breast cancer 관련 유전자 (signatures)

   breast cancer 의 prognosis 나 drug-response 에 관련된 유전자 등 breast cancer 에 관련된 것으로 알려진 유전자 목록을 모아 보자. 이렇게 관심있는 특성과 밀접한 연관을 갖는 유전자들을 signature gene 이라고 하는데, 일반적으는 van 't Veer 의 70 signature 나 Wang 의 76-gene signature 가 많이 알려져 있다. 그러나 그 이후에 몇몇 study 에서 보다 많은 경우에 의미있을 것으로 추측되는 signature 들이 발표되었다. 뭔가 할 때마다 찾아 가서 정리하는 것이 귀찮아서 여기다 지금까지 알려진 것들을 계속적으로 추가한다. 초기 목록은 이 논문^[각주:1]에 근거하고, signature 목록은 이 논문의 supplementary appendix 에서 갖고 왔다. text file의 format 은, linux 의 관례에 따라 # 으로 시작하는 줄은 주석이다. 또한 tab-deliminated 되어 있다. 각 column 은 self-explainatory 하다.


Prognosis 관련 Signatures

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1. NKI 70-signature

a. Source Gene expression profiling predicts clinical outcome of breast cancer, Nature 2002, 415, 530-436. van 't Veer et al. ( pubmed link : PMID 11823860 )
b. Notes lymph node negative 에서 distant metastasis free duration 에 관련된 signature 이다. 실제 gene list는 원 논문의 supple. 의 table 2. 에서 correlation 의 절대값이 큰 gene 70 개이다.
c. Gene List

# RawID    HPRD    Symbol    RefSeq    Protein    EntrezGene    OMIM    Swiss-Prot    Name
AL080059    15576    TSPYL5    NM_033512.2    NP_277047.2    85453    -    -    TSPY-like 5
Contig63649_RC    -
Contig46218_RC    -
NM_016359    14857    NUSAP1    AF290612.1    AAK28023.1    51203    -    -    Nucleolar and spindle associated protein 1
AA555029_RC    -
NM_003748    06009    ALDH4A1    NM_003748.2    NP_003739.2    8659    606811    P30038    Pyrroline 5 carboxylate dehydrogenase, delta 1
Contig38288_RC    -
NM_003862    04766    FGF18    NM_003862.1    NP_003853.1    8817    603726    O76093    Fibroblast growth factor 18
Contig28552_RC    -
Contig32125_RC    -
U82987    16165    BBC3    NM_014417.2    NP_055232.1    27113    605854    Q9BXH1    BCL2 binding component 3
AL137718    10884    DIAPH3    NM_001042517.1    NP_001035982.1    81624    -    Q9NSV4    DIAPH3
AB037863    13860    EBF4    NM_020833.1    NP_065884.1    57593    609935    Q9BQW3    Early B-cell factor 4
NM_020188    16783    C16orf61    NM_020188.2    NP_064573.1    56942    -    Q9NRP2    DC13 protein
NM_020974    18030    SCUBE2    NM_020974.1    NP_066025.1    57758    -    Q9NQ36    Signal peptide CUB domain EGF like 2
NM_000127    00598    EXT1    NM_000127.2    NP_000118.2    2131    608177    Q16394    Exostosin 1
NM_002019    01297    FLT1    NM_002019.2    NP_002010.1    2321    165070    P17948    VEGF receptor 1
NM_002073    00746    GNAZ    NM_002073.2    NP_002064.1    2781    139160    P19086    Guanine nucleotide binding protein, alpha Z polypeptide
NM_000436    02001    OXCT1    NM_000436.3    NP_000427.1    5019    601424    P55809    3-oxoacid CoA transferase
NM_004994    00387    MMP9    NM_004994.2    NP_004985.2    4318    120361    P14780    Matrix metalloproteinase 9
Contig55377_RC    -
Contig35251_RC    -
Contig25991    11860    ECT2    NM_018098.4    NP_060568.3    1894    600586    Q9H8V3    Epithelial cell transforming sequence 2 oncogene
NM_003875    10927    GMPS    NM_003875.2    NP_003866.1    8833    600358    P49915    Guanine monophosphate synthetase
NM_006101    06277    NDC80    NM_006101.1    NP_006092.1    10403    607272    O14777    Kinetochore associated 2
NM_003882    16019    WISP1    NM_003882.2    NP_003873.1    8840    603398    O95388    WNT1 inducible signaling pathway protein 1
NM_003607    04562    CDC42BPA    NM_003607.3    NP_003598.2    8476    603412    Q5VT25    CDC42 binding protein kinase alpha
AF073519    04308    SERF1A    NM_021967.1    NP_068802.1    8293    603011    O75920    Small EDRK rich factor 1A
AF052162    08572    AYTL2    NM_024830.3    NP_079106.3    79888    610472    Q8NF37    Acyltransferase like 2
NM_000849    00712    GSTM3    NM_000849.3    NP_000840.2    2947    138390    P21266    Glutathione S-transferase Mu3
Contig32185_RC    -
NM_016577    11474    RAB6B    NM_016577.3    NP_057661.3    51560    -    Q9NRW1    RAB6B
Contig48328_RC    -
Contig46223_RC    -
NM_015984    10293    UCHL5    NM_015984.2    NP_057068.1    51377    610667    Q9Y5K5    Ubiquitin thiolesterase L5
NM_006117    16269    PECI    NM_006117.2    NP_006108.2    10455    608024    O75521    Dodecenoyl-CoA delta-isomerase
AK000745    17459    MTDH    NM_178812.2    NP_848927.1    92140    610323    Q86UE4    Metadherin
Contig40831_RC    -
NM_003239    01829    TGFB3    NM_003239.1    NP_003230.1    7043    190230    P10600    TGF beta 3
NM_014791    06119    MELK    NM_014791.2    NP_055606.1    9833    607025    Q14680    Maternal embryonic leucine zipper kinase
X05610    00355    COL4A2    NM_001846.2    NP_001837.2    1284    120090    P08572    Collagen, type IV, alpha 2
NM_016448    17952    DTL    NM_016448.1    NP_057532.1    51514    610617    Q9NZJ0    RA regulated nuclear matrix associated protein
NM_018401    15446    STK32B    NM_018401.1    NP_060871.1    55351    -    Q9NY57    Serine/threonine kinase 32B
NM_000788    00507    DCK    NM_000788.1    NP_000779.1    1633    125450    P27707    Deoxycytidine kinase
Contig51464_RC    -
AL080079    17059    GPR126    NM_198569.1    NP_940971.1    57211    -    Q86SQ4    G protein coupled receptor 126
NM_006931    00686    SLC2A3    NM_006931.1    NP_008862.1    6515    138170    P11169    Solute carrier family 2, member 3
AF257175    16269    PECI    NM_006117.2    NP_006108.2    10455    608024    O75521    Dodecenoyl-CoA delta-isomerase
NM_014321    06237    ORC6L    NM_014321.2    NP_055136.1    23594    607213    Q9Y5N6    ORC6
NM_002916    00022    RFC4    NM_002916.3    NP_002907.1    5984    102577    P35249    Replication factor C4
Contig55725_RC    -
Contig24252_RC    -
AF201951    07579    MS4A7    NM_021201.4    NP_067024.1    58475    606502    Q9GZW8    Membrane spanning 4 domains subfamily A member 7
NM_005915    03485    MCM6    NM_005915.4    NP_005906.2    4175    601806    Q14566    MCM6
NM_001282    03015    AP2B1    BC006201.2    AAH06201.1    163    601025    P63010    Adaptor related protein complex 2 beta 1 subunit
Contig56457_RC    04570    TMEFF1    NM_003692.2    NP_003683.2    8577    603421    -    TMEFF1
NM_000599    00901    IGFBP5    NM_000599.2    NP_000590.1    3488    146734    P24593    IGF binding protein 5
NM_020386    07577    HRASLS    NM_020386.2    NP_065119.1    57110    606487    Q9HDD0    HRAS like suppressor
NM_014889    07142    PITRM1    NM_014889.2    NP_055704.2    10531    -    Q5JRX3    Pitrilysin metalloproteinase 1
AF055033    00901    IGFBP5    NM_000599.2    NP_000590.1    3488    146734    P24593    IGF binding protein 5
NM_006681    05485    NMU    NM_006681.1    NP_006672.1    10874    605103    P48645    Neuromedin U
NM_007203    18661    -    NM_147150.1    NP_671492.1    445815    -    -    PALM2-AKAP2 protein
Contig63102_RC    -
NM_003981    17899    PRC1    NM_003981.2    NP_003972.1    9055    603484    O43663    Protein regulator of cytokinesis 1
Contig20217_RC    -
NM_001809    00313    CENPA    NM_001809.3    NP_001800.1    1058    117139    P49450    Centromeric protein a
Contig2399_RC    -
NM_004702    04801    CCNE2    NM_057749.1    NP_477097.1    9134    603775    O96020    Cyclin E2
NM_007036    03310    ESM1    NM_007036.3    NP_008967.1    11082    601521    Q9NQ30    ESM1
NM_018354    12772    C20orf46    NM_018354.1    NP_060824.1    55321    -    Q9NUR3    C20orf46 protein

NKI-70.txt.converted.txt

2. 76-signature.

a. Source Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer, Lancet 2005, 365, 671-679. Wang Y, et al. ( pubmed link : PMID 15721472 )
b. Notes
c. Gene List

# RawID    HPRD    Symbol    RefSeq    Protein    EntrezGene    OMIM    Swiss-Prot    Name
# For ER-positive group
219340_s_at    06383    CLN8    NM_018941.3    NP_061764.2    2055    607837    Q9UBY8    Ceroid lipofuscinosis, neuronal 8
217771_at    08428    GOLPH2    NM_016548.2    NP_057632.2    51280    606804    Q8NBJ4    Golgi PhosphoProtein 2
202418_at    06755    YIF1A    NM_020470.1    NP_065203.1    10897    -    O95070    Yip1 interacting factor homolog
206295_at    02976    IL18    NM_001562.2    NP_001553.1    3606    600953    Q14116    Interleukin 18
201091_s_at    05130    CBX3    NM_016587.2    NP_057671.2    11335    604477    Q13185    Chromobox homolog 3
204015_s_at    04123    DUSP4    NM_001394.5    NP_001385.1    1846    602747    Q13115    Dual specificity phosphatase 4
200726_at    08911    PPP1CC    NM_002710.1    NP_002701.1    5501    176914    P36873    Protein phosphatase 1, catalytic subunit, gamma isoform
200965_s_at    03819    ABLIM1    NM_002313.5    NP_002304.3    3983    602330    O14639    Actin binding LIM protein 1
210314_x_at    05128    TNFSF13    NM_003808.2    NP_003799.1    8741    604472    O75888    Tumour necrosis factor ligand superfamily, member 13
221882_s_at    11636    TMEM8    NM_021259.1    NP_067082.1    58986    -    Q9HCN3    Transmembrane protein 8
217767_at    00400    C3    NM_000064.2    NP_000055.2    718    120700    P01024    Complement component 3
219588_s_at    10539    NCAPG2    NM_017760.5    NP_060230.5    54892    608532    Q86XI2    More than blood homolog
204073_s_at    12213    C11orf9    NM_013279.1    NP_037411.1    745    608329    -    Chromosome 11 open reading frame 9
212567_s_at    01141    MAP4    NM_002375.3    NP_002366.2    4134    157132    P27816    Microtubule associated protein 4
211382_s_at    05600    TACC2    NM_206862.1    NP_996744.1    10579    605302    O95359    TACC2
201663_s_at    09276    SMC4    NM_005496.3    NP_005487.3    10051    605575    Q9NTJ3    SMC4 structural maintenance of chromosomes 4
221344_at    17678    OR12D2    NM_013936.2    NP_039224.2    26529    -    P58182    Olfactory receptor 12D2
210028_s_at    05398    ORC3L    NM_181837.1    NP_862820.1    23595    604972    Q9UBD5    ORC3
218782_s_at    10678    ATAD2    NM_014109.2    NP_054828.2    29028    -    Q6PL18    ATAD2
201664_at    09276    SMC4    NM_005496.3    NP_005487.3    10051    605575    Q9NTJ3    SMC4 structural maintenance of chromosomes 4
219724_s_at    -    -    NM_014796.1    NP_055611.1    9840    -    -    KIAA0748
204014_at    04123    DUSP4    NM_001394.5    NP_001385.1    1846    602747    Q13115    Dual specificity phosphatase 4
212014_x_at    00115    CD44    NM_000610.3    NP_000601.3    960    107269    P16070    CD44
202240_at    03652    PLK1    NM_005030.3    NP_005021.2    5347    602098    P53350    Polo like kinase
204740_at    11937    CNKSR1    BC011604.2    AAH11604.1    10256    603272    Q969H4    Connector enhancer of kinase suppressor of Ras 1
208180_s_at    11919    HIST1H4H    NM_003543.3    NP_003534.1    8365    602828    -    Histone 1 H4h
204768_s_at    02670    FEN1    NM_004111.4    NP_004102.1    2237    600393    P39748    Flap endonuclease 1
203391_at    01742    FKBP2    NM_004470.2    NP_004461.2    2286    186946    P26885    FK506 binding protein 2
211762_s_at    02818    KPNA2    NM_002266.2    NP_002257.1    3838    600685    P52292    Karyopherin alpha 2
218914_at    10824    C1orf66    NM_015997.2    NP_057081.2    51093    -    -    CGI 41 protein
221028_s_at    14419    GFOD2    NM_030819.2    NP_110446.2    81577    -    Q3B7J2    Glucose-fructose oxidoreductase domain containing 2
211779_x_at    06256    AP2A2    NM_012305.2    NP_036437.1    161    607242    O94973    Adaptor related protein complex 2, alpha2 subunit
218883_s_at    14722    MLF1IP    NM_024629.2    NP_078905.2    79682    -    Q71F23    MLF1 interacting protein
204888_s_at    04815    NEURL    NM_004210.3    NP_004201.2    9148    603804    O76050    NEURL
217815_at    16088    SUPT16H    NM_007192.2    NP_009123.1    11198    605012    Q9Y5B9    FACTp140
201368_at    18319    ZFP36L2    NM_006887.3    NP_008818.3    678    -    P47974    Zinc finger protein 36 C3H type like 2
201288_at    04162    ARHGDIB    NM_001175.4    NP_001166.3    397    602843    P52566    RHO GDP dissociation inhibitor beta
201068_s_at    01105    PSMC2    NM_002803.2    NP_002794.1    5701    154365    P35998    Proteasome 26S subunit, ATPase 2
218478_s_at    11698    ZCCHC8    NM_017612.2    NP_060082.2    55596    -    Q6NZY4    Zinc finger, CCHC domain containing 8
214919_s_at    16489    ANKHD1    NM_017747.1    NP_060217.1    54882    610500    Q8IWG5    Ankyrin repeat and KH domain containing 1
209835_x_at    00115    CD44    NM_000610.3    NP_000601.3    960    107269    P16070    CD44
217471_at    10452    HELZ    NM_014877.3    NP_055692.2    9931    606699    P42694    Helicase with zinc finger domain
203306_s_at    09290    SLC35A1    NM_006416.3    NP_006407.1    10559    605634    P78382    Solute carrier family 35 member A1
205034_at    04801    CCNE2    NM_057749.1    NP_477097.1    9134    603775    O96020    Cyclin E2
221816_s_at    08480    PHF11    AB011031.1    BAA32101.1    51131    607796    Q9UIL8    PHD finger protein 11
219510_at    10375    POLQ    NM_006596.3    NP_006587.3    10721    604419    O75417    DNA polymerase theta
217102_at    -    -    AF041410.1    -    -    -    -    -    -
208683_at    00254    CAPN2    NM_001748.3    NP_001739.1    824    114230    P17655    Calpain 2
215510_at    -    -    AV693985    -    -    -    -    -
218533_s_at    15607    UCKL1    NM_017859.2    NP_060329.2    54963    610866    Q9NWZ5    Uridine cytidine kinase 1 like 1
215633_x_at    -    -    AV713720    -    -    -    -    -
221928_at    07044    ACACB    NM_001093.3    NP_001084.3    32    601557    O00763    Acetyl-CoA carboxylase beta
214806_at    03730    BICD1    NM_001714.2    NP_001705.2    636    602204    Q96G01    Bicaudal D homolog 1
204540_at    04265    EEF1A2    NM_001958.2    NP_001949.1    1917    602959    Q05639    Elongation factor 1, alpha 2
221916_at    01206    NEFL    NM_006158.2    NP_006149.2    4747    162280    P07196    Neurofilament light polypeptide
216693_x_at    17096    -    NM_016073.2    NP_057157.1    50810    -    -    Hepatoma derived growth factor related protein 3
209500_x_at    05128    TNFSF13    NM_003808.2    NP_003799.1    8741    604472    O75888    Tumour necrosis factor ligand superfamily, member 13
209524_at    -    -    FLJ10418    -    -    -    -    -
207118_s_at    04502    MMP23A    NM_004659.1    NP_004650.1    8511    603320    -    Matrix metalloproteinase 23A
211040_x_at    09593    GTSE1    NM_016426.4    NP_057510.2    51512    607477    Q9NYZ3    G2 and S phase expressed 1
#For ER-negative group
218430_s_at    07807    RFXDC2    NM_022841.5    NP_073752.5    64864    -    -    Regulatory factor X domain containing 2
217404_s_at    00361    COL2A1    NM_001844.4    NP_001835.3    1280    120140    P02458    Collagen, type II, alpha 1
205848_at    04158    GAS2    NM_005256.2    NP_005247.1    2620    602835    O43903    Growth arrest specific Protein 2
214915_at    -    -    FLJ11780    -    -    -    -    -
216010_x_at    00196    FUT3    NM_000149.1    NP_000140.1    2525    111100    P21217    Fucosyltransferase 3
204631_at    01173    MYH2    NM_017534.4    NP_060004.2    4620    160740    Q9UKX2    Myosin heavy chain 2, skeletal muscle, adult
202687_s_at    04670    TNFSF10    NM_003810.2    NP_003801.1    8743    603598    P50591    TRAIL
221634_at    -    -    BC000596.1    -    -    -    -    -
220886_at    02284    GABRQ    NM_018558.1    NP_061028.1    55879    300349    Q9UN88    Gamma aminobutyric acid receptor theta
202239_at    09598    PARP4    NM_006437.3    NP_006428.2    143    607519    Q9UKK3    ADP-ribosyltransferase like 1
204218_at    13172    C11orf51    NM_014042.2    NP_054761.1    25906    -    P60006    DKFZP564M082 protein
221241_s_at    05841    BCL2L14    NM_138722.1    NP_620048.1    79370    606126    Q9BZR8    BCL2-like 14 (apoptosis facilitator)
209862_s_at    16261    CEP57    NM_014679.3    NP_055494.2    9702    607951    Q86XR8    Translokin
217019_at    -    RPS4XP3    ng_000967.3    -    -    -    -    -
210593_at    02431    SAT1    NM_002970.1    NP_002961.1    6303    313020    P21673    Spermidine/spermine N(1) acetyltransferase
216103_at    07075    ACOT11    NM_015547.2    NP_056362.1    26027    606803    Q8WXI4    Acyl-CoA thioesterase 11

76-signature.txt.converted.txt

1. Gene-Expression Signatures in Breast Cancer, N Engl J Med, 2009, 360:790-800, Christos Sotiriou, et al. [본문으로]