%PDF-1.6
%
1 0 obj
<>
endobj
2 0 obj
<>stream
Sandra Martínez-Canales, Francisco Cifuentes, Miguel López De Rodas Gregorio, Leticia Serrano-Oviedo, Eva María Galán-Moya, Eitan Amir, Atanasio Pandiella, Balázs Győrffy, Alberto Ocaña
Transcriptomic immunologic signature associated with favorable clinical outcome in basal-like breast tumors
www.plosone.org
www.plosone.org
endstream
endobj
3 0 obj
<>/XObject<>>>/CropBox[0 0 612 792]/MediaBox[0 0 612 792]/Parent 12 0 R/Annots 13 0 R/Contents 14 0 R/TrimBox[0 0 612 792]>>
endobj
13 0 obj
[15 0 R 16 0 R 17 0 R 18 0 R 19 0 R 20 0 R 21 0 R 22 0 R 23 0 R 24 0 R 25 0 R 26 0 R 27 0 R]
endobj
15 0 obj
<>/Border[0 0 0]/Dest(Rpone.0175128.ref001)>>
endobj
16 0 obj
<>/Border[0 0 0]/Dest(Rpone.0175128.ref001)>>
endobj
17 0 obj
<>/Border[0 0 0]/Dest(Rpone.0175128.ref002)>>
endobj
18 0 obj
<>/Border[0 0 0]/Dest(Rpone.0175128.ref003)>>
endobj
19 0 obj
<>/Border[0 0 0]/Dest(Rpone.0175128.ref004)>>
endobj
20 0 obj
<>/Border[0 0 0]/Dest(Rpone.0175128.ref005)>>
endobj
21 0 obj
<>/Border[0 0 0]/Dest(Rpone.0175128.ref006)>>
endobj
22 0 obj
<>/Border[0 0 0]/Dest(Rpone.0175128.ref007)>>
endobj
23 0 obj
<>/Border[0 0 0]/Dest(Rpone.0175128.ref008)>>
endobj
24 0 obj
<>/Border[0 0 0]/Dest(Rpone.0175128.ref008)>>
endobj
25 0 obj
<>/Border[0 0 0]/Dest(Rpone.0175128.ref009)>>
endobj
26 0 obj
<>/Border[0 0 0]/Dest(Rpone.0175128.ref010)>>
endobj
27 0 obj
<>/Border[0 0 0]/A 28 0 R>>
endobj
28 0 obj
<>
endobj
14 0 obj
[29 0 R 30 0 R 31 0 R 32 0 R 33 0 R 34 0 R 35 0 R 36 0 R 37 0 R 38 0 R 39 0 R 40 0 R 41 0 R 42 0 R]
endobj
29 0 obj
<>stream
q
0.45 0.36 0.35 0.01 k
0 w
575.9997 647.9101 m
199.9998 647.9101 l
199.9998 648.4102 l
575.9997 648.4102 l
f*
0.83 0.64 0.02 0 k
485.5748 575.3764 m
490.337 575.3764 l
h
f*
375.137 549.3543 m
379.8992 549.3543 l
h
f*
459.8362 458.3622 m
464.5984 458.3622 l
h
f*
484.7244 432.3969 m
489.4866 432.3969 l
h
f*
203.4142 380.3528 m
208.1764 380.3528 l
h
f*
212.5984 380.3528 m
217.3606 380.3528 l
h
f*
483.874 354.3874 m
488.6362 354.3874 l
h
f*
400.7055 341.4047 m
405.4677 341.4047 l
h
f*
455.7543 315.3827 m
460.5165 315.3827 l
h
f*
405.6945 302.4 m
410.4567 302.4 l
h
f*
374.6268 263.3953 m
379.389 263.3953 l
h
f*
482.7969 146.948 m
492.3213 146.948 l
h
f*
0 g
1 j
1 J
11.4998 0 0 11.4998 200.0125 706.3937 cm
BT
/F2 1 Tf
1 TL
-0.0035 Tc
0 0 Td
(Conclusion)Tj
ET
Q
q
1 j
1 J
0 w
9.5 0 0 9.5 200.0125 689.3858 cm
BT
/F0 1 Tf
1 TL
-0.0042 Tc
0 0 Td
(We)Tj
1.7127 0 Td
(describe)Tj
3.9506 0 Td
(a)Tj
0.7698 0 Td
(gene)Tj
2.4169 0 Td
(signature)Tj
4.2788 0 Td
(associated)Tj
4.9472 0 Td
(with)Tj
1.9753 0 Td
(immune)Tj
3.7417 0 Td
(function)Tj
3.682 0 Td
(and)Tj
1.8679 0 Td
(favorable)Tj
4.2788 0 Td
(outcome)Tj
4.0222 0 Td
(in)Tj
-37.6439 -1.474 Td
(basal-like)Tj
4.3802 0 Td
(breast)Tj
2.9719 0 Td
(cancer.)Tj
3.4672 0 Td
(Incorporation)Tj
5.9856 0 Td
(of)Tj
1.0443 0 Td
(this)Tj
1.7605 0 Td
(signature)Tj
4.2788 0 Td
(in)Tj
0.9846 0 Td
(prospective)Tj
5.2754 0 Td
(studies)Tj
3.3539 0 Td
(may)Tj
2.0946 0 Td
(help)Tj
2.0827 0 Td
(to)Tj
-37.6797 -1.468 Td
(stratify)Tj
3.1389 0 Td
(risk)Tj
1.7545 0 Td
(of)Tj
1.0503 0 Td
(early)Tj
2.3573 0 Td
(stage)Tj
2.6377 0 Td
(TNBC.)Tj
ET
Q
q
1 j
1 J
0 w
11.9999 0 0 11.9999 200.0125 593.4614 cm
BT
/F2 1 Tf
1 TL
-0.0033 Tc
0 0 Td
(Introduction)Tj
ET
Q
q
1 j
1 J
0 w
10 0 0 10 200.0125 576.4535 cm
BT
/F8 1 Tf
1 TL
-0.004 Tc
0 0 Td
(Metastatic)Tj
4.3483 0 Td
(triple)Tj
2.347 0 Td
(negative)Tj
3.532 0 Td
(breast)Tj
2.6135 0 Td
(cancer)Tj
2.846 0 Td
(\(TNBC\))Tj
3.4922 0 Td
(is)Tj
0.8448 0 Td
(an)Tj
1.2075 0 Td
(incurable)Tj
3.9685 0 Td
(disease)Tj
3.016 0 Td
([)Tj
0.83 0.64 0.02 0 k
(1)Tj
0 g
(].)Tj
1.5988 0 Td
(However,)Tj
4.0762 0 Td
(in)Tj
1.0374 0 Td
(early)Tj
-34.9282 -1.2982 Td
(stage)Tj
2.1996 0 Td
(disease,)Tj
3.2428 0 Td
(surgical)Tj
3.3165 0 Td
(resection)Tj
3.8438 0 Td
(and)Tj
1.7291 0 Td
(adjuvant)Tj
3.7021 0 Td
(treatment)Tj
4.1385 0 Td
(with)Tj
1.9956 0 Td
(chemotherapy)Tj
5.947 0 Td
(can)Tj
1.6271 0 Td
(contribute)Tj
4.3937 0 Td
(to)Tj
-36.1358 -1.3039 Td
(cure)Tj
1.9672 0 Td
(in)Tj
1.0318 0 Td
(a)Tj
0.6576 0 Td
(substantial)Tj
4.5014 0 Td
(proportion)Tj
4.6318 0 Td
(of)Tj
1.0148 0 Td
(patients)Tj
3.3675 0 Td
([)Tj
0.83 0.64 0.02 0 k
(1)Tj
0 g
(].)Tj
-15.9759 -1.2983 Td
(Decisions)Tj
4.1158 0 Td
(for)Tj
1.389 0 Td
(recommendation)Tj
7.1376 0 Td
(for)Tj
1.389 0 Td
(adjuvant)Tj
3.702 0 Td
(treatment)Tj
4.1329 0 Td
(in)Tj
1.0375 0 Td
(breast)Tj
2.6135 0 Td
(cancer)Tj
2.8459 0 Td
(are)Tj
1.4457 0 Td
(based)Tj
2.4718 0 Td
(on)Tj
1.2756 0 Td
(the)Tj
-34.7525 -1.2983 Td
(overall)Tj
2.9026 0 Td
(risk)Tj
1.7121 0 Td
(of)Tj
1.0148 0 Td
(cancer)Tj
2.846 0 Td
(recurrence)Tj
4.5297 0 Td
(which)Tj
2.6476 0 Td
(can)Tj
1.627 0 Td
(be)Tj
1.1509 0 Td
(estimated)Tj
4.0762 0 Td
(based)Tj
2.4718 0 Td
(on)Tj
1.2756 0 Td
(the)Tj
1.4683 0 Td
(extent)Tj
2.6759 0 Td
(of)Tj
1.0148 0 Td
(disease,)Tj
3.2428 0 Td
(as)Tj
1.0148 0 Td
(well)Tj
-35.6709 -1.3039 Td
(as)Tj
1.0147 0 Td
(biological)Tj
4.0876 0 Td
(factors)Tj
2.9026 0 Td
(such)Tj
2.0636 0 Td
(as)Tj
1.0148 0 Td
(histologic)Tj
4.0876 0 Td
(grade)Tj
2.4434 0 Td
(and)Tj
1.7292 0 Td
(receptor)Tj
3.5546 0 Td
(status.)Tj
2.7269 0 Td
(For)Tj
1.6271 0 Td
(TNBC)Tj
2.8062 0 Td
(given)Tj
2.3811 0 Td
(the)Tj
1.4684 0 Td
(high)Tj
2.0126 0 Td
(risk)Tj
-35.9204 -1.2982 Td
(of)Tj
1.0147 0 Td
(relapse)Tj
2.9934 0 Td
(and)Tj
1.7348 0 Td
(the)Tj
1.4683 0 Td
(poor)Tj
2.1203 0 Td
(prognosis,)Tj
4.354 0 Td
(treatment)Tj
4.1329 0 Td
(with)Tj
1.9956 0 Td
(chemotherapy)Tj
5.9527 0 Td
(is)Tj
0.8447 0 Td
(offered)Tj
3.0501 0 Td
(to)Tj
1.0261 0 Td
(most)Tj
2.2054 0 Td
(patients.)Tj
-32.893 -1.2983 Td
(However,)Tj
4.0761 0 Td
(in)Tj
1.0375 0 Td
(some)Tj
2.3301 0 Td
(circumstances)Tj
5.9017 0 Td
(the)Tj
1.4683 0 Td
(benefit)Tj
2.9764 0 Td
(from)Tj
2.2053 0 Td
(adjuvant)Tj
3.702 0 Td
(chemotherapy)Tj
5.9471 0 Td
(in)Tj
1.0375 0 Td
(TNBC)Tj
2.8119 0 Td
(can)Tj
1.6271 0 Td
(be)Tj
-35.121 -1.2983 Td
(less)Tj
1.61 0 Td
(clear,)Tj
2.3414 0 Td
(for)Tj
1.389 0 Td
(instance)Tj
3.5263 0 Td
(when)Tj
2.4037 0 Td
(tumors)Tj
3.1011 0 Td
(are)Tj
1.4513 0 Td
(very)Tj
1.9219 0 Td
(small,)Tj
2.5569 0 Td
(when)Tj
2.4037 0 Td
(patients)Tj
3.3676 0 Td
(are)Tj
1.4456 0 Td
(older)Tj
2.2961 0 Td
(or)Tj
1.0998 0 Td
(when)Tj
2.4038 0 Td
(medical)Tj
-33.3182 -1.3039 Td
(co-morbidities)Tj
6.1171 0 Td
(make)Tj
2.3924 0 Td
(the)Tj
1.4683 0 Td
(toxicity)Tj
3.2032 0 Td
(of)Tj
1.0148 0 Td
(chemotherapy)Tj
5.947 0 Td
(less)Tj
1.6101 0 Td
(favorable)Tj
3.8891 0 Td
([)Tj
0.83 0.64 0.02 0 k
(2)Tj
0 g
(].)Tj
1.5987 0 Td
(In)Tj
1.1112 0 Td
(these)Tj
2.2507 0 Td
(circumstances)Tj
5.9074 0 Td
(it)Tj
-36.51 -1.2983 Td
(would)Tj
2.7099 0 Td
(be)Tj
1.1508 0 Td
(desirable)Tj
3.7814 0 Td
(to)Tj
1.0261 0 Td
(have)Tj
2.058 0 Td
(better)Tj
2.5455 0 Td
(information)Tj
5.074 0 Td
(about)Tj
2.4944 0 Td
(prognosis.)Tj
-19.6439 -1.2982 Td
(Inhibition)Tj
4.3029 0 Td
(of)Tj
1.0148 0 Td
(immune)Tj
3.6227 0 Td
(surveillance)Tj
4.9492 0 Td
(is)Tj
0.8504 0 Td
(one)Tj
1.6951 0 Td
(of)Tj
1.0148 0 Td
(the)Tj
1.4684 0 Td
(hallmarks)Tj
4.1612 0 Td
(of)Tj
1.0148 0 Td
(cancer)Tj
2.8403 0 Td
([)Tj
0.83 0.64 0.02 0 k
(3)Tj
0 g
(].)Tj
1.6044 0 Td
(Activation)Tj
4.3993 0 Td
(of)Tj
-34.1345 -1.3039 Td
(immune)Tj
3.6169 0 Td
(system)Tj
2.931 0 Td
(against)Tj
3.0161 0 Td
(the)Tj
1.4627 0 Td
(tumor)Tj
2.7325 0 Td
(can)Tj
1.6158 0 Td
(lead)Tj
1.8425 0 Td
(to)Tj
1.0204 0 Td
(an)Tj
1.1906 0 Td
(anti-tumor)Tj
4.6318 0 Td
(response)Tj
3.7247 0 Td
(and)Tj
1.7234 0 Td
(therefore)Tj
3.8438 0 Td
(potentially)Tj
-33.3522 -1.2983 Td
(improve)Tj
3.5773 0 Td
(clinical)Tj
3.0784 0 Td
(outcome.)Tj
3.9514 0 Td
(In)Tj
1.1112 0 Td
(TNBC)Tj
2.8063 0 Td
(the)Tj
1.474 0 Td
(presence)Tj
3.7077 0 Td
(of)Tj
1.0148 0 Td
(tumor)Tj
2.7439 0 Td
(infiltrating)Tj
4.5241 0 Td
(lymphocytes)Tj
5.2497 0 Td
(\(TIL\))Tj
2.3924 0 Td
(is)Tj
0.8447 0 Td
(a)Tj
-36.4759 -1.2983 Td
(marker)Tj
3.135 0 Td
(of)Tj
1.0148 0 Td
(the)Tj
1.4684 0 Td
(activation)Tj
4.1555 0 Td
(of)Tj
1.0148 0 Td
(the)Tj
1.4684 0 Td
(immune)Tj
3.6283 0 Td
(system)Tj
2.9367 0 Td
(and)Tj
1.7291 0 Td
(is)Tj
0.8504 0 Td
(associated)Tj
4.2519 0 Td
(with)Tj
2.0013 0 Td
(improved)Tj
4.1045 0 Td
(outcome)Tj
-31.7591 -1.3039 Td
([)Tj
0.83 0.64 0.02 0 k
(4)Tj
0 g
(,)Tj
0.83 0.64 0.02 0 k
1.2585 0 Td
(5)Tj
0 g
(].)Tj
1.2643 0 Td
(Indeed,)Tj
3.2371 0 Td
(therapeutic)Tj
4.7282 0 Td
(strategies)Tj
3.9231 0 Td
(to)Tj
1.0261 0 Td
(activate)Tj
3.2542 0 Td
(the)Tj
1.4683 0 Td
(immune)Tj
3.6283 0 Td
(system,)Tj
3.1635 0 Td
(like)Tj
1.6554 0 Td
(those)Tj
2.3357 0 Td
(blocking)Tj
3.6794 0 Td
(the)Tj
-34.6221 -1.2982 Td
(programmed)Tj
5.4765 0 Td
(death)Tj
2.4321 0 Td
(receptor-1)Tj
4.3823 0 Td
(\(PD-1\))Tj
3.0217 0 Td
(or)Tj
1.0942 0 Td
(its)Tj
1.1452 0 Td
(ligand;)Tj
2.9366 0 Td
(or)Tj
1.0999 0 Td
(cytotoxic)Tj
3.8607 0 Td
(T-lymphocyte)Tj
5.8564 0 Td
(associated)Tj
4.2576 0 Td
(pro-)Tj
-35.5632 -1.2983 Td
(tein)Tj
1.7574 0 Td
(4)Tj
0.6917 0 Td
(\(CTLA-4\))Tj
4.2236 0 Td
(receptors,)Tj
4.1442 0 Td
(have)Tj
2.0579 0 Td
(shown)Tj
2.8517 0 Td
(activity)Tj
3.1181 0 Td
(in)Tj
1.0318 0 Td
(several)Tj
2.9366 0 Td
(solid)Tj
2.1317 0 Td
(tumors)Tj
3.1011 0 Td
([)Tj
0.83 0.64 0.02 0 k
(6)Tj
0 g
(].)Tj
1.6044 0 Td
(In)Tj
1.1055 0 Td
(TNBC)Tj
2.8119 0 Td
(these)Tj
-33.5676 -1.2983 Td
(agents)Tj
2.7495 0 Td
(are)Tj
1.4457 0 Td
(currently)Tj
3.8891 0 Td
(in)Tj
1.0375 0 Td
(late)Tj
1.6214 0 Td
(stages)Tj
2.5625 0 Td
(of)Tj
1.0148 0 Td
(development)Tj
5.4085 0 Td
([)Tj
0.83 0.64 0.02 0 k
(7)Tj
0 g
(].)Tj
-18.5328 -1.3039 Td
(Different)Tj
3.8664 0 Td
(cell)Tj
1.559 0 Td
(membrane)Tj
4.5695 0 Td
(proteins)Tj
3.5149 0 Td
(are)Tj
1.4457 0 Td
(associated)Tj
4.2576 0 Td
(with)Tj
1.9955 0 Td
(the)Tj
1.4741 0 Td
(identification)Tj
5.5842 0 Td
(of)Tj
1.0148 0 Td
(neoantigens)Tj
5.0456 0 Td
(and)Tj
-35.5235 -1.2983 Td
(activation)Tj
4.1498 0 Td
(of)Tj
1.0148 0 Td
(effector)Tj
3.2429 0 Td
(T-cells,)Tj
3.1067 0 Td
(or)Tj
1.0998 0 Td
(the)Tj
1.4684 0 Td
(regulation)Tj
4.3086 0 Td
(of)Tj
1.0148 0 Td
(this)Tj
1.6781 0 Td
(activation)Tj
4.1499 0 Td
([)Tj
0.83 0.64 0.02 0 k
(8)Tj
0 g
(].)Tj
1.6044 0 Td
(This)Tj
1.9842 0 Td
(has)Tj
1.5421 0 Td
(been)Tj
2.126 0 Td
(the)Tj
1.4683 0 Td
(case)Tj
1.8595 0 Td
(for)Tj
-35.8183 -1.2982 Td
(antibodies)Tj
4.3596 0 Td
(against)Tj
3.0274 0 Td
(PD1)Tj
1.9899 0 Td
(and)Tj
1.7348 0 Td
(CTLA4,)Tj
3.4129 0 Td
(among)Tj
2.999 0 Td
(others)Tj
2.7043 0 Td
([)Tj
0.83 0.64 0.02 0 k
(8)Tj
0 g
(].)Tj
1.6044 0 Td
(However,)Tj
4.0761 0 Td
(many)Tj
2.4775 0 Td
(other)Tj
2.3471 0 Td
(cell)Tj
1.559 0 Td
(surface)Tj
3.0501 0 Td
(regu-)Tj
-35.3421 -1.3039 Td
(lators)Tj
2.4377 0 Td
(involved)Tj
3.651 0 Td
(in)Tj
1.0318 0 Td
(this)Tj
1.6781 0 Td
(activation)Tj
4.1499 0 Td
(exist)Tj
2.0353 0 Td
(and)Tj
1.7291 0 Td
(have)Tj
2.058 0 Td
(not)Tj
1.576 0 Td
(been)Tj
2.1203 0 Td
(explored.)Tj
3.9288 0 Td
(An)Tj
1.4513 0 Td
(example)Tj
3.5547 0 Td
(includes)Tj
3.5432 0 Td
(the)Tj
-34.9452 -1.2983 Td
(family)Tj
2.7212 0 Td
(of)Tj
1.0035 0 Td
(Human)Tj
3.3108 0 Td
(Leucocyte)Tj
4.2349 0 Td
(Antigens)Tj
3.8041 0 Td
(\(HLA\),)Tj
3.1124 0 Td
(or)Tj
1.0885 0 Td
(the)Tj
1.4627 0 Td
(novel)Tj
2.3924 0 Td
(regulatory)Tj
4.3086 0 Td
(protein)Tj
3.1465 0 Td
(T)Tj
0.822 0 Td
(cell)Tj
1.5534 0 Td
(immunore-)Tj
-32.961 -1.2983 Td
(ceptor)Tj
2.7609 0 Td
(with)Tj
1.9956 0 Td
(Ig)Tj
1.0261 0 Td
(and)Tj
1.7291 0 Td
(ITIM)Tj
2.4038 0 Td
(domains)Tj
3.685 0 Td
(\(TIGIT\))Tj
3.5206 0 Td
([)Tj
0.83 0.64 0.02 0 k
(9)Tj
0 g
(].)Tj
-15.9249 -1.3039 Td
(In)Tj
1.1111 0 Td
(our)Tj
1.6271 0 Td
(study,)Tj
2.6135 0 Td
(by)Tj
1.1792 0 Td
(using)Tj
2.3925 0 Td
(an)Tj
/F12 1 Tf
1.2019 0 Td
[()12()]TJ
1.0148 0 Td
[()10()4()12()4()7()]TJ
/F8 1 Tf
2.1543 0 Td
(approach,)Tj
4.1782 0 Td
(we)Tj
1.3266 0 Td
(aimed)Tj
2.6929 0 Td
(to)Tj
1.0261 0 Td
(identify)Tj
3.2939 0 Td
(genes)Tj
2.4434 0 Td
(that)Tj
1.7802 0 Td
(code)Tj
2.0976 0 Td
(for)Tj
1.389 0 Td
(cell)Tj
-34.7185 -1.2983 Td
(surface)Tj
3.05 0 Td
(proteins)Tj
3.5093 0 Td
(and)Tj
1.7348 0 Td
(then)Tj
2.0182 0 Td
(select)Tj
2.3925 0 Td
(those)Tj
2.3414 0 Td
(involved)Tj
3.6453 0 Td
(in)Tj
1.0375 0 Td
(the)Tj
1.4683 0 Td
(regulation)Tj
4.3086 0 Td
(of)Tj
1.0148 0 Td
(the)Tj
1.4684 0 Td
(immune)Tj
3.6283 0 Td
(system)Tj
2.9367 0 Td
(for)Tj
1.3889 0 Td
(fur-)Tj
-35.943 -1.2982 Td
(ther)Tj
1.8425 0 Td
(evaluation.)Tj
4.5864 0 Td
(We)Tj
1.6044 0 Td
(subsequently)Tj
5.4085 0 Td
(examined)Tj
4.1272 0 Td
(their)Tj
2.1089 0 Td
(prognostic)Tj
4.4844 0 Td
(influence)Tj
3.9175 0 Td
(to)Tj
1.0261 0 Td
(help)Tj
1.9332 0 Td
(identify)Tj
3.2995 0 Td
(patients)Tj
-34.3386 -1.3039 Td
(at)Tj
0.9524 0 Td
(lower)Tj
2.4491 0 Td
(risk)Tj
1.7178 0 Td
(of)Tj
1.0148 0 Td
(relapse)Tj
2.999 0 Td
(and)Tj
1.7291 0 Td
(for)Tj
1.3833 0 Td
(whom)Tj
2.761 0 Td
(treatment)Tj
4.1329 0 Td
(with)Tj
2.0012 0 Td
(chemotherapy)Tj
5.9471 0 Td
(may)Tj
1.9275 0 Td
(not)Tj
1.5761 0 Td
(be)Tj
1.1508 0 Td
(needed.)Tj
ET
Q
q
1 j
1 J
0 w
11.9999 0 0 11.9999 200.0125 183.0047 cm
BT
/F2 1 Tf
1 TL
-0.0033 Tc
0 0 Td
(Material)Tj
3.959 0 Td
(and)Tj
1.989 0 Td
(methods)Tj
/F0 1 Tf
-5.948 -1.5023 Td
(Transcriptomic)Tj
6.7087 0 Td
(and)Tj
1.8661 0 Td
(gene-set)Tj
4.063 0 Td
(enrichment)Tj
5.1119 0 Td
(analyses)Tj
ET
Q
q
1 j
1 J
0 w
10 0 0 10 200.0125 148.0251 cm
BT
/F8 1 Tf
1 TL
-0.004 Tc
0 0 Td
(We)Tj
1.61 0 Td
(used)Tj
2.058 0 Td
(a)Tj
0.6519 0 Td
(public)Tj
2.7099 0 Td
(dataset)Tj
2.9991 0 Td
(\(GEO)Tj
2.5908 0 Td
(DataSet)Tj
3.3165 0 Td
(accession)Tj
3.9742 0 Td
(number:)Tj
3.6396 0 Td
(GDS2250\))Tj
4.388 0 Td
([)Tj
0.83 0.64 0.02 0 k
(10)Tj
0 g
(])Tj
1.8539 0 Td
(of)Tj
1.0148 0 Td
(mRNA)Tj
3.0841 0 Td
(level)Tj
-33.8908 -1.3039 Td
(data)Tj
1.9105 0 Td
(from)Tj
2.2053 0 Td
(normal)Tj
3.1521 0 Td
(breast)Tj
2.6136 0 Td
(tissue)Tj
2.4548 0 Td
(and)Tj
1.7347 0 Td
(basal-like)Tj
3.9855 0 Td
(breast)Tj
2.6136 0 Td
(tumors)Tj
3.1067 0 Td
(to)Tj
1.0205 0 Td
(identify)Tj
3.2995 0 Td
(upregulated)Tj
4.9833 0 Td
(genes.)Tj
-33.0801 -1.2982 Td
(Affymetrix)Tj
4.5807 0 Td
(CEL)Tj
1.9899 0 Td
(files)Tj
1.8028 0 Td
(were)Tj
2.126 0 Td
(downloaded)Tj
5.1534 0 Td
(and)Tj
1.7291 0 Td
(analyzed)Tj
3.702 0 Td
(with)Tj
1.9956 0 Td
(Affymetrix)Tj
4.5807 0 Td
(Transcriptome)Tj
6.1739 0 Td
(Analysis)Tj
-33.8341 -1.2983 Td
(Console)Tj
3.4752 0 Td
(3.0.)Tj
1.6214 0 Td
(We)Tj
1.6101 0 Td
(obtained)Tj
3.7303 0 Td
(genes)Tj
2.4435 0 Td
(with)Tj
1.9956 0 Td
(different)Tj
3.6566 0 Td
(expression)Tj
4.4674 0 Td
(values)Tj
2.6646 0 Td
(from)Tj
2.2053 0 Td
(the)Tj
1.474 0 Td
(two)Tj
1.7065 0 Td
(samples)Tj
3.3845 0 Td
(and)Tj
-34.435 -1.3039 Td
(unregulated)Tj
5.0116 0 Td
(genes)Tj
2.4434 0 Td
(were)Tj
2.1203 0 Td
(defined)Tj
3.2258 0 Td
(as)Tj
1.0148 0 Td
(those)Tj
2.3414 0 Td
(with)Tj
1.9956 0 Td
(a)Tj
0.652 0 Td
(minimum)Tj
4.2916 0 Td
(2)Tj
0.6973 0 Td
(fold)Tj
1.7858 0 Td
(differential)Tj
4.6035 0 Td
(expression)Tj
-30.1831 -1.2983 Td
(between)Tj
3.5262 0 Td
(normal)Tj
3.1465 0 Td
(and)Tj
1.7291 0 Td
(malignant)Tj
4.2859 0 Td
(tissue.)Tj
2.6816 0 Td
(We)Tj
1.6101 0 Td
(selected)Tj
3.3448 0 Td
(this)Tj
1.6781 0 Td
(cut-off)Tj
2.9027 0 Td
(level)Tj
2.0126 0 Td
(to)Tj
1.0261 0 Td
(include)Tj
3.1861 0 Td
(a)Tj
0.652 0 Td
(large)Tj
2.16 0 Td
(number)Tj
ET
Q
q
1 j
1 J
0 w
576 737.1 m
36 737.1 l
36 737.6 l
576 737.6 l
f*
36 741.2598 107.1496 23.6976 re
W* n
q
107.0929 0 0 23.6409 36 741.3165 cm
q
/I0 Do
Q
Q
Q
q
0 0 612 792 re
W* n
1 j
1 J
0 w
7.9999 0 0 7.9999 240.0944 745.7952 cm
BT
/F0 1 Tf
1 TL
-0.005 Tc
0 0 Td
(Transcript)Tj
4.3724 0 Td
(omic)Tj
2.3032 0 Td
(immunolog)Tj
4.8048 0 Td
(ic)Tj
0.9212 0 Td
(signature)Tj
4.2591 0 Td
(associat)Tj
3.6 0 Td
(ed)Tj
1.3111 0 Td
(with)Tj
1.9701 0 Td
(clinical)Tj
3.1464 0 Td
(outcome)Tj
3.9969 0 Td
(in)Tj
0.978 0 Td
(basal-like)Tj
4.3583 0 Td
(breast)Tj
2.948 0 Td
(tumors)Tj
ET
Q
q
1 j
1 J
0 w
36 48.0002 m
576 48.0002 l
576 47.5002 l
36 47.5002 l
f*
0.83 0.64 0.02 0 k
81.5811 34.9228 m
237.8835 34.9228 l
h
f*
0 g
7.9999 0 0 7.9999 36 36 cm
BT
/F0 1 Tf
1 TL
-0.005 Tc
0 0 Td
(PLOS)Tj
2.8559 0 Td
(ONE)Tj
2.3669 0 Td
(|)Tj
0.83 0.64 0.02 0 k
0.4748 0 Td
(https://doi.or)Tj
5.4142 0 Td
(g/10.137)Tj
3.8198 0 Td
(1/journal.po)Tj
5.1236 0 Td
(ne.01751)Tj
4.089 0 Td
(28)Tj
0 g
2.0906 0 Td
(May)Tj
2.0906 0 Td
(4,)Tj
1.0346 0 Td
(2017)Tj
35.7806 0 Td
(2)Tj
0.7654 0 Td
(/)Tj
0.496 0 Td
(10)Tj
/F10 1 Tf
-0.025 Tc
-66.402 84.0904 Td
(Competitive)Tj
4.3866 0 Td
(ness)Tj
1.9559 0 Td
(of)Tj
0.9496 0 Td
(Spain)Tj
2.3103 0 Td
(\(BFU2015-)Tj
4.0394 0 Td
(71371-R\),)Tj
4.0181 0 Td
(the)Tj
-17.6599 -1.3748 Td
(Instituto)Tj
3.274 0 Td
(de)Tj
1.1197 0 Td
(Salud)Tj
2.3032 0 Td
(Carlos)Tj
2.5653 0 Td
(III)Tj
0.9851 0 Td
(through)Tj
3.1465 0 Td
(the)Tj
1.3748 0 Td
(Spanis)Tj
2.5016 0 Td
(h)Tj
-17.2702 -1.3749 Td
(Cancer)Tj
2.7921 0 Td
(Centers)Tj
3.0473 0 Td
(Networ)Tj
2.6787 0 Td
(k)Tj
0.6449 0 Td
(Program)Tj
3.4796 0 Td
(\(RD12/003)Tj
4.1032 0 Td
(6/)Tj
-16.7458 -1.3748 Td
(0003\))Tj
2.4236 0 Td
(and)Tj
1.5874 0 Td
(CIBERONC,)Tj
4.5071 0 Td
(the)Tj
1.3748 0 Td
(scientific)Tj
3.4654 0 Td
(foundation)Tj
4.1882 0 Td
(of)Tj
-17.5465 -1.3748 Td
(the)Tj
1.3677 0 Td
(AECC)Tj
2.2748 0 Td
(and)Tj
1.5874 0 Td
(the)Tj
1.3677 0 Td
(CRIS)Tj
2.1119 0 Td
(Foundation)Tj
4.3512 0 Td
(\(to)Tj
1.2614 0 Td
(AP\).)Tj
1.8 0 Td
(The)Tj
-16.1221 -1.3748 Td
(work)Tj
2.0622 0 Td
(carried)Tj
2.7638 0 Td
(out)Tj
1.4244 0 Td
(in)Tj
0.8858 0 Td
(our)Tj
1.4741 0 Td
(laboratories)Tj
4.585 0 Td
(receive)Tj
2.6008 0 Td
(d)Tj
-15.7961 -1.3748 Td
(support)Tj
3.0968 0 Td
(from)Tj
2.0126 0 Td
(the)Tj
1.3678 0 Td
(European)Tj
3.7346 0 Td
(Community)Tj
4.5497 0 Td
(through)Tj
-14.7615 -1.3748 Td
(the)Tj
1.3677 0 Td
(regional)Tj
3.1819 0 Td
(developm)Tj
3.6284 0 Td
(ent)Tj
1.3677 0 Td
(funding)Tj
3.0402 0 Td
(program)Tj
-12.5859 -1.3748 Td
(\(FEDER\).)Tj
3.6 0 Td
(The)Tj
1.5874 0 Td
(funders)Tj
3.0473 0 Td
(had)Tj
1.5874 0 Td
(no)Tj
1.1693 0 Td
(role)Tj
1.6157 0 Td
(in)Tj
0.8859 0 Td
(study)Tj
2.2677 0 Td
(design,)Tj
-15.7607 -1.3748 Td
(data)Tj
1.7929 0 Td
(collection)Tj
3.7347 0 Td
(and)Tj
1.5945 0 Td
(analysis)Tj
2.9622 0 Td
(,)Tj
0.4464 0 Td
(decision)Tj
3.2883 0 Td
(to)Tj
0.9496 0 Td
(publish,)Tj
3.1465 0 Td
(or)Tj
-17.9151 -1.3749 Td
(preparation)Tj
4.4433 0 Td
(of)Tj
0.9496 0 Td
(the)Tj
1.3677 0 Td
(manuscript.)Tj
/F9 1 Tf
-6.7606 -2.126 Td
(Competing)Tj
4.3795 0 Td
(interests)Tj
3.3307 0 Td
(:)Tj
/F10 1 Tf
0.4819 0 Td
(The)Tj
1.5875 0 Td
(authors)Tj
3.0401 0 Td
(have)Tj
1.963 0 Td
(declared)Tj
-14.7827 -1.3748 Td
(that)Tj
1.6228 0 Td
(no)Tj
1.1693 0 Td
(competing)Tj
4.1599 0 Td
(interests)Tj
ET
endstream
endobj
30 0 obj
<>stream
endstream
endobj
31 0 obj
<>stream
endstream
endobj
32 0 obj
<>stream
endstream
endobj
33 0 obj
<>stream
endstream
endobj
34 0 obj
<>stream
endstream
endobj
35 0 obj
<>stream
endstream
endobj
36 0 obj
<>stream
endstream
endobj
37 0 obj
<>stream
endstream
endobj
38 0 obj
<>stream
endstream
endobj
39 0 obj
<>stream
endstream
endobj
40 0 obj
<>stream
endstream
endobj
41 0 obj
<>stream
endstream
endobj
42 0 obj
<>stream
BT
10.3394 66.8414 Td
(exist.)Tj
ET
Q
endstream
endobj
43 0 obj
<>/XObject<>>>/CropBox[0 0 612 792]/MediaBox[0 0 612 792]/Parent 12 0 R/Annots 44 0 R/Contents 45 0 R/TrimBox[0 0 612 792]>>
endobj
44 0 obj
[46 0 R 47 0 R 48 0 R 49 0 R 50 0 R 51 0 R 52 0 R 53 0 R 54 0 R 55 0 R 56 0 R 57 0 R 58 0 R 59 0 R 60 0 R 61 0 R 62 0 R]
endobj
46 0 obj
<>/Border[0 0 0]/A 63 0 R>>
endobj
63 0 obj
<>
endobj
47 0 obj
<>/Border[0 0 0]/A 64 0 R>>
endobj
64 0 obj
<>
endobj
48 0 obj
<>/Border[0 0 0]/A 65 0 R>>
endobj
65 0 obj
<>
endobj
49 0 obj
<>/Border[0 0 0]/Dest(Rpone.0175128.ref011)>>
endobj
50 0 obj
<>/Border[0 0 0]/Dest(Rpone.0175128.ref012)>>
endobj
51 0 obj
<>/Border[0 0 0]/Dest(Rpone.0175128.ref013)>>
endobj
52 0 obj
<>/Border[0 0 0]/Dest(Rpone.0175128.ref014)>>
endobj
53 0 obj
<>/Border[0 0 0]/A 66 0 R>>
endobj
66 0 obj
<>
endobj
54 0 obj
<>/Border[0 0 0]/Dest(Rpone.0175128.ref015)>>
endobj
55 0 obj
<>/Border[0 0 0]/Dest(Rpone.0175128.ref010)>>
endobj
56 0 obj
<>/Border[0 0 0]/A 67 0 R>>
endobj
67 0 obj
<>
endobj
57 0 obj
<>/Border[0 0 0]/Dest(Rpone.0175128.g001)>>
endobj
58 0 obj
<>/Border[0 0 0]/Dest(Rpone.0175128.s002)>>
endobj
59 0 obj
<>/Border[0 0 0]/Dest(Rpone.0175128.g001)>>
endobj
60 0 obj
<>/Border[0 0 0]/Dest(Rpone.0175128.s003)>>
endobj
61 0 obj
<>/Border[0 0 0]/Dest(Rpone.0175128.ref011)>>
endobj
62 0 obj
<>/Border[0 0 0]/A 68 0 R>>
endobj
68 0 obj
<>
endobj
45 0 obj
[69 0 R 70 0 R 71 0 R 72 0 R 73 0 R 74 0 R 75 0 R 76 0 R 77 0 R 78 0 R 79 0 R 80 0 R 81 0 R 82 0 R 83 0 R]
endobj
69 0 obj
<>stream
q
0.83 0.64 0.02 0 k
307.8425 693.2976 m
406.9984 693.2976 l
h
f*
285.1654 667.3323 m
364.0819 667.3323 l
h
f*
383.7543 593.9717 m
480.4157 593.9717 l
h
f*
510.2929 580.989 m
519.8173 580.989 l
h
f*
339.3071 541.9843 m
348.7748 541.9843 l
h
f*
507.3449 476.9575 m
516.8693 476.9575 l
h
f*
276.9449 463.9748 m
286.4693 463.9748 l
h
f*
338.3433 377.6315 m
417.6 377.6315 l
h
f*
426.6142 377.6315 m
436.1386 377.6315 l
h
f*
342.7087 285.2787 m
352.2331 285.2787 l
h
f*
288 259.2567 m
387.1559 259.2567 l
h
f*
420.6047 220.252 m
446.9669 220.252 l
h
f*
313.3417 207.2693 m
347.2441 207.2693 l
h
f*
518.1732 133.9087 m
543.5717 133.9087 l
h
f*
200.0126 120.926 m
233.915 120.926 l
h
f*
526.5071 107.9433 m
536.0315 107.9433 l
h
f*
0 g
1 j
1 J
0 w
10 0 0 10 200.0125 707.4141 cm
BT
/F8 1 Tf
1 TL
-0.004 Tc
0 0 Td
(of)Tj
1.0147 0 Td
(genes.)Tj
2.6646 0 Td
(The)Tj
1.7858 0 Td
(list)Tj
1.389 0 Td
(of)Tj
1.0148 0 Td
(genes)Tj
2.4434 0 Td
(was)Tj
1.7008 0 Td
(analyzed)Tj
3.702 0 Td
(using)Tj
2.3868 0 Td
(gene-set)Tj
3.5149 0 Td
(enrichment)Tj
4.8699 0 Td
(analyses)Tj
3.4866 0 Td
(using)Tj
2.3868 0 Td
(DAVID)Tj
3.4129 0 Td
(Bio-)Tj
-35.773 -1.3039 Td
(informatics)Tj
4.8018 0 Td
(Resources)Tj
4.2406 0 Td
(6.8)Tj
1.4003 0 Td
(\()Tj
0.83 0.64 0.02 0 k
(https://david.ncifcrf.gov/)Tj
0 g
(\))Tj
10.8113 0 Td
(in)Tj
1.0375 0 Td
(order)Tj
2.4207 0 Td
(to)Tj
1.0262 0 Td
(identify)Tj
3.2938 0 Td
(functions)Tj
3.9912 0 Td
(of)Tj
1.0148 0 Td
(these)Tj
-34.0382 -1.2982 Td
(genes.)Tj
2.6645 0 Td
(We)Tj
1.6101 0 Td
(used)Tj
2.0579 0 Td
(an)Tj
1.2076 0 Td
(adjusted)Tj
3.5716 0 Td
(p-value)Tj
3.1748 0 Td
(of)Tj
1.0148 0 Td
(less)Tj
1.6157 0 Td
(than)Tj
2.0239 0 Td
(0.05)Tj
1.8766 0 Td
(to)Tj
1.0204 0 Td
(select)Tj
2.3981 0 Td
(the)Tj
1.4684 0 Td
(enriched)Tj
3.736 0 Td
(gene)Tj
2.0806 0 Td
(sets.)Tj
1.8879 0 Td
(Data)Tj
2.1203 0 Td
(con-)Tj
-35.5292 -1.2983 Td
(tained)Tj
2.7155 0 Td
(at)Tj
0.9525 0 Td
(Oncomine)Tj
4.507 0 Td
(\()Tj
0.83 0.64 0.02 0 k
(www.oncomine.org)Tj
0 g
(\))Tj
8.793 0 Td
(was)Tj
1.6951 0 Td
(used)Tj
2.0636 0 Td
(to)Tj
1.0262 0 Td
(independently)Tj
5.9754 0 Td
(confirm)Tj
3.4412 0 Td
(the)Tj
1.474 0 Td
(difference)Tj
-32.6435 -1.2983 Td
(among)Tj
2.9933 0 Td
(the)Tj
1.4684 0 Td
(selected)Tj
3.3505 0 Td
(genes.)Tj
ET
Q
q
1 j
1 J
0 w
11.9999 0 0 11.9999 200.0125 625.0393 cm
BT
/F0 1 Tf
1 TL
-0.0033 Tc
0 0 Td
(Outcome)Tj
4.2425 0 Td
(analyses)Tj
ET
Q
q
1 j
1 J
0 w
10 0 0 10 200.0125 608.0314 cm
BT
/F8 1 Tf
1 TL
-0.004 Tc
0 0 Td
(The)Tj
1.7801 0 Td
(KM)Tj
1.7858 0 Td
(Plotter)Tj
2.9253 0 Td
(Online)Tj
2.9991 0 Td
(Tool)Tj
2.0919 0 Td
(was)Tj
1.7008 0 Td
(used)Tj
2.058 0 Td
(to)Tj
1.0261 0 Td
(analyze)Tj
3.1748 0 Td
(the)Tj
1.4683 0 Td
(relationship)Tj
4.989 0 Td
(between)Tj
3.5319 0 Td
(the)Tj
1.4683 0 Td
(gene)Tj
2.0807 0 Td
(expression)Tj
-33.0801 -1.2982 Td
(and)Tj
1.7291 0 Td
(patient)Tj
3.0047 0 Td
(clinical)Tj
3.0784 0 Td
(outcome)Tj
3.7247 0 Td
(in)Tj
1.0375 0 Td
(breast)Tj
2.6135 0 Td
(cancer)Tj
2.846 0 Td
(\()Tj
0.83 0.64 0.02 0 k
(http://www.kmplot.com)Tj
0 g
(\);)Tj
10.7885 0 Td
(this)Tj
1.6781 0 Td
(public)Tj
2.7043 0 Td
(database)Tj
-33.2048 -1.2983 Td
(allowed)Tj
3.2881 0 Td
(us)Tj
1.1055 0 Td
(to)Tj
1.0262 0 Td
(investigate)Tj
4.4617 0 Td
(overall)Tj
2.9026 0 Td
(survival)Tj
3.3392 0 Td
(\(OS\))Tj
2.1203 0 Td
(and)Tj
1.7291 0 Td
(relapse-free)Tj
4.8586 0 Td
(survival)Tj
3.3335 0 Td
(\(RFS\))Tj
2.5285 0 Td
([)Tj
0.83 0.64 0.02 0 k
(11)Tj
0 g
(].)Tj
2.0749 0 Td
(Definitions)Tj
-32.7682 -1.3039 Td
(of)Tj
1.0147 0 Td
(breast)Tj
2.6136 0 Td
(cancer)Tj
2.8459 0 Td
(subgroups)Tj
4.3654 0 Td
(reported)Tj
3.6566 0 Td
(in)Tj
1.0375 0 Td
(this)Tj
1.6724 0 Td
(online)Tj
2.761 0 Td
(tool)Tj
1.7801 0 Td
(are:)Tj
1.6724 0 Td
(triple)Tj
2.3471 0 Td
(negative)Tj
3.532 0 Td
(\(ER-/HER2-\),)Tj
5.7826 0 Td
(lumi-)Tj
-35.0813 -1.2983 Td
(nal)Tj
1.4456 0 Td
(A)Tj
0.9071 0 Td
(\(ESR1+/HER2-/MK167-low\),)Tj
12.0698 0 Td
(luminal)Tj
3.3109 0 Td
(B)Tj
0.7993 0 Td
(\(ESR1+/HER2-/MK167-)Tj
9.8532 0 Td
(high)Tj
2.0069 0 Td
(or)Tj
1.0942 0 Td
(ESR1+/HER2)Tj
-31.487 -1.2982 Td
(+\),)Tj
1.3662 0 Td
(and)Tj
1.7292 0 Td
(basal-like)Tj
3.9855 0 Td
(\(ESR1-/HER2-\))Tj
6.5083 0 Td
([)Tj
0.83 0.64 0.02 0 k
(12)Tj
0 g
(].)Tj
2.0749 0 Td
(Analysis)Tj
3.5773 0 Td
(was)Tj
1.7008 0 Td
(carried)Tj
3.0387 0 Td
(out)Tj
1.5477 0 Td
(in)Tj
1.0375 0 Td
(multiple)Tj
3.5659 0 Td
(steps.)Tj
2.4095 0 Td
(First,)Tj
2.2677 0 Td
(we)Tj
-34.8092 -1.3039 Td
(restricted)Tj
3.9854 0 Td
(analysis)Tj
3.3279 0 Td
(to)Tj
1.0205 0 Td
(the)Tj
1.474 0 Td
(basal-like)Tj
3.9854 0 Td
(breast)Tj
2.6136 0 Td
(cancer)Tj
2.8459 0 Td
(subgroup.)Tj
4.2293 0 Td
(Then,)Tj
2.5568 0 Td
(the)Tj
1.4684 0 Td
(association)Tj
4.6261 0 Td
(between)Tj
3.5319 0 Td
(the)Tj
-35.6652 -1.2983 Td
(genes)Tj
2.4377 0 Td
(of)Tj
1.0148 0 Td
(interest)Tj
3.2145 0 Td
(and)Tj
1.7291 0 Td
(outcome)Tj
3.7304 0 Td
(was)Tj
1.6951 0 Td
(explored)Tj
3.702 0 Td
(after)Tj
2.0353 0 Td
(selection)Tj
3.719 0 Td
(of)Tj
1.0148 0 Td
(the)Tj
1.4683 0 Td
(specific)Tj
3.1918 0 Td
(probe)Tj
2.5455 0 Td
(utilized)Tj
3.1918 0 Td
(ini-)Tj
-34.6901 -1.2983 Td
(tially.)Tj
2.3924 0 Td
(Finally,)Tj
3.1691 0 Td
(we)Tj
1.3266 0 Td
(evaluated)Tj
3.9912 0 Td
(all)Tj
1.1451 0 Td
(immunologic-related)Tj
8.691 0 Td
(genes)Tj
2.4435 0 Td
(and)Tj
1.7291 0 Td
(their)Tj
2.1089 0 Td
(association)Tj
4.6318 0 Td
(with)Tj
1.9956 0 Td
(both)Tj
2.0579 0 Td
(RFS)Tj
-35.6822 -1.2982 Td
(and)Tj
1.7291 0 Td
(OS)Tj
1.44 0 Td
(in)Tj
1.0374 0 Td
(basal)Tj
2.1997 0 Td
(like)Tj
1.6554 0 Td
(breast)Tj
2.6136 0 Td
(cancer,)Tj
3.0727 0 Td
(and)Tj
1.7291 0 Td
(confirmed)Tj
4.3937 0 Td
(these)Tj
2.2564 0 Td
(data)Tj
1.9162 0 Td
(in)Tj
1.0318 0 Td
(the)Tj
1.474 0 Td
(Oncomine)Tj
4.5014 0 Td
(dataset.)Tj
-29.8543 -1.304 Td
(We)Tj
1.61 0 Td
(also)Tj
1.7688 0 Td
(confirmed)Tj
4.3994 0 Td
(the)Tj
1.4683 0 Td
(results)Tj
2.8063 0 Td
(using)Tj
2.3924 0 Td
(two)Tj
1.7065 0 Td
(additional)Tj
4.2803 0 Td
(datasets:)Tj
3.5829 0 Td
(METABRIC)Tj
5.1817 0 Td
([)Tj
0.83 0.64 0.02 0 k
(13)Tj
0 g
(])Tj
1.8539 0 Td
(and)Tj
1.7291 0 Td
(the)Tj
-33.9758 -1.2982 Td
(GSE25066)Tj
4.3596 0 Td
(dataset)Tj
2.9934 0 Td
([)Tj
0.83 0.64 0.02 0 k
(14)Tj
0 g
(].)Tj
2.0806 0 Td
(METABRIC)Tj
5.1817 0 Td
(contains)Tj
3.6056 0 Td
(information)Tj
5.074 0 Td
(about)Tj
2.4945 0 Td
(331)Tj
1.6497 0 Td
(basal-like)Tj
3.9855 0 Td
(tumors)Tj
3.1068 0 Td
(with)Tj
-34.5314 -1.2983 Td
(data)Tj
1.9105 0 Td
(available)Tj
3.668 0 Td
(for)Tj
1.389 0 Td
(OS,)Tj
1.6667 0 Td
(while)Tj
2.3698 0 Td
(the)Tj
1.4683 0 Td
(GSE25066)Tj
4.3597 0 Td
(dataset)Tj
2.9933 0 Td
(comprises)Tj
4.2747 0 Td
(RFS)Tj
1.8425 0 Td
(data)Tj
1.9162 0 Td
(on)Tj
1.2756 0 Td
(142)Tj
1.644 0 Td
(basal-like)Tj
-30.7783 -1.3039 Td
(tumors.)Tj
ET
Q
q
1 j
1 J
0 w
11.9999 0 0 11.9999 200.0125 408.6992 cm
BT
/F0 1 Tf
1 TL
-0.0033 Tc
0 0 Td
(Evaluation)Tj
4.8283 0 Td
(of)Tj
1.0441 0 Td
(molecular)Tj
4.4977 0 Td
(alterations)Tj
ET
Q
q
1 j
1 J
0 w
10 0 0 10 200.0125 391.6913 cm
BT
/F8 1 Tf
1 TL
-0.004 Tc
0 0 Td
(To)Tj
1.3379 0 Td
(explore)Tj
3.1748 0 Td
(the)Tj
1.4683 0 Td
(presence)Tj
3.7134 0 Td
(of)Tj
1.0148 0 Td
(mutations,)Tj
4.507 0 Td
(deletions)Tj
3.8211 0 Td
(or)Tj
1.0998 0 Td
(amplifications)Tj
5.8961 0 Td
(in)Tj
1.0374 0 Td
(the)Tj
1.4684 0 Td
(identified)Tj
4.0592 0 Td
(genes)Tj
2.4434 0 Td
(we)Tj
-35.0416 -1.2982 Td
(used)Tj
2.0579 0 Td
(data)Tj
1.9162 0 Td
(contained)Tj
4.1952 0 Td
(at)Tj
0.9525 0 Td
(cBioportal)Tj
4.371 0 Td
(\()Tj
0.83 0.64 0.02 0 k
(www.cbioportal.org)Tj
0 g
(\))Tj
8.827 0 Td
([)Tj
0.83 0.64 0.02 0 k
(15)Tj
0 g
(].)Tj
ET
Q
q
1 j
1 J
0 w
11.9999 0 0 11.9999 200.0125 348.3779 cm
BT
/F2 1 Tf
1 TL
-0.0033 Tc
0 0 Td
(Results)Tj
/F0 1 Tf
0 -1.5023 Td
(Identification)Tj
5.7591 0 Td
(of)Tj
1.0488 0 Td
(upregulated)Tj
5.4284 0 Td
(genes)Tj
2.9102 0 Td
(coding)Tj
3.1229 0 Td
(for)Tj
1.3748 0 Td
(membrane)Tj
4.9512 0 Td
(cell)Tj
1.6961 0 Td
(surface)Tj
-26.2915 -1.167 Td
(proteins)Tj
ET
Q
q
1 j
1 J
0 w
10 0 0 10 200.0125 299.3385 cm
BT
/F8 1 Tf
1 TL
-0.004 Tc
0 0 Td
(To)Tj
1.3379 0 Td
(identify)Tj
3.2938 0 Td
(upregulated)Tj
4.9833 0 Td
(genes)Tj
2.4435 0 Td
(in)Tj
1.0318 0 Td
(TNBC)Tj
2.8119 0 Td
(we)Tj
1.3266 0 Td
(analyzed)Tj
3.702 0 Td
(data)Tj
1.9163 0 Td
(from)Tj
2.2053 0 Td
(a)Tj
0.652 0 Td
(public)Tj
2.7099 0 Td
(GEO)Tj
2.2507 0 Td
(Dataset)Tj
3.2088 0 Td
(\(acces-)Tj
-33.8738 -1.2982 Td
(sion)Tj
1.9048 0 Td
(number:)Tj
3.6397 0 Td
(GDS2250/GSE3744\))Tj
8.3848 0 Td
([)Tj
0.83 0.64 0.02 0 k
(10)Tj
0 g
(].)Tj
2.075 0 Td
(Using)Tj
2.5965 0 Td
(a)Tj
0.6576 0 Td
(minimum)Tj
4.286 0 Td
(fold)Tj
1.7915 0 Td
(change)Tj
3.0443 0 Td
(of)Tj
1.0148 0 Td
(2,)Tj
0.9185 0 Td
(we)Tj
1.3266 0 Td
(selected)Tj
3.3505 0 Td
(1564)Tj
-34.9906 -1.2983 Td
(upregulated)Tj
4.9832 0 Td
(genes.)Tj
2.6646 0 Td
(We)Tj
1.61 0 Td
(evaluated)Tj
3.9912 0 Td
(these)Tj
2.2507 0 Td
(genes)Tj
2.4434 0 Td
(using)Tj
2.3868 0 Td
(functional)Tj
4.3143 0 Td
(genomics)Tj
4.0308 0 Td
(with)Tj
2.0013 0 Td
(David)Tj
2.6362 0 Td
(Bioinfor-)Tj
-33.3125 -1.3039 Td
(matics)Tj
2.8232 0 Td
(Resources)Tj
4.2406 0 Td
(6.8)Tj
1.3947 0 Td
(\()Tj
0.83 0.64 0.02 0 k
(https://david.ncifcrf.gov/)Tj
0 g
(\).)Tj
11.0437 0 Td
(As)Tj
1.2642 0 Td
(genes)Tj
2.4378 0 Td
(that)Tj
1.7802 0 Td
(code)Tj
2.1033 0 Td
(for)Tj
1.3833 0 Td
(proteins)Tj
3.5149 0 Td
(that)Tj
1.7801 0 Td
(are)Tj
1.4457 0 Td
(at)Tj
0.9524 0 Td
(the)Tj
-36.1641 -1.2983 Td
(plasma)Tj
3.033 0 Td
(membrane)Tj
4.5638 0 Td
(can)Tj
1.627 0 Td
(be)Tj
1.1509 0 Td
(involved)Tj
3.651 0 Td
(in)Tj
1.0318 0 Td
(several)Tj
2.9367 0 Td
(functions)Tj
3.9911 0 Td
(we)Tj
1.3266 0 Td
(extracted)Tj
3.8835 0 Td
(different)Tj
3.6566 0 Td
(functions)Tj
-30.852 -1.2982 Td
(including)Tj
4.0421 0 Td
(cell)Tj
1.5591 0 Td
(differentiation,)Tj
6.2021 0 Td
(communication,)Tj
6.8372 0 Td
(adhesion,)Tj
4.0421 0 Td
(transmembrane)Tj
6.582 0 Td
(transport)Tj
3.9232 0 Td
(and)Tj
1.7348 0 Td
(trans-)Tj
-34.9226 -1.3039 Td
(membrane)Tj
4.5637 0 Td
(receptor)Tj
3.5603 0 Td
(tyrosine)Tj
3.4469 0 Td
(kinase)Tj
2.7553 0 Td
(signaling)Tj
3.821 0 Td
(pathway)Tj
3.5717 0 Td
(\()Tj
0.83 0.64 0.02 0 k
(Fig)Tj
1.8198 0 Td
(1A)Tj
0 g
(\).)Tj
1.9446 0 Td
(A)Tj
0.9014 0 Td
(total)Tj
2.0069 0 Td
(of)Tj
1.0148 0 Td
(934)Tj
1.6441 0 Td
(genes)Tj
2.4434 0 Td
(were)Tj
-33.4939 -1.2983 Td
(included)Tj
3.7133 0 Td
(in)Tj
1.0318 0 Td
(these)Tj
2.2564 0 Td
(functions)Tj
3.9911 0 Td
(\()Tj
0.83 0.64 0.02 0 k
(S1)Tj
1.5081 0 Td
(Table)Tj
0 g
(\).)Tj
ET
Q
q
1 j
1 J
0 w
11.9999 0 0 11.9999 200.0125 178.0157 cm
BT
/F0 1 Tf
1 TL
-0.0033 Tc
0 0 Td
(Selection)Tj
4.2803 0 Td
(of)Tj
1.0441 0 Td
(immune)Tj
3.737 0 Td
(genes)Tj
2.9103 0 Td
(linked)Tj
2.7921 0 Td
(with)Tj
1.9749 0 Td
(outcome)Tj
ET
Q
q
1 j
1 J
0 w
10 0 0 10 200.0125 161.0078 cm
BT
/F8 1 Tf
1 TL
-0.004 Tc
0 0 Td
(Using)Tj
2.5965 0 Td
(information)Tj
5.074 0 Td
(from)Tj
2.211 0 Td
(genes)Tj
2.4377 0 Td
(that)Tj
1.7802 0 Td
(code)Tj
2.1033 0 Td
(for)Tj
1.3833 0 Td
(proteins)Tj
3.5149 0 Td
(at)Tj
0.9525 0 Td
(the)Tj
1.4683 0 Td
(cell)Tj
1.559 0 Td
(membrane,)Tj
4.7962 0 Td
(we)Tj
1.3266 0 Td
(explored)Tj
3.7021 0 Td
(only)Tj
-34.9056 -1.2982 Td
(those)Tj
2.3357 0 Td
(involved)Tj
3.651 0 Td
(in)Tj
1.0375 0 Td
(immunological)Tj
6.2985 0 Td
(processes)Tj
3.9685 0 Td
(that)Tj
1.7745 0 Td
(are)Tj
1.4513 0 Td
(associated)Tj
4.2576 0 Td
(with)Tj
1.9956 0 Td
(outcome,)Tj
3.9514 0 Td
(and)Tj
1.7292 0 Td
(confirmed)Tj
-32.4508 -1.3039 Td
(their)Tj
2.1089 0 Td
(upregulated)Tj
4.9833 0 Td
(expression)Tj
4.4617 0 Td
(in)Tj
1.0375 0 Td
(breast)Tj
2.6135 0 Td
(cancer)Tj
2.846 0 Td
(using)Tj
2.3867 0 Td
(data)Tj
1.9162 0 Td
(available)Tj
3.668 0 Td
(at)Tj
0.9525 0 Td
(Oncomine)Tj
4.5014 0 Td
(\()Tj
0.83 0.64 0.02 0 k
(Fig)Tj
1.8198 0 Td
(1B)Tj
0 g
1.2756 0 Td
(and)Tj
0.83 0.64 0.02 0 k
-34.5711 -1.2983 Td
(S2)Tj
1.1678 0 Td
(Table)Tj
0 g
(\).)Tj
3.0104 0 Td
(A)Tj
0.9014 0 Td
(total)Tj
2.0069 0 Td
(of)Tj
1.0148 0 Td
(16)Tj
1.1679 0 Td
(genes)Tj
2.4434 0 Td
(were)Tj
2.1203 0 Td
(identified,)Tj
4.286 0 Td
(but)Tj
1.5534 0 Td
(only)Tj
1.9785 0 Td
(ten)Tj
1.4911 0 Td
(confirmed)Tj
4.3936 0 Td
(as)Tj
1.0148 0 Td
(upregulated)Tj
4.9833 0 Td
(using)Tj
-33.5336 -1.2983 Td
(data)Tj
1.9105 0 Td
(from)Tj
2.2053 0 Td
(Oncomine)Tj
4.5071 0 Td
(and)Tj
1.7291 0 Td
(linked)Tj
2.7326 0 Td
(with)Tj
1.9956 0 Td
(outcome.)Tj
3.9514 0 Td
(Using)Tj
2.5966 0 Td
(the)Tj
1.474 0 Td
(online)Tj
2.7609 0 Td
(tool)Tj
1.7745 0 Td
(KM)Tj
1.7858 0 Td
(plotter)Tj
2.8856 0 Td
([)Tj
0.83 0.64 0.02 0 k
(11)Tj
0 g
(])Tj
1.8482 0 Td
(and)Tj
-34.1572 -1.3039 Td
(making)Tj
3.2484 0 Td
(the)Tj
1.4684 0 Td
(analyses)Tj
3.4866 0 Td
(for)Tj
1.3833 0 Td
(those)Tj
2.3414 0 Td
(ten)Tj
1.4853 0 Td
(genes)Tj
2.4435 0 Td
(we)Tj
1.3266 0 Td
(observed)Tj
3.7984 0 Td
(that,)Tj
2.0012 0 Td
(CD300A,)Tj
3.9572 0 Td
(CD6,)Tj
2.3187 0 Td
(DAPP1,)Tj
3.4639 0 Td
(TLR6,)Tj
-32.7229 -1.2982 Td
(CSF2RA)Tj
3.668 0 Td
(and)Tj
1.7291 0 Td
(BTN2A2)Tj
3.7814 0 Td
(were)Tj
2.1259 0 Td
(associated)Tj
4.252 0 Td
(with)Tj
2.0012 0 Td
(improved)Tj
4.1046 0 Td
(RFS)Tj
1.8482 0 Td
(only,)Tj
2.1996 0 Td
(while)Tj
2.3698 0 Td
(HLA-C,)Tj
3.4469 0 Td
(HLA-F,)Tj
ET
Q
q
1 j
1 J
0 w
576 737.1 m
36 737.1 l
36 737.6 l
576 737.6 l
f*
36 741.2598 107.1496 23.6976 re
W* n
q
107.0929 0 0 23.6409 36 741.3165 cm
q
/I0 Do
Q
Q
Q
q
0 0 612 792 re
W* n
1 j
1 J
0 w
7.9999 0 0 7.9999 240.0944 745.7952 cm
BT
/F0 1 Tf
1 TL
-0.005 Tc
0 0 Td
(Transcript)Tj
4.3724 0 Td
(omic)Tj
2.3032 0 Td
(immunolog)Tj
4.8048 0 Td
(ic)Tj
0.9212 0 Td
(signature)Tj
4.2591 0 Td
(associat)Tj
3.6 0 Td
(ed)Tj
1.3111 0 Td
(with)Tj
1.9701 0 Td
(clinical)Tj
3.1464 0 Td
(outcome)Tj
3.9969 0 Td
(in)Tj
0.978 0 Td
(basal-like)Tj
4.3583 0 Td
(breast)Tj
2.948 0 Td
(tumors)Tj
ET
Q
q
1 j
1 J
0 w
36 48.0002 m
576 48.0002 l
576 47.5002 l
36 47.5002 l
f*
0.83 0.64 0.02 0 k
81.5811 34.9228 m
237.8835 34.9228 l
h
f*
0 g
7.9999 0 0 7.9999 36 36 cm
BT
/F0 1 Tf
1 TL
-0.005 Tc
0 0 Td
(PLOS)Tj
2.8559 0 Td
(ONE)Tj
2.3669 0 Td
(|)Tj
0.83 0.64 0.02 0 k
0.4748 0 Td
(https://doi.or)Tj
5.4142 0 Td
(g/10.137)Tj
3.8198 0 Td
(1/journal.po)Tj
5.1236 0 Td
(ne.01751)Tj
4.089 0 Td
(28)Tj
0 g
2.0906 0 Td
(May)Tj
2.0906 0 Td
(4,)Tj
1.0346 0 Td
(2017)Tj
35.7806 0 Td
(3)Tj
0.7654 0 Td
(/)Tj
ET
endstream
endobj
70 0 obj
<>stream
endstream
endobj
71 0 obj
<>stream
endstream
endobj
72 0 obj
<>stream
endstream
endobj
73 0 obj
<>stream
endstream
endobj
74 0 obj
<>stream
endstream
endobj
75 0 obj
<>stream
endstream
endobj
76 0 obj
<>stream
endstream
endobj
77 0 obj
<>stream
endstream
endobj
78 0 obj
<>stream
endstream
endobj
79 0 obj
<>stream
endstream
endobj
80 0 obj
<>stream
endstream
endobj
81 0 obj
<>stream
endstream
endobj
82 0 obj
<>stream
endstream
endobj
83 0 obj
<>stream
BT
66.402 0 Td
(10)Tj
ET
Q
endstream
endobj
84 0 obj
<>/XObject<>>>/CropBox[0 0 612 792]/MediaBox[0 0 612 792]/Parent 12 0 R/Annots 87 0 R/Contents 88 0 R/TrimBox[0 0 612 792]>>
endobj
85 0 obj
<>
endobj
89 0 obj
<>
endobj
90 0 obj
<>stream
%!PS-AdobeFont-1.0
11 dict begin
/FontName /TeX_CM_Maths_Italic def
/FontType 1 def
/FontBBox {-31 -239 1041 750} readonly def
/FontMatrix [0.001 0 0 0.001 0 0] readonly def
/PaintType 0 def
/FontInfo 8 dict dup begin
/FullName (TeX_CM_Maths_Italic) readonly def
/BaseFontName (TeX_CM_Maths_Italic) def
end def
/Encoding 256 array
0 1 255 {1 index exch /.notdef put} for
dup 0 /C0 put
dup 1 /C1 put
dup 2 /C2 put
dup 3 /C3 put
dup 4 /C4 put
dup 5 /C5 put
dup 6 /C6 put
dup 7 /C7 put
dup 8 /C8 put
dup 9 /C9 put
dup 10 /C10 put
dup 11 /C11 put
dup 12 /C12 put
dup 13 /C13 put
dup 14 /C14 put
dup 15 /C15 put
dup 16 /C16 put
dup 17 /C17 put
dup 18 /C18 put
dup 19 /C19 put
dup 20 /C20 put
dup 21 /C21 put
dup 22 /C22 put
dup 23 /C23 put
dup 24 /C24 put
dup 25 /C25 put
dup 26 /C26 put
dup 27 /C27 put
dup 28 /C28 put
dup 29 /C29 put
dup 30 /C30 put
dup 31 /C31 put
dup 32 /space put
dup 33 /exclam put
dup 34 /quotedbl put
dup 35 /numbersign put
dup 36 /dollar put
dup 37 /percent put
dup 38 /ampersand put
dup 39 /quoteright put
dup 40 /parenleft put
dup 41 /parenright put
dup 42 /asterisk put
dup 43 /plus put
dup 44 /comma put
dup 45 /hyphen put
dup 46 /period put
dup 47 /slash put
dup 48 /zero put
dup 49 /one put
dup 50 /two put
dup 51 /three put
dup 52 /four put
dup 53 /five put
dup 54 /six put
dup 55 /seven put
dup 56 /eight put
dup 57 /nine put
dup 58 /colon put
dup 59 /semicolon put
dup 60 /less put
dup 61 /equal put
dup 62 /greater put
dup 63 /question put
dup 64 /at put
dup 65 /A put
dup 66 /B put
dup 67 /C put
dup 68 /D put
dup 69 /E put
dup 70 /F put
dup 71 /G put
dup 72 /H put
dup 73 /I put
dup 74 /J put
dup 75 /K put
dup 76 /L put
dup 77 /M put
dup 78 /N put
dup 79 /O put
dup 80 /P put
dup 81 /Q put
dup 82 /R put
dup 83 /S put
dup 84 /T put
dup 85 /U put
dup 86 /V put
dup 87 /W put
dup 88 /X put
dup 89 /Y put
dup 90 /Z put
dup 91 /bracketleft put
dup 92 /backslash put
dup 93 /bracketright put
dup 94 /asciicircum put
dup 95 /underscore put
dup 96 /quoteleft put
dup 97 /a put
dup 98 /b put
dup 99 /c put
dup 100 /d put
dup 101 /e put
dup 102 /f put
dup 103 /g put
dup 104 /h put
dup 105 /i put
dup 106 /j put
dup 107 /k put
dup 108 /l put
dup 109 /m put
dup 110 /n put
dup 111 /o put
dup 112 /p put
dup 113 /q put
dup 114 /r put
dup 115 /s put
dup 116 /t put
dup 117 /u put
dup 118 /v put
dup 119 /w put
dup 120 /x put
dup 121 /y put
dup 122 /z put
dup 123 /braceleft put
dup 124 /bar put
dup 125 /braceright put
dup 126 /asciitilde put
dup 127 /Euro put
readonly def
currentdict end
currentfile eexec
M#1H5 J6o\&rtS(#v\0\V7Fe༙OYx5-cY9^%Y6
(efIOldN"wȰ;)UƽoFg/rvV$JS8_oc@
o9-eGJp}[Do]mN=4*{ܯq=eU^t6¤.vA2*Sr 2@Y0}Rcx,TX|ZP
;o<[1?
T<=qo:-62/]8~i wX?wJ`lLkI@EjYׅq5ڧHtvc6i 0M]YUN;M]ť0]z[{s1uO[6be#9k~d/YpMA.=뤎P\|W#?W$iz81ZL
Ңri^?WP]X A.@
z[
75y6k .U*3}hA\t&HW!Q
=+Г A 5