Module 258

Jump to: General properties | Gene sets | Enriched clinical annotations | Enriched Go annotations | Visual display

General Properties
Below we list the number of gene sets from which the module was composed was originally composed, and the number of genes and experiments that it contains. Clicking on the number of genes will display a detailed list of all the genes in the module. Clicking on the number of experiments will display a detailed list of all the experiments in the module.
Num gene sets:	2
Num genes:	26 (see 19 additional genes for this module)
Num experiments:	270 (108 induced, 162 repressed)

Jump to: General properties | Gene sets | Enriched clinical annotations | Enriched Go annotations | Visual display

Gene sets
Below we list the gene sets from which the module was originally composed. Clicking on a gene set will display all the genes associated with that gene set. Also listed are all the other modules in which the gene set participates.
secondary metabolism	258 348 449 541
Pollack99 25	258 348 449 541

Jump to: General properties | Gene sets | Enriched clinical annotations | Enriched Go annotations | Visual display

Enriched clinical annotations
For each of the clinical annotations, we tested whether it was enriched in the set of experiments in which the module is significantly induced (or repressed). Below we list all such annotations that were enriched in this module with an FDR corrected p-value of 0.05 ('P-value' column), along with the number ('Hits' column) of induced (or repressed) experiments in which they appear. We also show the fraction of experiments with the given annotation that are included in this module ('Hits (%)' column). Rows that correspond to annotations that were enriched in the induced experiments of the module have a red background, while rows corresponding to annotations enriched in the repressed experiments have a green background. For each annotation, we also list the other modules in which it was enriched.
Clinical annotation	P-value	Hits	Hits(%)	Modules
CLL	6.39e-11	20	12.345	3 5 8 16 17 18 21 37 52 53 54 56 57 61 64 69 72 76 79 84 97 98 102 105 118 119 124 125 126 128 136 145 156 158 161 169 170 171 179 182 187 188 197 198 210 212 219 236 237 238 240 244 245 252 254 255 258 261 292 300 301 302 303 308 312 313 315 317 337 344 345 348 358 361 378 399 403 436 451 456 459 485 502 513 522 525 531 532 537 547 554 562 573
Activated B like	1.18e-09	13	12.037	2 5 6 16 27 33 37 38 44 45 46 52 53 55 60 63 64 69 75 76 79 84 85 88 97 108 117 118 119 128 134 136 145 169 170 171 172 174 179 182 188 193 199 204 208 223 238 241 255 258 259 261 263 288 289 291 292 300 301 311 317 345 348 358 361 367 375 378 399 436 449 459 502 513 522 525 532 556 562
Breat cancer	3.80e-09	24	22.222	1 2 6 11 12 23 24 26 27 33 44 46 47 55 63 64 66 67 75 84 88 99 100 112 117 122 137 139 147 154 161 166 171 172 180 192 195 205 206 207 208 209 211 213 220 234 256 258 262 279 285 292 297 324 325 333 334 342 345 356 357 389 427 467 480 481 503 513 544 559 561 567 576 578
Female hormonal cancer	2.20e-08	24	22.222	6 11 12 23 24 26 27 33 44 46 47 55 63 66 67 75 84 88 99 100 112 117 122 137 139 147 154 161 166 172 180 192 195 205 206 207 209 213 220 234 256 258 279 285 297 324 325 333 334 342 356 357 389 427 480 481 503 513 559 567 576 578
Breast tissue or cancer	2.60e-08	24	22.222	1 2 5 6 11 12 19 23 24 26 27 33 44 46 47 55 60 63 64 66 67 75 84 88 99 100 112 117 122 129 137 139 147 154 161 166 171 172 176 180 192 195 205 206 207 208 209 213 220 234 256 258 279 285 297 324 325 333 334 342 345 356 357 385 389 427 480 481 503 513 559 567 576 578
After chemo (doxo, BC)	3.71e-08	10	9.259	1 2 5 6 11 12 23 24 26 27 33 38 44 46 47 55 60 63 64 66 75 84 88 100 107 112 117 122 129 137 139 161 171 172 180 206 207 208 209 211 213 220 234 258 289 292 320 324 342 345 348 385 389 424 436 461 467 478 513
Female hormonal tissue and cancer	2.18e-07	24	22.222	1 2 6 11 12 19 23 24 26 27 33 44 46 47 55 63 64 66 67 75 84 88 99 100 112 117 122 137 139 147 154 161 166 172 176 180 192 195 206 207 209 213 220 234 256 258 279 285 297 324 333 334 342 356 357 385 389 427 480 503 513 559 567 576 578
DLBCL tissue	5.36e-07	23	21.296	33 37 47 60 69 70 76 79 84 97 118 120 128 136 138 145 169 170 171 174 175 179 182 188 201 204 208 210 211 214 237 238 241 255 258 261 291 292 300 301 317 329 345 348 358 361 378 387 398 399 436 449 456 459 466 468 512 513 522 525 532 562
Breast cancer or cell line	5.77e-07	25	23.148	0 6 11 12 23 24 26 27 30 33 44 46 47 55 63 66 67 71 75 88 99 100 112 117 122 129 134 137 139 147 154 156 161 166 172 176 180 186 187 192 193 195 205 206 207 209 213 220 234 240 256 258 279 285 288 297 324 325 331 333 334 342 356 357 389 397 411 418 427 433 443 461 465 480 481 482 485 503 509 511 513 544 559 561 567 576 578
DLBCL tissue and cell line	1.54e-06	23	21.296	33 37 47 52 61 69 70 76 79 84 97 118 120 128 136 138 145 169 170 174 175 179 182 188 201 204 208 210 211 214 237 238 241 255 258 261 291 292 300 301 317 329 345 348 358 361 378 387 398 399 436 449 456 459 466 468 512 513 522 525 532 562
IPI=3	2.91e-06	10	9.259	70 76 97 120 138 175 182 201 214 258 261 263 292 329 358 361 387 512 525
Stage T3 - breast	3.51e-06	12	11.111	26 67 139 180 206 207 258 285 325 389 559 567 578
Breast	5.18e-06	25	23.148	0 1 2 6 11 12 23 24 26 27 33 44 46 47 55 63 66 67 75 88 99 100 112 117 122 129 134 137 139 147 154 161 166 172 176 180 192 195 201 205 206 207 209 213 220 234 256 258 279 285 297 324 325 329 330 333 334 342 356 357 385 389 411 427 433 461 465 480 481 503 511 513 544 561 567 576 578
Female hormonal cancer and cell line	6.38e-06	25	23.148	0 6 11 12 23 24 26 33 46 47 55 63 66 67 75 88 99 100 112 117 122 129 134 137 139 147 154 166 172 176 180 192 195 206 207 209 213 220 234 256 258 279 285 297 324 325 333 334 342 356 357 389 411 418 427 433 465 480 485 503 511 513 544 559 561 567 576 578
Adenocarcinoma (various tissues)	7.28e-06	46	42.592	2 6 7 9 10 11 12 19 20 23 24 26 36 38 40 41 43 48 55 58 60 66 67 68 78 83 88 89 90 92 93 94 95 96 100 101 104 106 107 108 112 113 117 122 129 130 131 135 137 139 140 142 143 148 153 154 157 162 163 164 165 166 167 172 176 180 181 189 190 192 203 204 205 206 207 209 211 220 221 222 223 230 234 235 239 242 249 257 258 263 279 280 285 286 290 293 295 297 298 306 310 322 324 326 334 342 343 357 364 373 374 379 382 384 385 389 397 401 404 417 421 422 426 427 431 435 438 440 443 447 461 464 469 479 480 486 487 495 506 513 514 515 520 521 523 542 551 552 564 567 573
Breast cell line	2.88e-05	13	8.024	0 1 3 14 15 18 26 30 33 34 44 45 47 52 63 68 71 79 85 99 107 119 122 128 134 139 146 154 170 171 172 178 180 186 191 193 199 207 208 258 262 279 288 292 293 297 321 324 325 331 334 341 342 345 348 357 361 362 389 411 418 424 432 455 467 478 485 509 511 513 516 526 561
Dead - B lymphoma	3.80e-05	12	11.111	33 37 69 70 76 79 84 97 118 120 128 136 138 145 169 170 174 175 179 182 188 201 204 208 210 214 237 238 241 255 258 261 291 292 300 301 317 329 345 348 358 361 378 387 436 459 468 512 513 522 525 532 562
Ref CRA BC	3.80e-05	12	11.111	11 26 66 67 88 100 112 117 137 139 154 180 205 206 207 258 285 297 325 342 357 364 389 567
Liver cell line	4.69e-05	6	3.703	1 3 9 10 17 18 19 23 24 27 32 38 40 43 44 45 46 48 49 52 54 57 58 60 63 64 72 73 75 76 78 79 93 95 96 98 99 101 106 107 108 109 112 117 118 119 121 123 124 125 126 128 129 130 131 132 135 139 158 163 164 165 167 169 170 171 172 176 177 180 184 185 198 199 205 208 209 212 213 221 223 235 238 244 246 247 249 252 258 259 263 265 283 286 292 294 295 301 302 305 309 310 320 327 337 342 343 345 349 353 373 388 395 397 401 403 410 415 416 418 424 426 430 436 438 440 443 451 454 456 457 458 461 462 467 477 478 479 496 505 529 536 556 572
Female hormonal tissue, cancer or cell line	5.59e-05	25	23.148	0 1 2 6 11 12 23 24 26 33 47 55 63 66 67 80 88 99 100 112 117 122 129 134 137 139 147 154 161 166 176 180 192 195 201 206 207 209 213 220 234 256 258 279 285 297 324 325 329 330 333 334 342 356 357 385 389 411 418 427 433 465 480 503 511 513 559 561 567 576 578
ER or DC pos BC	6.53e-05	12	11.111	26 67 117 139 180 205 206 207 234 258 285 342 389 443 559 567 578
mut p53 breast	7.23e-05	9	8.333	16 26 53 67 118 139 154 166 192 206 207 258 279 333 334 389 397 427 480
Lymphoma tissue or cell line	0.00012	23	21.296	33 37 61 69 70 79 97 118 120 128 136 138 145 169 170 174 175 179 182 188 201 204 214 237 238 241 255 258 261 278 291 292 301 317 329 345 348 358 361 378 387 398 399 436 456 459 468 512 513 525 532 562
Grade 3-breast	0.00014	9	8.333	26 53 54 57 67 98 118 158 166 192 198 206 207 252 258 279 315 333 334 389 397 427 480
No Ig mut	0.00014	7	4.320	16 37 53 54 57 61 69 79 98 118 119 124 126 128 136 145 156 169 170 179 187 188 237 238 240 254 255 258 301 308 312 313 315 317 361 378 399 403 451 456 459 485 502 525 532 537 554
Dead - all	0.00026	20	18.518	26 52 70 79 84 97 118 128 145 169 170 174 182 201 214 258 261 274 291 329 387 389 483 512 513 525 562 563
Stage T3	0.00026	13	12.037	26 159 206 207 258 285 321 389 443 460 497 559 567
Breast cancer or cell line	0.00035	26	16.049	0 6 11 12 23 24 26 27 30 33 44 46 47 55 63 66 67 71 75 88 99 100 112 117 122 129 134 137 139 147 154 156 161 166 172 176 180 186 187 192 193 195 205 206 207 209 213 220 234 240 256 258 279 285 288 297 324 325 331 333 334 342 356 357 389 397 411 418 427 433 443 461 465 480 481 482 485 503 509 511 513 544 559 561 567 576 578
Dead - Breast cancer	0.00036	8	7.407	26 67 139 154 180 192 206 207 258 279 333 334 389 397 427 480

Jump to: General properties | Gene sets | Enriched clinical annotations | Enriched Go annotations | Visual display

Enriched GO annotations

For each GO annotation, we tested whether it was enriched in the set of genes of the module. Below we list all such annotations that were enriched in this module with an FDR corrected p-value of 0.05 ('P-value' column), along with the number ('Hits' column) of genes in which they appear. We also show the fraction of genes with the given GO annotation that are included in this module ('Hits (%)' column).

Jump to: General properties | Gene sets | Enriched clinical annotations | Enriched Go annotations | Visual display

Visual display
Below is a visual display of the module. Shown are those arrays in which the module's genes significantly change, and the direction of change (induction/repression) in each array is indicated (middle, labeled 'Module changes'; red/green row). The arrays that correspond to the significant clinical attributes are also shown (top; brown rows). The gene sets that compose the module are also shown (left) along with an indication of the membership of the module genes in these gene sets.
You can also view the images within GeneXPress by loading the module gxp file file.
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