Dataset: Expression data from paired matched breast cancer Fine needle aspiration (FNA) or Core needle biopsies (CBX)
Paired FNA and CBX specimens were prospectively collected from 37 breast cancers before any systemic therapy during a biomarker discovery...
Paired FNA and CBX specimens were prospectively collected from 37 breast cancers before any systemic therapy during a biomarker discovery study at The University of Texas M. D. Anderson Cancer Center. We identified 293 probe sets overexpressed in core biopsies; these included five highly coexpressed gene clusters (metagenes) corresponding to immune functions and extracellular matrix components. We compared gene expression profiles of pairs of fine-needle (stroma-poor) and core-needle (stroma-rich) biopsies from 37 cancers to identify stroma-associated genes Pre-treatment paird matched FNA and CBX from primary tumors were obtained and RNA extracted and hybridized to afymetrix microarrays according to manufacturer protocol.
- Species:
- human
- Samples:
- 74
- Source:
- E-GEOD-32518
- PubMed:
- 20805453
- Updated:
- Dec.12, 2014
- Registered:
- Jun.18, 2014
Factors:
(via ArrayExpress)
| Sample | PRE N | PRE MBNG | PR STATUS BY IHC | ER BY GENE | PRE T | PR (%) BY IHC | AGE AT DX | ER (%) BY IHC | MATCHED PAIR | SAMPLE TYPE | ER STATUS BY IHC | HER2 STATUS IHC (AND FISH) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| GSM805375 | 0 | 3 | N | ERneg | 2 | 0 | 56 | 0 | 39 | core needle biopsy | N | N |
| GSM805374 | 0 | 3 | N | ERneg | 2 | 0 | 56 | 0 | 39 | fine needle aspiration | N | N |
| GSM805373 | 2 | 3 | N | ERneg | 2 | 0 | 34 | 0 | 38 | core needle biopsy | N | N |
| GSM805372 | 2 | 3 | N | ERneg | 2 | 0 | 34 | 0 | 38 | fine needle aspiration | N | N |
| GSM80537 | 2 | 3 | N | ERneg | 4 | 0 | 49 | 0 | 37 | core needle biopsy | N | P |
| GSM805370 | 2 | 3 | N | ERneg | 4 | 0 | 49 | 0 | 37 | fine needle aspiration | N | P |
| GSM805369 | 1 | 2 | P | ERpos | 4 | 80 | 52 | 80 | 36 | core needle biopsy | P | P |
| GSM805368 | 1 | 2 | P | ERpos | 4 | 80 | 52 | 80 | 36 | fine needle aspiration | P | P |
| GSM805367 | 0 | 1 | P | ERpos | 3 | 60 | 49 | 95 | 35 | core needle biopsy | P | N |
| GSM805366 | 0 | 1 | P | ERpos | 3 | 60 | 49 | 95 | 35 | fine needle aspiration | P | N |
| GSM805365 | 1 | 3 | P | ERpos | 3 | 30 | 45 | 30 | 34 | core needle biopsy | P | N |
| GSM805364 | 1 | 3 | P | ERpos | 3 | 30 | 45 | 30 | 34 | fine needle aspiration | P | N |
| GSM805363 | 1 | 3 | N | ERneg | 4 | 0 | 46 | 0 | 33 | core needle biopsy | N | N |
| GSM805362 | 1 | 3 | N | ERneg | 4 | 0 | 46 | 0 | 33 | fine needle aspiration | N | N |
| GSM80536 | 1 | 3 | N | ERneg | 2 | 0 | 50 | 0 | 32 | core needle biopsy | N | P |
| GSM805360 | 1 | 3 | N | ERneg | 2 | 0 | 50 | 0 | 32 | fine needle aspiration | N | P |
| GSM805359 | 0 | 3 | N | ERneg | 2 | 1 | 47 | 5 | 31 | core needle biopsy | N | N |
| GSM805358 | 0 | 3 | N | ERneg | 2 | 1 | 47 | 5 | 31 | fine needle aspiration | N | N |
| GSM805357 | 1 | 3 | N | ERneg | 4 | 0 | 61 | 0 | 30 | core needle biopsy | N | N |
| GSM805356 | 1 | 3 | N | ERneg | 4 | 0 | 61 | 0 | 30 | fine needle aspiration | N | N |
| GSM805355 | 1 | 1 | P | ERpos | 2 | 30 | 60 | 100 | 28 | core needle biopsy | P | N |
| GSM805354 | 1 | 1 | P | ERpos | 2 | 30 | 60 | 100 | 28 | fine needle aspiration | P | N |
| GSM805353 | NA | NA | NA | ERpos | NA | NA | NA | NA | 27 | core needle biopsy | NA | NA |
| GSM805352 | NA | NA | NA | ERpos | NA | NA | NA | NA | 27 | fine needle aspiration | NA | NA |
| GSM80535 | NA | NA | NA | ERpos | NA | NA | NA | NA | 26 | core needle biopsy | NA | NA |
| GSM805350 | NA | NA | NA | ERpos | NA | NA | NA | NA | 26 | fine needle aspiration | NA | NA |
| GSM805349 | NA | NA | NA | ERpos | NA | NA | NA | NA | 25 | core needle biopsy | NA | NA |
| GSM805348 | NA | NA | NA | ERpos | NA | NA | NA | NA | 25 | fine needle aspiration | NA | NA |
| GSM805347 | NA | NA | NA | ERpos | NA | NA | NA | NA | 24 | core needle biopsy | NA | NA |
| GSM805346 | NA | NA | NA | ERpos | NA | NA | NA | NA | 24 | fine needle aspiration | NA | NA |
| GSM805345 | NA | NA | NA | ERneg | NA | NA | NA | NA | 23 | core needle biopsy | NA | NA |
| GSM805344 | NA | NA | NA | ERneg | NA | NA | NA | NA | 23 | fine needle aspiration | NA | NA |
| GSM805343 | NA | NA | NA | ERpos | NA | NA | NA | NA | 22 | core needle biopsy | NA | NA |
| GSM805342 | NA | NA | NA | ERpos | NA | NA | NA | NA | 22 | fine needle aspiration | NA | NA |
| GSM80534 | NA | NA | NA | ERpos | NA | NA | NA | NA | 21 | core needle biopsy | NA | NA |
| GSM805340 | NA | NA | NA | ERpos | NA | NA | NA | NA | 21 | fine needle aspiration | NA | NA |
| GSM805339 | NA | NA | NA | ERneg | NA | NA | NA | NA | 20 | core needle biopsy | NA | NA |
| GSM805338 | NA | NA | NA | ERneg | NA | NA | NA | NA | 20 | fine needle aspiration | NA | NA |
| GSM805337 | 1 | 3 | N | ERpos | 1 | 0 | 51 | 90 | 19 | core needle biopsy | P | N |
| GSM805336 | 1 | 3 | N | ERpos | 1 | 0 | 51 | 90 | 19 | fine needle aspiration | P | N |
| GSM805335 | NA | NA | NA | NA | NA | NA | NA | NA | 18 | core needle biopsy | NA | NA |
| GSM805334 | 1 | 2 | N | ERpos | 2 | 0 | 45 | 91 | 18 | fine needle aspiration | P | N |
| GSM805333 | 1 | 2 | N | ERneg | 3 | 0 | 37 | 0 | 17 | core needle biopsy | N | N |
| GSM805332 | 1 | 2 | N | ERneg | 3 | 0 | 37 | 0 | 17 | fine needle aspiration | N | N |
| GSM80533 | NA | NA | NA | NA | NA | NA | NA | NA | 16 | core needle biopsy | NA | NA |
| GSM805330 | 1 | 3 | N | ERpos | 2 | 0 | 63 | 0 | 16 | fine needle aspiration | N | N |
| GSM805329 | 0 | 3 | N | ERneg | 2 | 0 | 44 | 0 | 15 | core needle biopsy | N | N |
| GSM805328 | 0 | 3 | N | ERneg | 2 | 0 | 44 | 0 | 15 | fine needle aspiration | N | N |
| GSM805327 | 3 | 3 | P | ERpos | 4 | 10 | 46 | 30 | 14 | core needle biopsy | P | N |
| GSM805326 | 3 | 3 | P | ERpos | 4 | 10 | 46 | 30 | 14 | fine needle aspiration | P | N |
| GSM805325 | 2 | 2 | N | ERneg | 3 | 0 | 45 | 0 | 13 | core needle biopsy | N | P |
| GSM805324 | 2 | 2 | N | ERneg | 3 | 0 | 45 | 0 | 13 | fine needle aspiration | N | P |
| GSM805323 | 0 | 3 | N | ERneg | 2 | 0 | 55 | 0 | 12 | core needle biopsy | N | P |
| GSM805322 | 0 | 3 | N | ERneg | 2 | 0 | 55 | 0 | 12 | fine needle aspiration | N | P |
| GSM80532 | NA | NA | NA | NA | NA | NA | NA | NA | 10 | core needle biopsy | NA | NA |
| GSM805320 | 0 | 3 | N | ERneg | 3 | 0 | 53 | 0 | 10 | fine needle aspiration | N | N |
| GSM805319 | 0 | 3 | P | ERpos | 2 | 60 | 47 | 80 | 9 | core needle biopsy | P | N |
| GSM805318 | 0 | 3 | P | ERpos | 2 | 60 | 47 | 80 | 9 | fine needle aspiration | P | N |
| GSM805317 | 0 | 2 | P | ERpos | 1 | 100 | 46 | 100 | 8 | core needle biopsy | P | N |
| GSM805316 | 0 | 2 | P | ERpos | 1 | 100 | 46 | 100 | 8 | fine needle aspiration | P | N |
| GSM805315 | 0 | 3 | N | ERpos | 3 | 5 | 41 | 80 | 7 | core needle biopsy | P | N |
| GSM805314 | 0 | 3 | N | ERpos | 3 | 5 | 41 | 80 | 7 | fine needle aspiration | P | N |
| GSM805313 | 0 | 2 | P | ERpos | 2 | 80 | 57 | 90 | 6 | core needle biopsy | P | N |
| GSM805312 | 0 | 2 | P | ERpos | 2 | 80 | 57 | 90 | 6 | fine needle aspiration | P | N |
| GSM8053 | 1 | 3 | N | ERneg | 3 | 0 | 30 | 0 | 5 | core needle biopsy | N | P |
| GSM805310 | 1 | 3 | N | ERneg | 3 | 0 | 30 | 0 | 5 | fine needle aspiration | N | P |
| GSM805309 | 1 | 3 | P | ERpos | 3 | 80 | 45 | 80 | 4 | core needle biopsy | P | P |
| GSM805308 | 1 | 3 | P | ERpos | 3 | 80 | 45 | 80 | 4 | fine needle aspiration | P | P |
| GSM805307 | 0 | 3 | P | ERneg | 1 | 90 | 37 | 0 | 3 | core needle biopsy | N | N |
| GSM805306 | 0 | 3 | P | ERneg | 1 | 90 | 37 | 0 | 3 | fine needle aspiration | N | N |
| GSM805305 | 0 | 3 | N | ERpos | 3 | 0 | 50 | 95 | 2 | core needle biopsy | P | P |
| GSM805304 | 0 | 3 | N | ERpos | 3 | 0 | 50 | 95 | 2 | fine needle aspiration | P | P |
| GSM805303 | 1 | 1 | N | ERpos | 3 | 5 | 51 | 95 | 1 | core needle biopsy | P | N |
| GSM805302 | 1 | 1 | N | ERpos | 3 | 5 | 51 | 95 | 1 | fine needle aspiration | P | N |