Note that this is a very raw representation of only the new data. I still need to make the tables more aesthetically pleasing/readable. Also, I need to fix the C stack issue and map my ensembl IDs to entrez IDs to produce some of my figures.
## GO.ID Term Annotated
## 1 GO:0008324 cation transmembrane transporter activit... 653
## 2 GO:0015075 ion transmembrane transporter activity 863
## 3 GO:0005198 structural molecule activity 685
## 4 GO:0022824 transmitter-gated ion channel activity 48
## 5 GO:0022835 transmitter-gated channel activity 48
## 6 GO:0022891 substrate-specific transmembrane transpo... 931
## 7 GO:0005230 extracellular ligand-gated ion channel a... 74
## 8 GO:0022890 inorganic cation transmembrane transport... 546
## 9 GO:0022836 gated channel activity 329
## 10 GO:0022892 substrate-specific transporter activity 1119
## 11 GO:0005261 cation channel activity 314
## 12 GO:0022857 transmembrane transporter activity 1019
## 13 GO:0046873 metal ion transmembrane transporter acti... 440
## 14 GO:0005216 ion channel activity 425
## 15 GO:0005179 hormone activity 116
## 16 GO:0030594 neurotransmitter receptor activity 89
## 17 GO:0022838 substrate-specific channel activity 435
## 18 GO:0015267 channel activity 464
## 19 GO:0022803 passive transmembrane transporter activi... 465
## 20 GO:0005215 transporter activity 1308
## Significant Expected Rank in Fisher.classic Fisher.elim Fisher.classic
## 1 48 18.16 1 0.050 7.8e-10
## 2 57 24.00 2 0.706 1.0e-09
## 3 48 19.05 3 5.8e-07 3.7e-09
## 4 12 1.33 4 2.1e-05 5.2e-09
## 5 12 1.33 5 1.000 5.2e-09
## 6 58 25.89 6 0.764 6.3e-09
## 7 14 2.06 7 0.156 1.3e-08
## 8 40 15.18 8 0.408 2.4e-08
## 9 29 9.15 9 0.236 4.5e-08
## 10 63 31.12 10 0.717 6.1e-08
## 11 28 8.73 11 0.018 6.1e-08
## 12 59 28.34 12 0.844 6.4e-08
## 13 34 12.24 13 0.226 8.0e-08
## 14 33 11.82 14 0.466 1.1e-07
## 15 16 3.23 15 5.2e-06 1.3e-07
## 16 14 2.47 16 0.306 1.5e-07
## 17 33 12.10 17 0.516 1.9e-07
## 18 34 12.90 18 0.475 2.8e-07
## 19 34 12.93 19 0.480 3.0e-07
## 20 67 36.37 20 0.812 7.3e-07
Top 20 molecular function GO terms ordered by classic Fisher test results.
## GO.ID Term Annotated Significant
## 1 GO:0018149 peptide cross-linking 55 23
## 2 GO:0031424 keratinization 179 34
## 3 GO:0030216 keratinocyte differentiation 246 38
## 4 GO:0009913 epidermal cell differentiation 295 41
## 5 GO:0070268 cornification 109 25
## 6 GO:0032501 multicellular organismal process 6776 280
## 7 GO:0008544 epidermis development 401 44
## 8 GO:0043588 skin development 358 41
## 9 GO:0030855 epithelial cell differentiation 676 58
## 10 GO:0044707 single-multicellular organism process 5989 248
## 11 GO:0032502 developmental process 5776 232
## 12 GO:0044767 single-organism developmental process 5690 229
## 13 GO:0009888 tissue development 1824 98
## 14 GO:0060429 epithelium development 1172 72
## 15 GO:0048856 anatomical structure development 5369 217
## 16 GO:0048513 animal organ development 3171 145
## 17 GO:0007275 multicellular organism development 4921 202
## 18 GO:0007586 digestion 171 22
## 19 GO:0030154 cell differentiation 3725 162
## 20 GO:0048731 system development 4366 182
## Expected Rank in Fisher.classic Fisher.elim Fisher.classic
## 1 1.59 1 1.9e-21 1.9e-21
## 2 5.18 2 0.00013 1.5e-18
## 3 7.12 3 0.10883 2.2e-17
## 4 8.54 4 0.03883 5.4e-17
## 5 3.15 5 5.5e-16 5.5e-16
## 6 196.12 6 0.14916 2.6e-15
## 7 11.61 7 0.08170 2.6e-14
## 8 10.36 8 0.21472 4.9e-14
## 9 19.57 9 0.07286 9.6e-14
## 10 173.34 10 0.03834 9.5e-13
## 11 167.18 11 0.01780 3.8e-10
## 12 164.69 12 0.02274 4.7e-10
## 13 52.79 13 0.16299 7.2e-10
## 14 33.92 14 0.24399 8.1e-10
## 15 155.40 15 0.05514 1.6e-09
## 16 91.78 16 0.09798 2.0e-09
## 17 142.43 17 0.10605 2.7e-09
## 18 4.95 18 5.4e-08 4.7e-09
## 19 107.82 19 0.01268 5.7e-09
## 20 126.37 20 0.15313 1.0e-08
Top 20 biological process GO terms ordered by classic Fisher test results.
## GO.ID Term Annotated Significant
## 1 GO:0001533 cornified envelope 59 25
## 2 GO:0005615 extracellular space 1390 84
## 3 GO:0034702 ion channel complex 285 25
## 4 GO:1902495 transmembrane transporter complex 321 26
## 5 GO:0044456 synapse part 676 42
## 6 GO:0098590 plasma membrane region 957 53
## 7 GO:1990351 transporter complex 328 26
## 8 GO:0005886 plasma membrane 4853 184
## 9 GO:0071944 cell periphery 4952 186
## 10 GO:0097060 synaptic membrane 291 23
## 11 GO:0045202 synapse 811 45
## 12 GO:0005887 integral component of plasma membrane 1536 72
## 13 GO:0045211 postsynaptic membrane 220 19
## 14 GO:0044459 plasma membrane part 2531 106
## 15 GO:0005903 brush border 98 12
## 16 GO:0005576 extracellular region 4470 167
## 17 GO:0031226 intrinsic component of plasma membrane 1602 72
## 18 GO:0005892 acetylcholine-gated channel complex 17 5
## 19 GO:0034703 cation channel complex 206 17
## 20 GO:0098794 postsynapse 407 26
## Expected Rank in Fisher.classic Fisher.elim Fisher.classic
## 1 1.68 1 1.5e-23 1.5e-23
## 2 39.55 2 3.0e-10 2.6e-11
## 3 8.11 3 0.2436 6.7e-07
## 4 9.13 4 0.2846 1.8e-06
## 5 19.24 5 0.0705 1.9e-06
## 6 27.23 6 0.0993 2.6e-06
## 7 9.33 7 0.3282 2.7e-06
## 8 138.10 8 0.4628 3.5e-06
## 9 140.92 9 0.4873 5.5e-06
## 10 8.28 10 0.1341 1.1e-05
## 11 23.08 11 0.1826 1.5e-05
## 12 43.71 12 0.0015 1.6e-05
## 13 6.26 13 1.8e-05 1.8e-05
## 14 72.02 14 0.3068 1.9e-05
## 15 2.79 15 0.0092 2.2e-05
## 16 127.20 16 0.5727 3.3e-05
## 17 45.59 17 1.0000 6.4e-05
## 18 0.48 18 8.5e-05 8.5e-05
## 19 5.86 19 0.0052 8.8e-05
## 20 11.58 20 0.2625 0.00011
Top 20 cellular component GO terms ordered by classic Fisher test result
## GO.ID Term Annotated
## 1 GO:0022836 gated channel activity 329
## 2 GO:0004930 G-protein coupled receptor activity 623
## 3 GO:0022838 substrate-specific channel activity 435
## 4 GO:0022803 passive transmembrane transporter activi... 465
## 5 GO:0015267 channel activity 464
## 6 GO:0005216 ion channel activity 425
## 7 GO:0005261 cation channel activity 314
## 8 GO:0005244 voltage-gated ion channel activity 195
## 9 GO:0022832 voltage-gated channel activity 195
## 10 GO:0008324 cation transmembrane transporter activit... 653
## 11 GO:0022857 transmembrane transporter activity 1019
## 12 GO:0046873 metal ion transmembrane transporter acti... 440
## 13 GO:0022890 inorganic cation transmembrane transport... 546
## 14 GO:0015077 monovalent inorganic cation transmembran... 359
## 15 GO:0015075 ion transmembrane transporter activity 863
## 16 GO:0022891 substrate-specific transmembrane transpo... 931
## 17 GO:0099600 transmembrane receptor activity 1074
## 18 GO:0022843 voltage-gated cation channel activity 132
## 19 GO:0005267 potassium channel activity 126
## 20 GO:0015079 potassium ion transmembrane transporter ... 159
## Significant Expected Rank in KS.classic KS.elim KS.classic
## 1 29 9.15 1 0.0229 1.1e-16
## 2 26 17.32 2 1.1e-09 2.1e-16
## 3 33 12.10 3 0.0546 4.4e-16
## 4 34 12.93 4 0.0316 6.2e-16
## 5 34 12.90 5 0.0393 9.2e-16
## 6 33 11.82 6 0.1198 2.0e-15
## 7 28 8.73 7 0.0320 1.2e-14
## 8 15 5.42 8 0.0128 5.7e-14
## 9 15 5.42 9 0.0128 5.7e-14
## 10 48 18.16 10 0.0488 9.1e-14
## 11 59 28.34 11 0.0084 1.1e-13
## 12 34 12.24 12 0.1291 1.2e-13
## 13 40 15.18 13 0.1316 1.4e-13
## 14 28 9.98 14 0.0895 1.4e-13
## 15 57 24.00 15 0.1541 3.7e-13
## 16 58 25.89 16 0.0372 5.0e-13
## 17 40 29.87 17 0.4266 1.4e-12
## 18 11 3.67 18 0.2394 3.2e-12
## 19 13 3.50 19 0.0033 4.7e-12
## 20 15 4.42 20 0.2814 3.2e-11
Top 20 molecular function GO terms ordered by classic Kolmogorov–Smirnov test test results.
## GO.ID Term Annotated
## 1 GO:0050877 neurological system process 1038
## 2 GO:0099536 synaptic signaling 596
## 3 GO:0099537 trans-synaptic signaling 596
## 4 GO:0098916 anterograde trans-synaptic signaling 594
## 5 GO:0007268 chemical synaptic transmission 594
## 6 GO:0007600 sensory perception 709
## 7 GO:0003008 system process 1752
## 8 GO:0006811 ion transport 1540
## 9 GO:0007156 homophilic cell adhesion via plasma memb... 157
## 10 GO:0007186 G-protein coupled receptor signaling pat... 1011
## 11 GO:0007218 neuropeptide signaling pathway 96
## 12 GO:0006812 cation transport 1065
## 13 GO:0034220 ion transmembrane transport 1030
## 14 GO:0007267 cell-cell signaling 1541
## 15 GO:0006813 potassium ion transport 226
## 16 GO:0098742 cell-cell adhesion via plasma-membrane a... 231
## 17 GO:0007586 digestion 171
## 18 GO:0043269 regulation of ion transport 595
## 19 GO:0015672 monovalent inorganic cation transport 518
## 20 GO:0071804 cellular potassium ion transport 192
## Significant Expected Rank in KS.classic KS.elim KS.classic
## 1 41 30.04 1 0.07309 3.6e-15
## 2 32 17.25 2 0.45375 7.7e-14
## 3 32 17.25 3 0.45375 7.7e-14
## 4 32 17.19 4 1.00000 8.3e-14
## 5 32 17.19 5 3.2e-05 8.3e-14
## 6 26 20.52 6 0.14634 2.4e-13
## 7 78 50.71 7 0.22039 2.4e-13
## 8 77 44.57 8 0.00041 2.6e-13
## 9 2 4.54 9 1.9e-12 1.9e-12
## 10 50 29.26 10 6.9e-05 2.2e-12
## 11 10 2.78 11 7.9e-12 7.9e-12
## 12 58 30.83 12 0.08704 1.2e-10
## 13 57 29.81 13 0.03724 6.0e-10
## 14 70 44.60 14 0.04025 6.3e-10
## 15 17 6.54 15 0.12559 1.4e-09
## 16 6 6.69 16 0.13770 1.9e-09
## 17 22 4.95 17 0.00011 1.9e-09
## 18 32 17.22 18 0.31547 2.1e-09
## 19 30 14.99 19 0.25699 3.9e-09
## 20 15 5.56 20 1.00000 4.0e-09
Top 20 biological process GO terms ordered by classic Kolmogorov–Smirnov test test results.
## GO.ID Term Annotated
## 1 GO:0031224 intrinsic component of membrane 5153
## 2 GO:0016021 integral component of membrane 5025
## 3 GO:0031226 intrinsic component of plasma membrane 1602
## 4 GO:0005887 integral component of plasma membrane 1536
## 5 GO:1990351 transporter complex 328
## 6 GO:1902495 transmembrane transporter complex 321
## 7 GO:0044424 intracellular part 13746
## 8 GO:0005622 intracellular 14031
## 9 GO:0034702 ion channel complex 285
## 10 GO:0005615 extracellular space 1390
## 11 GO:0044446 intracellular organelle part 8581
## 12 GO:0034703 cation channel complex 206
## 13 GO:0044422 organelle part 8784
## 14 GO:0043229 intracellular organelle 11995
## 15 GO:0043231 intracellular membrane-bounded organelle 10351
## 16 GO:0043226 organelle 12952
## 17 GO:0043227 membrane-bounded organelle 12056
## 18 GO:0044425 membrane part 6261
## 19 GO:0044391 ribosomal subunit 183
## 20 GO:0044444 cytoplasmic part 9042
## Significant Expected Rank in KS.classic KS.elim KS.classic
## 1 160 146.64 1 0.52427 1.1e-22
## 2 155 142.99 2 1.3e-08 5.8e-19
## 3 72 45.59 3 0.19943 6.6e-15
## 4 72 43.71 4 4.6e-10 9.4e-15
## 5 26 9.33 5 0.06618 6.9e-14
## 6 26 9.13 6 0.03568 8.8e-14
## 7 314 391.16 7 0.08474 1.2e-13
## 8 330 399.27 8 0.04997 1.9e-13
## 9 25 8.11 9 0.00083 4.2e-13
## 10 84 39.55 10 1.3e-11 1.3e-11
## 11 140 244.18 11 2.8e-07 2.5e-11
## 12 17 5.86 12 0.07092 5.9e-11
## 13 145 249.96 13 0.63998 6.2e-11
## 14 253 341.34 14 0.74384 1.3e-10
## 15 206 294.55 15 5.1e-06 1.8e-10
## 16 304 368.57 16 0.23381 3.1e-10
## 17 286 343.07 17 0.16911 5.1e-10
## 18 181 178.17 18 0.23336 1.4e-09
## 19 0 5.21 19 0.00236 2.2e-09
## 20 179 257.30 20 0.00064 2.6e-08
Top 20 cellular component GO terms ordered by classic Kolmogorov–Smirnov test test results.
Histogram of p-values based on classic Fisher test.
Scatter plot of p-values for classic vs. elim Fisher test. Dot size is proportional to the number of annotated genes for the respective GO term; coloring reprsents the number of significantly differentially exrepressed genes: Dark red = more genes, yellow = less genes.
Distribution of the genes’ rank for a single GO ID, compared to the null distribution
Distribution of the genes’ rank for a single GO ID, compared to the null distribution