 |
| Q5FKU6 | -128.0 |
| Q5FKV3 | -59.5 |
| Q5FJJ9 | -21.0 |
| Q5FI54 | 185.0 |
| Q5FL42 | 294.0 |
| Q5FJX9 | 307.0 |
| Q5FIS8 | 361.0 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q5FMA3 | -401.0 |
| Q5FKV2 | -264.0 |
| Q5FME5 | -255.0 |
| Q5FL56 | -249.0 |
| Q5FMB5 | -241.0 |
| Q5FKR7 | -240.0 |
| Q5FKE0 | -214.0 |
| Q5FKG3 | -175.0 |
| Q5FL88 | -173.0 |
| Q5FKR6 | -159.0 |
| Q5FKX6 | -131.0 |
| Q5FKU6 | -128.0 |
| Q5FKV3 | -59.5 |
| Q5FJJ9 | -21.0 |
| Q5FI54 | 185.0 |
| Q5FL42 | 294.0 |
| Q5FJX9 | 307.0 |
| Q5FIS8 | 361.0 |
intermediate filament organization
| set | intermediate filament organization |
| setSize | 5 |
| pANOVA | 0.103 |
| s.dist | 0.422 |
| p.adjustANOVA | 0.43 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| O77727 | 363.5 |
| P04264 | 180.0 |
| P35527 | 159.0 |
| P35908 | 124.0 |
| P13645 | 97.0 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| O77727 | 363.5 |
| P04264 | 180.0 |
| P35527 | 159.0 |
| P35908 | 124.0 |
| P13645 | 97.0 |
threonine biosynthetic process
| set | threonine biosynthetic process |
| setSize | 6 |
| pANOVA | 0.115 |
| s.dist | -0.373 |
| p.adjustANOVA | 0.454 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q5FJS5 | -400 |
| Q5FJS7 | -391 |
| Q5FJS6 | -354 |
| Q5FJS4 | -236 |
| Q5FKQ6 | 100 |
| Q5FKR3 | 388 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q5FJS5 | -400 |
| Q5FJS7 | -391 |
| Q5FJS6 | -354 |
| Q5FJS4 | -236 |
| Q5FKQ6 | 100 |
| Q5FKR3 | 388 |
FtsZ-dependent cytokinesis
| set | FtsZ-dependent cytokinesis |
| setSize | 4 |
| pANOVA | 0.125 |
| s.dist | -0.444 |
| p.adjustANOVA | 0.463 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q5FKU8 | -219.0 |
| Q5FKV1 | -195.0 |
| Q5FKU9 | -168.5 |
| Q5FKV0 | -134.0 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q5FKU8 | -219.0 |
| Q5FKV1 | -195.0 |
| Q5FKU9 | -168.5 |
| Q5FKV0 | -134.0 |
protein transport
| set | protein transport |
| setSize | 7 |
| pANOVA | 0.13 |
| s.dist | -0.332 |
| p.adjustANOVA | 0.463 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q5FMH8 | -280 |
| Q5FMH6 | -250 |
| Q5FKR7 | -240 |
| Q5FLX1 | -190 |
| Q5FHQ4 | -152 |
| Q5FI74 | -101 |
| Q5FJJ0 | 292 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q5FMH8 | -280 |
| Q5FMH6 | -250 |
| Q5FKR7 | -240 |
| Q5FLX1 | -190 |
| Q5FHQ4 | -152 |
| Q5FI74 | -101 |
| Q5FJJ0 | 292 |
peptide transport
| set | peptide transport |
| setSize | 10 |
| pANOVA | 0.137 |
| s.dist | -0.273 |
| p.adjustANOVA | 0.467 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q5FMH7 | -334.0 |
| Q5FIJ7 | -289.0 |
| Q5FMH8 | -280.0 |
| Q5FMH6 | -250.0 |
| Q5FMI2 | -174.0 |
| Q5FJ99 | -165.5 |
| Q5FMI1 | -81.0 |
| Q5FJJ4 | -4.0 |
| Q5FJI9 | 220.5 |
| Q5FJJ0 | 292.0 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q5FMH7 | -334.0 |
| Q5FIJ7 | -289.0 |
| Q5FMH8 | -280.0 |
| Q5FMH6 | -250.0 |
| Q5FMI2 | -174.0 |
| Q5FJ99 | -165.5 |
| Q5FMI1 | -81.0 |
| Q5FJJ4 | -4.0 |
| Q5FJI9 | 220.5 |
| Q5FJJ0 | 292.0 |
rRNA processing
| set | rRNA processing |
| setSize | 5 |
| pANOVA | 0.154 |
| s.dist | -0.37 |
| p.adjustANOVA | 0.49 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q5FKT4 | -383 |
| Q5FMG4 | -377 |
| Q5FKS0 | -319 |
| Q5FM33 | 108 |
| Q5FJT6 | 233 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q5FKT4 | -383 |
| Q5FMG4 | -377 |
| Q5FKS0 | -319 |
| Q5FM33 | 108 |
| Q5FJT6 | 233 |
epithelial cell differentiation
| set | epithelial cell differentiation |
| setSize | 3 |
| pANOVA | 0.157 |
| s.dist | 0.473 |
| p.adjustANOVA | 0.49 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| O77727 | 363.5 |
| P35527 | 159.0 |
| P13645 | 97.0 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| O77727 | 363.5 |
| P35527 | 159.0 |
| P13645 | 97.0 |
cellular response to heat
| set | cellular response to heat |
| setSize | 3 |
| pANOVA | 0.166 |
| s.dist | 0.463 |
| p.adjustANOVA | 0.497 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q5FLA7 | 395 |
| Q5FHW6 | 349 |
| Q5FM98 | -137 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q5FLA7 | 395 |
| Q5FHW6 | 349 |
| Q5FM98 | -137 |
tRNA threonylcarbamoyladenosine modification
| set | tRNA threonylcarbamoyladenosine modification |
| setSize | 3 |
| pANOVA | 0.178 |
| s.dist | 0.45 |
| p.adjustANOVA | 0.514 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q5FL44 | 358 |
| Q5FLZ3 | 357 |
| Q5FLZ5 | -125 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q5FL44 | 358 |
| Q5FLZ3 | 357 |
| Q5FLZ5 | -125 |
glutamine metabolic process
| set | glutamine metabolic process |
| setSize | 5 |
| pANOVA | 0.219 |
| s.dist | 0.319 |
| p.adjustANOVA | 0.6 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q5FJC0 | 391.0 |
| Q5FJB9 | 322.0 |
| Q5FHX3 | 262.5 |
| Q5FJY6 | 98.0 |
| Q5FHZ2 | -367.0 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q5FJC0 | 391.0 |
| Q5FJB9 | 322.0 |
| Q5FHX3 | 262.5 |
| Q5FJY6 | 98.0 |
| Q5FHZ2 | -367.0 |
purine nucleotide biosynthetic process
| set | purine nucleotide biosynthetic process |
| setSize | 3 |
| pANOVA | 0.228 |
| s.dist | 0.403 |
| p.adjustANOVA | 0.6 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q5FMF5 | 280 |
| Q5FJG5 | 166 |
| Q5FMP2 | 85 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q5FMF5 | 280 |
| Q5FJG5 | 166 |
| Q5FMP2 | 85 |
negative regulation of DNA-templated transcription
| set | negative regulation of DNA-templated transcription |
| setSize | 8 |
| pANOVA | 0.232 |
| s.dist | -0.245 |
| p.adjustANOVA | 0.6 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q5FLA4 | -327.0 |
| Q5FLM6 | -312.0 |
| Q5FLY5 | -216.0 |
| Q5FIW0 | -124.0 |
| Q5FKN3 | -116.5 |
| Q5FMG1 | -61.0 |
| Q5FLF3 | 120.0 |
| Q84BU6 | 276.0 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q5FLA4 | -327.0 |
| Q5FLM6 | -312.0 |
| Q5FLY5 | -216.0 |
| Q5FIW0 | -124.0 |
| Q5FKN3 | -116.5 |
| Q5FMG1 | -61.0 |
| Q5FLF3 | 120.0 |
| Q84BU6 | 276.0 |
amino acid transport
| set | amino acid transport |
| setSize | 6 |
| pANOVA | 0.265 |
| s.dist | -0.264 |
| p.adjustANOVA | 0.631 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q5FMR1 | -389.0 |
| Q5FMN9 | -217.0 |
| Q5FLG3 | -177.0 |
| Q5FLG4 | -90.0 |
| Q5FHX1 | -0.5 |
| Q5FLS7 | 255.5 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q5FMR1 | -389.0 |
| Q5FMN9 | -217.0 |
| Q5FLG3 | -177.0 |
| Q5FLG4 | -90.0 |
| Q5FHX1 | -0.5 |
| Q5FLS7 | 255.5 |
methylation
| set | methylation |
| setSize | 9 |
| pANOVA | 0.266 |
| s.dist | 0.216 |
| p.adjustANOVA | 0.631 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q5FKL6 | 423.0 |
| Q5FIY4 | 328.0 |
| Q5FKI8 | 192.0 |
| Q5FM32 | 141.0 |
| Q5FJG9 | 125.5 |
| Q5FJM0 | 53.0 |
| Q5FL16 | -67.0 |
| Q5FM10 | -158.0 |
| Q5FJU6 | -160.0 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q5FKL6 | 423.0 |
| Q5FIY4 | 328.0 |
| Q5FKI8 | 192.0 |
| Q5FM32 | 141.0 |
| Q5FJG9 | 125.5 |
| Q5FJM0 | 53.0 |
| Q5FL16 | -67.0 |
| Q5FM10 | -158.0 |
| Q5FJU6 | -160.0 |
peptidoglycan biosynthetic process
| set | peptidoglycan biosynthetic process |
| setSize | 18 |
| pANOVA | 0.275 |
| s.dist | 0.15 |
| p.adjustANOVA | 0.631 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q5FMB2 | 421.0 |
| Q5FIS8 | 361.0 |
| Q5FL35 | 352.5 |
| Q5FJX6 | 343.0 |
| Q5FMN6 | 331.0 |
| Q5FL42 | 294.0 |
| Q5FMG0 | 277.0 |
| Q5FI54 | 185.0 |
| Q5FLV8 | 181.0 |
| Q5FKZ2 | 8.0 |
| Q5FIZ6 | 5.0 |
| Q5FKV3 | -59.5 |
| Q5FIQ6 | -138.0 |
| Q5FIR5 | -182.5 |
| Q5FMB5 | -241.0 |
| Q5FME5 | -255.0 |
| Q5FKV2 | -264.0 |
| Q5FHZ2 | -367.0 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q5FMB2 | 421.0 |
| Q5FIS8 | 361.0 |
| Q5FL35 | 352.5 |
| Q5FJX6 | 343.0 |
| Q5FMN6 | 331.0 |
| Q5FL42 | 294.0 |
| Q5FMG0 | 277.0 |
| Q5FI54 | 185.0 |
| Q5FLV8 | 181.0 |
| Q5FKZ2 | 8.0 |
| Q5FIZ6 | 5.0 |
| Q5FKV3 | -59.5 |
| Q5FIQ6 | -138.0 |
| Q5FIR5 | -182.5 |
| Q5FMB5 | -241.0 |
| Q5FME5 | -255.0 |
| Q5FKV2 | -264.0 |
| Q5FHZ2 | -367.0 |
carbohydrate metabolic process
| set | carbohydrate metabolic process |
| setSize | 17 |
| pANOVA | 0.278 |
| s.dist | 0.154 |
| p.adjustANOVA | 0.631 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q5FIH3 | 420.0 |
| Q5FHT1 | 405.0 |
| Q5FL35 | 352.5 |
| Q5FL62 | 327.0 |
| Q5FMN0 | 310.0 |
| Q5FI05 | 220.5 |
| Q5FM28 | 183.0 |
| Q5FLS5 | 129.0 |
| Q5FLE5 | 61.0 |
| Q5FL11 | 16.0 |
| Q5FL70 | -43.0 |
| Q5FKD7 | -64.0 |
| Q5FI03 | -91.0 |
| Q5FMJ1 | -198.0 |
| Q5FI04 | -234.5 |
| Q5FKV2 | -264.0 |
| Q5FIF2 | -321.5 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q5FIH3 | 420.0 |
| Q5FHT1 | 405.0 |
| Q5FL35 | 352.5 |
| Q5FL62 | 327.0 |
| Q5FMN0 | 310.0 |
| Q5FI05 | 220.5 |
| Q5FM28 | 183.0 |
| Q5FLS5 | 129.0 |
| Q5FLE5 | 61.0 |
| Q5FL11 | 16.0 |
| Q5FL70 | -43.0 |
| Q5FKD7 | -64.0 |
| Q5FI03 | -91.0 |
| Q5FMJ1 | -198.0 |
| Q5FI04 | -234.5 |
| Q5FKV2 | -264.0 |
| Q5FIF2 | -321.5 |
phospholipid biosynthetic process
| set | phospholipid biosynthetic process |
| setSize | 4 |
| pANOVA | 0.291 |
| s.dist | -0.306 |
| p.adjustANOVA | 0.643 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q5FJI7 | -288.0 |
| Q5FK09 | -220.5 |
| Q5FL70 | -43.0 |
| Q5FLK9 | 68.0 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q5FJI7 | -288.0 |
| Q5FK09 | -220.5 |
| Q5FL70 | -43.0 |
| Q5FLK9 | 68.0 |
proteolysis involved in protein catabolic process
| set | proteolysis involved in protein catabolic process |
| setSize | 3 |
| pANOVA | 0.327 |
| s.dist | 0.327 |
| p.adjustANOVA | 0.702 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q5FKD8 | 355.0 |
| Q5FKD9 | 239.5 |
| Q5FKR6 | -159.0 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q5FKD8 | 355.0 |
| Q5FKD9 | 239.5 |
| Q5FKR6 | -159.0 |
L-arginine biosynthetic process
| set | L-arginine biosynthetic process |
| setSize | 4 |
| pANOVA | 0.34 |
| s.dist | 0.276 |
| p.adjustANOVA | 0.706 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q5FJC0 | 391 |
| Q5FJB9 | 322 |
| Q5FJY6 | 98 |
| Q5FKD0 | -317 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q5FJC0 | 391 |
| Q5FJB9 | 322 |
| Q5FJY6 | 98 |
| Q5FKD0 | -317 |
gluconeogenesis
| set | gluconeogenesis |
| setSize | 6 |
| pANOVA | 0.363 |
| s.dist | 0.216 |
| p.adjustANOVA | 0.706 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q5FMJ3 | 264.5 |
| Q5FL50 | 227.0 |
| Q5FL49 | 164.5 |
| Q5FLS1 | 65.0 |
| Q5FL04 | -35.0 |
| Q5FJA1 | -99.0 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q5FMJ3 | 264.5 |
| Q5FL50 | 227.0 |
| Q5FL49 | 164.5 |
| Q5FLS1 | 65.0 |
| Q5FL04 | -35.0 |
| Q5FJA1 | -99.0 |
peptide cross-linking
| set | peptide cross-linking |
| setSize | 3 |
| pANOVA | 0.37 |
| s.dist | 0.3 |
| p.adjustANOVA | 0.706 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| P04264 | 180 |
| P35908 | 124 |
| P13645 | 97 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| P04264 | 180 |
| P35908 | 124 |
| P13645 | 97 |
DNA repair
| set | DNA repair |
| setSize | 12 |
| pANOVA | 0.383 |
| s.dist | -0.147 |
| p.adjustANOVA | 0.706 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q5FL82 | -405.0 |
| Q5FN08 | -259.5 |
| Q5FJP8 | -244.0 |
| Q5FJI6 | -220.5 |
| Q5FM04 | -211.0 |
| Q5FKC4 | -176.0 |
| Q5FLX2 | -79.0 |
| Q5FJH0 | 103.5 |
| Q5FLL4 | 110.0 |
| Q5FJL2 | 155.5 |
| Q5FLX3 | 168.0 |
| Q5FJX7 | 416.0 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q5FL82 | -405.0 |
| Q5FN08 | -259.5 |
| Q5FJP8 | -244.0 |
| Q5FJI6 | -220.5 |
| Q5FM04 | -211.0 |
| Q5FKC4 | -176.0 |
| Q5FLX2 | -79.0 |
| Q5FJH0 | 103.5 |
| Q5FLL4 | 110.0 |
| Q5FJL2 | 155.5 |
| Q5FLX3 | 168.0 |
| Q5FJX7 | 416.0 |
regulation of DNA-templated transcription elongation
| set | regulation of DNA-templated transcription elongation |
| setSize | 3 |
| pANOVA | 0.395 |
| s.dist | 0.284 |
| p.adjustANOVA | 0.706 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q5FMH3 | 429 |
| Q5FIY8 | 315 |
| Q5FM24 | -363 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q5FMH3 | 429 |
| Q5FIY8 | 315 |
| Q5FM24 | -363 |
epidermis development
| set | epidermis development |
| setSize | 3 |
| pANOVA | 0.397 |
| s.dist | 0.283 |
| p.adjustANOVA | 0.706 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| P35527 | 159 |
| P35908 | 124 |
| P13645 | 97 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| P35527 | 159 |
| P35908 | 124 |
| P13645 | 97 |
DNA-templated transcription termination
| set | DNA-templated transcription termination |
| setSize | 4 |
| pANOVA | 0.397 |
| s.dist | -0.245 |
| p.adjustANOVA | 0.706 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q5FM24 | -363 |
| Q5FJN3 | -340 |
| Q5FJB6 | 22 |
| Q5FLI0 | 299 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q5FM24 | -363 |
| Q5FJN3 | -340 |
| Q5FJB6 | 22 |
| Q5FLI0 | 299 |
tRNA methylation
| set | tRNA methylation |
| setSize | 3 |
| pANOVA | 0.417 |
| s.dist | 0.271 |
| p.adjustANOVA | 0.706 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q5FHQ5 | 200.5 |
| Q5FKE1 | 123.0 |
| Q5FHQ6 | 41.0 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q5FHQ5 | 200.5 |
| Q5FKE1 | 123.0 |
| Q5FHQ6 | 41.0 |
tRNA wobble uridine modification
| set | tRNA wobble uridine modification |
| setSize | 3 |
| pANOVA | 0.417 |
| s.dist | 0.271 |
| p.adjustANOVA | 0.706 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q5FHQ5 | 200.5 |
| Q5FKE1 | 123.0 |
| Q5FHQ6 | 41.0 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q5FHQ5 | 200.5 |
| Q5FKE1 | 123.0 |
| Q5FHQ6 | 41.0 |
purine ribonucleoside salvage
| set | purine ribonucleoside salvage |
| setSize | 3 |
| pANOVA | 0.433 |
| s.dist | 0.262 |
| p.adjustANOVA | 0.706 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q5FL62 | 327.0 |
| Q5FMD9 | 209.0 |
| Q5FLD2 | -182.5 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q5FL62 | 327.0 |
| Q5FMD9 | 209.0 |
| Q5FLD2 | -182.5 |
biosynthetic process
| set | biosynthetic process |
| setSize | 4 |
| pANOVA | 0.433 |
| s.dist | 0.227 |
| p.adjustANOVA | 0.706 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q5FLC0 | 250.0 |
| Q5FKK3 | 204.5 |
| Q5FKQ7 | 144.0 |
| Q5FKI3 | -187.0 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q5FLC0 | 250.0 |
| Q5FKK3 | 204.5 |
| Q5FKQ7 | 144.0 |
| Q5FKI3 | -187.0 |
methionine biosynthetic process
| set | methionine biosynthetic process |
| setSize | 3 |
| pANOVA | 0.447 |
| s.dist | -0.254 |
| p.adjustANOVA | 0.714 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q5FJS6 | -354 |
| Q5FK49 | -110 |
| Q5FJG5 | 166 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q5FJS6 | -354 |
| Q5FK49 | -110 |
| Q5FJG5 | 166 |
transmembrane transport
| set | transmembrane transport |
| setSize | 13 |
| pANOVA | 0.473 |
| s.dist | 0.116 |
| p.adjustANOVA | 0.738 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q5FII3 | 377.0 |
| Q5FJJ0 | 292.0 |
| Q5FN03 | 285.0 |
| Q5FJJ2 | 261.0 |
| Q5FLS7 | 255.5 |
| Q5FLF9 | 214.0 |
| Q5FIL9 | 200.5 |
| Q5FJJ1 | 56.0 |
| Q5FHX1 | -0.5 |
| Q5FMH6 | -250.0 |
| Q5FMH9 | -273.0 |
| Q5FMH8 | -280.0 |
| Q5FMM2 | -413.0 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q5FII3 | 377.0 |
| Q5FJJ0 | 292.0 |
| Q5FN03 | 285.0 |
| Q5FJJ2 | 261.0 |
| Q5FLS7 | 255.5 |
| Q5FLF9 | 214.0 |
| Q5FIL9 | 200.5 |
| Q5FJJ1 | 56.0 |
| Q5FHX1 | -0.5 |
| Q5FMH6 | -250.0 |
| Q5FMH9 | -273.0 |
| Q5FMH8 | -280.0 |
| Q5FMM2 | -413.0 |
DNA recombination
| set | DNA recombination |
| setSize | 13 |
| pANOVA | 0.487 |
| s.dist | -0.112 |
| p.adjustANOVA | 0.744 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q5FL82 | -405.0 |
| Q5FN08 | -259.5 |
| Q5FJP8 | -244.0 |
| Q5FJI6 | -220.5 |
| Q5FM04 | -211.0 |
| Q5FKC4 | -176.0 |
| Q5FLX2 | -79.0 |
| Q5FJT8 | -31.0 |
| Q5FKT7 | 77.0 |
| Q5FJH0 | 103.5 |
| Q5FLX3 | 168.0 |
| Q5FJH4 | 352.5 |
| Q5FJX7 | 416.0 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q5FL82 | -405.0 |
| Q5FN08 | -259.5 |
| Q5FJP8 | -244.0 |
| Q5FJI6 | -220.5 |
| Q5FM04 | -211.0 |
| Q5FKC4 | -176.0 |
| Q5FLX2 | -79.0 |
| Q5FJT8 | -31.0 |
| Q5FKT7 | 77.0 |
| Q5FJH0 | 103.5 |
| Q5FLX3 | 168.0 |
| Q5FJH4 | 352.5 |
| Q5FJX7 | 416.0 |
carbohydrate catabolic process
| set | carbohydrate catabolic process |
| setSize | 7 |
| pANOVA | 0.509 |
| s.dist | -0.145 |
| p.adjustANOVA | 0.744 |
Top enriched genes
| GeneID | Gene Rank |
|---|---|
| Q5FJZ4 | -387.0 |
| Q5FL27 | -77.5 |
| Q5FKN4 | -52.0 |
| Q5FKN0 | -41.0 |
| Q5FHV9 | -9.0 |
| Q5FLZ2 | 47.0 |
| Q5FKP1 | 147.0 |
Click HERE to show all gene set members
| GeneID | Gene Rank |
|---|---|
| Q5FJZ4 | -387.0 |
| Q5FL27 | -77.5 |
| Q5FKN4 | -52.0 |
| Q5FKN0 | -41.0 |
| Q5FHV9 | -9.0 |
| Q5FLZ2 | 47.0 |
| Q5FKP1 | 147.0 |
Network diagram
Only used for one-dimensional analysis.
Here, the network diagram is used to depict the similarity between some of the top ranked gene sets. It makes separate charts for up and downregulated sets. It works best when prioritisation is done by effect size during the mitch_calc() step. By default, we only show the top 20 genes, but you can use the networkplot() command yourself with other options. See ?networkplot for more detail. There is an element of stochasticity with regard to the network projection, so if you see a lot of overlapping labels or labels getting cut off, you could repeat the chart generation until you get a nice layout. See ?networkplot for more detail.
Below the network diagrams, you will see lists of genes that make up the up and downregulated sets respectively. For upregulated genes the score needs to be >2 and for downregulated genes it needs to be < -2. This is to remove genes that have uninteresting differential expression and do not contribute enrichment.
if (d==1) {
networkplot(eres=res,FDR=0.05,n_sets=20)
network_genes(eres=res,FDR=0.05,n_sets=20)
} else {
message("Network charts only generated in one-dimensional analysis.")
}## Can't plot upregulated sets. Fewer than 5 found.## Can't plot downregulated sets. Fewer than 5 found.## No significant upregulated sets to show.## [[1]]
## [[1]]$`DOWN genesets.translation`
## [1] "Q5FKT1" "Q5FKT2" "Q5FLL1" "Q5FLL0" "Q5FLL2" "Q5FMA5" "Q5FL79" "Q5FKI9"
## [9] "Q5FKF5" "Q5FKE5" "Q5FJM6" "Q5FMA9" "Q5FJN2" "Q5FM22" "Q5FM90" "Q5FM89"
## [17] "Q5FM78" "Q5FN05" "Q5FM13" "Q5FM23" "Q5FM12" "Q5FM59" "Q5FM80" "Q5FM72"
## [25] "Q5FM83" "Q5FM64" "Q5FM75" "Q5FJK8" "Q5FIW9" "Q5FJF9" "Q5FM85" "Q5FM88"
## [33] "Q5FM79" "Q5FJG0" "Q5FJI3" "Q5FM82" "Q5FM73" "Q5FMB6" "Q5FKH0" "Q5FIZ7"
## [41] "Q5FM68" "Q5FJM3" "Q5FM84" "Q5FKX2" "Q5FM74" "Q5FN09" "Q5FM93" "Q5FM77"
## [49] "Q5FM58" "Q5FM91" "Q5FM66" "Q5FM94" "Q5FM67" "Q5FJK5" "Q5FM81" "Q5FN07"
## [57] "Q5FM86" "Q5FJT3"Session information
Here is the session info with all the versions of packages used.
sessionInfo()## R version 4.5.0 (2025-04-11)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.5 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0 LAPACK version 3.10.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: Australia/Melbourne
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] gtools_3.9.5 mitch_1.20.0
##
## loaded via a namespace (and not attached):
## [1] gtable_0.3.6 beeswarm_0.4.0 xfun_0.52
## [4] bslib_0.9.0 ggplot2_3.5.2 htmlwidgets_1.6.4
## [7] caTools_1.18.3 GGally_2.2.1 lattice_0.22-7
## [10] vctrs_0.6.5 tools_4.5.0 bitops_1.0-9
## [13] generics_0.1.3 parallel_4.5.0 tibble_3.2.1
## [16] pkgconfig_2.0.3 KernSmooth_2.23-26 RColorBrewer_1.1-3
## [19] lifecycle_1.0.4 compiler_4.5.0 farver_2.1.2
## [22] stringr_1.5.1 gplots_3.2.0 httpuv_1.6.16
## [25] sass_0.4.10 htmltools_0.5.8.1 yaml_2.3.10
## [28] later_1.4.2 pillar_1.10.2 jquerylib_0.1.4
## [31] tidyr_1.3.1 MASS_7.3-65 cachem_1.1.0
## [34] mime_0.13 ggstats_0.9.0 network_1.19.0
## [37] tidyselect_1.2.1 digest_0.6.37 stringi_1.8.7
## [40] dplyr_1.1.4 reshape2_1.4.4 purrr_1.0.4
## [43] fastmap_1.2.0 grid_4.5.0 cli_3.6.5
## [46] magrittr_2.0.3 dichromat_2.0-0.1 withr_3.0.2
## [49] scales_1.4.0 promises_1.3.2 rmarkdown_2.29
## [52] gridExtra_2.3 kableExtra_1.4.0 coda_0.19-4.1
## [55] shiny_1.10.0 evaluate_1.0.3 knitr_1.50
## [58] viridisLite_0.4.2 rlang_1.1.6 Rcpp_1.0.14
## [61] xtable_1.8-4 glue_1.8.0 echarts4r_0.4.5
## [64] xml2_1.3.8 jsonlite_2.0.0 svglite_2.1.3
## [67] rstudioapi_0.17.1 R6_2.6.1 plyr_1.8.9
## [70] statnet.common_4.11.0 systemfonts_1.2.2END of report