                         SEQUENCE LISTING

<110>  RAY, Partha S.
       BAGARIA, Sanjay
       CUI, Xiaojiang
       WANG, Jinhua
 
<120>  METHODS FOR DIAGNOSIS, PROGNOSIS AND TREATMENT OF PRIMARY AND 
       METASTATIC BASAL-LIKE BREAST CANCER AND OTHER CANCER TYPES

<130>  71754.8001.WO00

<140>  PCT/US10/44817
<141>  2010-08-06

<150>  US 61/231,984
<151>  2009-08-06

<160>  14    

<170>  PatentIn version 3.5

<210>  1
<211>  57
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Mouse FoxC1 shRNA sequence

<400>  1
ccgggagcag agctactatc gcgctctcga gagcgcgata gtagctctgc tcttttg          57


<210>  2
<211>  58
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Mouse FoxC1 shRNA sequence

<400>  2
ccggtgggaa tagtagctgt cagatctcga gatctgacag ctactattcc catttttg         58


<210>  3
<211>  58
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Human FoxC1 shRNA sequence

<400>  3
ccggcaagaa gaaggacgcg gtgaactcga gttcaccgcg tccttcttct tgtttttg         58


<210>  4
<211>  57
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Human FoxC1 shRNA sequence

<400>  4
ccggcccgga caagaagatc accctctcga gagggtgatc ttcttgtccg ggttttt          57


<210>  5
<211>  57
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Control shRNA

<400>  5
ccggcaacaa gatgaagagc accaactcga gttggtgctc ttcatcttgt tgttttt          57


<210>  6
<211>  25
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  FOXC1 forward primer

<400>  6
cggtatccag ccagtctctg taccg                                             25


<210>  7
<211>  21
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  FOXC1 reverse primer

<400>  7
gttcggcttt gagggtgtgt c                                                 21


<210>  8
<211>  25
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  FOXC1 ERalpha forward primer

<400>  8
cggttagatt catcatgcgg aaccg                                             25


<210>  9
<211>  21
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  FOXC1 ERalpha reverse primer

<400>  9
tgtgtagagg gcatggtgga g                                                 21


<210>  10
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  ChIP assay ERalpha forward primer

<400>  10
agaagctaga cctctgcagg                                                   20


<210>  11
<211>  21
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  ChIP assay ERalpha reverse prime

<400>  11
aagcaggggc aaggaaatat c                                                 21


<210>  12
<211>  3946
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  FOXC1/FKHL7 gene

<300>
<308>  GenBank/AR140209
<309>  2001-06-16
<313>  (1)..(3946)

<400>  12
cgagaaaagg tgacgcgggg cccgggcagg cggccggcgc gcggcccccc ccccccccgc       60

cctggttatt tggccgcctt cgccggcagc tcagggcaga gtctcctgga aggcgcaggc      120

agtgtggcga gaagggcgcc tgcttgttct ttctttttgt ctgctttccc ccgtttgcgc      180

ctggaagctg cgccgcgagt tcctgcaagg cggtctgccg cggccgggcc cggccttctc      240

ccctcgcagc gaccccgcct cgcggccgcg cgggccccga ggtagcccga ggcgccggag      300

gagccagccc cagcgagcgc cgggagaggc ggcagcgcag ccggacgcac agcgcagcgg      360

gccggcacca gctcggccgg gcccggactc ggactcggcg gccggcgcgg cgcggcccgg      420

cccgagcgag ggtggggggc ggcgggcggc gcggggcggc ggcgagcggg ggccatgcag      480

gcgcgctact ccgtgtccag ccccaactcc ctgggagtgg tgccctacct cggcggcgag      540

cagagctact accgcgcggc ggccgcggcg gccgggggcg gctacaccgc catgccggcc      600

cccatgagcg tgtactcgca ccctgcgcac gccgagcagt acccgggcgg catggcccgc      660

gcctacgggc cctacacgcc gcagccgcag cccaaggaca tggtgaagcc gccctatagc      720

tacatcgcgc tcatcaccat ggccatccag aacgccccgg acaagaagat caccctgaac      780

ggcatctacc agttcatcat ggaccgcttc cccttctacc gggacaacaa gcagggctgg      840

cagaacagca tccgccacaa cctctcgctc aacgagtgct tcgtcaaggt gccgcgcgac      900

gacaagaagc cgggcaaggg cagctactgg acgctggacc cggactccta caacatgttc      960

gagaacggca gcttcctgcg gcggcggcgg cgcttcaaga agaaggacgc ggtgaaggac     1020

aaggaggaga aggacaggct gcacctcaag gagccgcccc cgcccggccg ccagcccccg     1080

cccgcgccgc cggagcaggc cgacggcaac gcgcccggtc cgcagccgcc gcccgtgcgc     1140

atccaggaca tcaagaccga gaacggtacg tgcccctcgc cgccccagcc cctgtccccg     1200

gccgccgccc tgggcagcgg cagcgccgcc gcggtgccca agatcgagag ccccgacagc     1260

agcagcagca gcctgtccag cgggagcagc cccccgggca gcctgccgtc ggcgcggccg     1320

ctcagcctgg acggtgcgga ttccgcgccg ccgccgcccg cgccctccgc cccgccgccg     1380

caccatagcc agggcttcag cgtggacaac atcatgacgt cgctgcgggg gtcgccgcag     1440

agcgcggccg cggagctcag ctccggcctt ctggcctcgg cggccgcgtc ctcgcgcgcg     1500

gggatcgcac ccccgctggc gctcggcgcc tactcgcccg gccagagctc cctctacagc     1560

tccccctgca gccagacctc cagcgcgggc agctcgggcg gcggcggcgg cggcgcgggg     1620

gccgcggggg gcgcgggcgg cgccgggacc taccactgca acctgcaagc catgagcctg     1680

tacgcggccg gcgagcgcgg gggccacttg cagggcgcgc ccgggggcgc gggcggctcg     1740

gccgtggaca accccctgcc cgactactct ctgcctccgg tcaccagcag cagctcgtcg     1800

tccctgagtc acggcggcgg cggcggcggc ggcgggggag gccaggaggc cggccaccac     1860

cctgcggccc accaaggccg cctcacctcg tggtacctga accaggcggg cggagacctg     1920

ggccacttgg caagcgcggc ggcggcggcg gcggccgcag gctacccggg ccagcagcag     1980

aacttccact cggtgcggga gatgttcgag tcacagagga tcggcttgaa caactctcca     2040

gtgaacggga atagtagctg tcaaatggcc ttcccttcca gccagtctct gtaccgcacg     2100

tccggagctt tcgtctacga ctgtagcaag ttttgacaca ccctcaaagc cgaactaaat     2160

cgaaccccaa agcaggaaaa gctaaaggaa cccatcaagg caaaatcgaa actaaaaaaa     2220

aaaaatccaa ttaaaaaaaa cccctgagaa tattcaccac accagcgaac agaatatccc     2280

tccaaaaatt cagctcacca gcaccagcac gaagaaaact ctattttctt aaccgattaa     2340

ttcagagcca cctccacttt gccttgtcta aataaacaaa cccgtaaact gttttataca     2400

gagacagcaa aatcttggtt tattaaagga cagtgttact ccagataaca cgtaagtttc     2460

ttcttgcttt tcagagacct gctttcccct cctcccgtct cccctctctt gccttcttcc     2520

ttgcctctca cctgtaagat attattttat cctatgttga agggaggggg aaagtccccg     2580

tttatgaaag tcgctttctt tttattcatg gacttgtttt aaaatgtaaa ttgcaacata     2640

gtaatttatt tttaatttgt agttggatgt cgtggaccaa acgccagaaa gtgttcccaa     2700

aacctgacgt taaattgcct gaaactttaa attgtgcttt ttttctcatt ataaaaaggg     2760

aaactgtatt aatcttattc tatcctcttt tctttctttt tgttgaacat attcattgtt     2820

tgtttattaa taaattacca ttcagtttga atgagaccta tatgtctgga tactttaata     2880

gagctttaat tattacgaaa aaagatttca gagataaaac actagaagtt acctattctc     2940

cacctaaatc tctgaaaaat ggagaaaccc tctgactagt ccatgtcaaa ttttactaaa     3000

agtctttttg tttagattta ttttcctgca gcatcttctg caaaatgtac tatatagtca     3060

gcttgctttg aggctagtaa aaagatattt ttctaaacag attggagttg gcatataaac     3120

aaatacgttt tctcactaat gacagtccat gattcggaaa ttttaagccc atgaatcagc     3180

cgcggtctta ccacggtgat gcctgtgtgc cgagagatgg gactgtgcgg ccagatatgc     3240

acagataaat atttggcttg tgtattccat ataaaattgc agtgcatatt atacatccct     3300

gtgagccaga tgctgaatag attttttcct attatttcag tcctttataa aaggaaaaat     3360

aaaccagttt ttaaatgtat gtatataatt ctcccccatt tacaatcctt catgtattac     3420

atagaaggat tgctttttta aaaatatact gcgggttgga aagggatatt taatctttga     3480

gaaactattt tagaaaatat gtttgtagaa caattatttt tgaaaaagat ttaaagcaat     3540

aacaagaagg aaggcgagag gagcagaaca ttttggtcta gggtggtttc tttttaaacc     3600

attttttctt gttaatttac agttaaacct aggggacaat ccggattggc cctccccctt     3660

ttgtaaataa cccaggaaat gtaataaatt cattatctta gggtgatctg ccctgccaat     3720

cagactttgg ggagatggcg atttgattac agacgttcgg gggggtgggg ggcttgcagt     3780

ttgttttgga gataatacag tttcctgcta tctgccgctc ctatctagag gcaacactta     3840

agcagtaatt gctgttgctt gttgtcaaaa tttgatcatt gttaaaggat tgctgcaaat     3900

aaatacactt taatttcagt caaaaaaaaa aaaaaaaaaa aaaaaa                    3946


<210>  13
<211>  1659
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  FOXC1/FKHL7 gene coding sequence

<300>
<308>  GenBank/AR140210
<309>  2001-06-16
<313>  (1)..(1659)

<400>  13
atgcaggcgc gctactccgt gtccagcccc aactccctgg gagtggtgcc ctacctcggc       60

ggcgagcaga gctactaccg cgcggcggcc gcggcggccg ggggcggcta caccgccatg      120

ccggccccca tgagcgtgta ctcgcaccct gcgcacgccg agcagtaccc gggcggcatg      180

gcccgcgcct acgggcccta cacgccgcag ccgcagccca aggacatggt gaagccgccc      240

tatagctaca tcgcgctcat caccatggcc atccagaacg ccccggacaa gaagatcacc      300

ctgaacggca tctaccagtt catcatggac cgcttcccct tctaccggga caacaagcag      360

ggctggcaga acagcatccg ccacaacctc tcgctcaacg agtgcttcgt caaggtgccg      420

cgcgacgaca agaagccggg caagggcagc tactggacgc tggacccgga ctcctacaac      480

atgttcgaga acggcagctt cctgcggcgg cggcggcgct tcaagaagaa ggacgcggtg      540

aaggacaagg aggagaagga caggctgcac ctcaaggagc cgcccccgcc cggccgccag      600

cccccgcccg cgccgccgga gcaggccgac ggcaacgcgc ccggtccgca gccgccgccc      660

gtgcgcatcc aggacatcaa gaccgagaac ggtacgtgcc cctcgccgcc ccagcccctg      720

tccccggccg ccgccctggg cagcggcagc gccgccgcgg tgcccaagat cgagagcccc      780

gacagcagca gcagcagcct gtccagcggg agcagccccc cgggcagcct gccgtcggcg      840

cggccgctca gcctggacgg tgcggattcc gcgccgccgc cgcccgcgcc ctccgccccg      900

ccgccgcacc atagccaggg cttcagcgtg gacaacatca tgacgtcgct gcgggggtcg      960

ccgcagagcg cggccgcgga gctcagctcc ggccttctgg cctcggcggc cgcgtcctcg     1020

cgcgcgggga tcgcaccccc gctggcgctc ggcgcctact cgcccggcca gagctccctc     1080

tacagctccc cctgcagcca gacctccagc gcgggcagct cgggcggcgg cggcggcggc     1140

gcgggggccg cggggggcgc gggcggcgcc gggacctacc actgcaacct gcaagccatg     1200

agcctgtacg cggccggcga gcgcgggggc cacttgcagg gcgcgcccgg gggcgcgggc     1260

ggctcggccg tggacaaccc cctgcccgac tactctctgc ctccggtcac cagcagcagc     1320

tcgtcgtccc tgagtcacgg cggcggcggc ggcggcggcg ggggaggcca ggaggccggc     1380

caccaccctg cggcccacca aggccgcctc acctcgtggt acctgaacca ggcgggcgga     1440

gacctgggcc acttggcaag cgcggcggcg gcggcggcgg ccgcaggcta cccgggccag     1500

cagcagaact tccactcggt gcgggagatg ttcgagtcac agaggatcgg cttgaacaac     1560

tctccagtga acgggaatag tagctgtcaa atggccttcc cttccagcca gtctctgtac     1620

cgcacgtccg gagctttcgt ctacgactgt agcaagttt                            1659


<210>  14
<211>  553
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  FOXC1/FKHL7 protein sequence

<300>
<308>  GenBank/AAE63616
<309>  2001-06-16
<313>  (1)..(553)

<400>  14

Met Gln Ala Arg Tyr Ser Val Ser Ser Pro Asn Ser Leu Gly Val Val 
1               5                   10                  15      


Pro Tyr Leu Gly Gly Glu Gln Ser Tyr Tyr Arg Ala Ala Ala Ala Ala 
            20                  25                  30          


Ala Gly Gly Gly Tyr Thr Ala Met Pro Ala Pro Met Ser Val Tyr Ser 
        35                  40                  45              


His Pro Ala His Ala Glu Gln Tyr Pro Gly Gly Met Ala Arg Ala Tyr 
    50                  55                  60                  


Gly Pro Tyr Thr Pro Gln Pro Gln Pro Lys Asp Met Val Lys Pro Pro 
65                  70                  75                  80  


Tyr Ser Tyr Ile Ala Leu Ile Thr Met Ala Ile Gln Asn Ala Pro Asp 
                85                  90                  95      


Lys Lys Ile Thr Leu Asn Gly Ile Tyr Gln Phe Ile Met Asp Arg Phe 
            100                 105                 110         


Pro Phe Tyr Arg Asp Asn Lys Gln Gly Trp Gln Asn Ser Ile Arg His 
        115                 120                 125             


Asn Leu Ser Leu Asn Glu Cys Phe Val Lys Val Pro Arg Asp Asp Lys 
    130                 135                 140                 


Lys Pro Gly Lys Gly Ser Tyr Trp Thr Leu Asp Pro Asp Ser Tyr Asn 
145                 150                 155                 160 


Met Phe Glu Asn Gly Ser Phe Leu Arg Arg Arg Arg Arg Phe Lys Lys 
                165                 170                 175     


Lys Asp Ala Val Lys Asp Lys Glu Glu Lys Asp Arg Leu His Leu Lys 
            180                 185                 190         


Glu Pro Pro Pro Pro Gly Arg Gln Pro Pro Pro Ala Pro Pro Glu Gln 
        195                 200                 205             


Ala Asp Gly Asn Ala Pro Gly Pro Gln Pro Pro Pro Val Arg Ile Gln 
    210                 215                 220                 


Asp Ile Lys Thr Glu Asn Gly Thr Cys Pro Ser Pro Pro Gln Pro Leu 
225                 230                 235                 240 


Ser Pro Ala Ala Ala Leu Gly Ser Gly Ser Ala Ala Ala Val Pro Lys 
                245                 250                 255     


Ile Glu Ser Pro Asp Ser Ser Ser Ser Ser Leu Ser Ser Gly Ser Ser 
            260                 265                 270         


Pro Pro Gly Ser Leu Pro Ser Ala Arg Pro Leu Ser Leu Asp Gly Ala 
        275                 280                 285             


Asp Ser Ala Pro Pro Pro Pro Ala Pro Ser Ala Pro Pro Pro His His 
    290                 295                 300                 


Ser Gln Gly Phe Ser Val Asp Asn Ile Met Thr Ser Leu Arg Gly Ser 
305                 310                 315                 320 


Pro Gln Ser Ala Ala Ala Glu Leu Ser Ser Gly Leu Leu Ala Ser Ala 
                325                 330                 335     


Ala Ala Ser Ser Arg Ala Gly Ile Ala Pro Pro Leu Ala Leu Gly Ala 
            340                 345                 350         


Tyr Ser Pro Gly Gln Ser Ser Leu Tyr Ser Ser Pro Cys Ser Gln Thr 
        355                 360                 365             


Ser Ser Ala Gly Ser Ser Gly Gly Gly Gly Gly Gly Ala Gly Ala Ala 
    370                 375                 380                 


Gly Gly Ala Gly Gly Ala Gly Thr Tyr His Cys Asn Leu Gln Ala Met 
385                 390                 395                 400 


Ser Leu Tyr Ala Ala Gly Glu Arg Gly Gly His Leu Gln Gly Ala Pro 
                405                 410                 415     


Gly Gly Ala Gly Gly Ser Ala Val Asp Asn Pro Leu Pro Asp Tyr Ser 
            420                 425                 430         


Leu Pro Pro Val Thr Ser Ser Ser Ser Ser Ser Leu Ser His Gly Gly 
        435                 440                 445             


Gly Gly Gly Gly Gly Gly Gly Gly Gln Glu Ala Gly His His Pro Ala 
    450                 455                 460                 


Ala His Gln Gly Arg Leu Thr Ser Trp Tyr Leu Asn Gln Ala Gly Gly 
465                 470                 475                 480 


Asp Leu Gly His Leu Ala Ser Ala Ala Ala Ala Ala Ala Ala Ala Gly 
                485                 490                 495     


Tyr Pro Gly Gln Gln Gln Asn Phe His Ser Val Arg Glu Met Phe Glu 
            500                 505                 510         


Ser Gln Arg Ile Gly Leu Asn Asn Ser Pro Val Asn Gly Asn Ser Ser 
        515                 520                 525             


Cys Gln Met Ala Phe Pro Ser Ser Gln Ser Leu Tyr Arg Thr Ser Gly 
    530                 535                 540                 


Ala Phe Val Tyr Asp Cys Ser Lys Phe 
545                 550             


