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					Potential SRC-3/RFX1 Target Genes with Human Disease Associations

   Sources: MorbidMap: http://www.ncbi.nlm.nih.gov/Omim/getmorbid.cgi
             Sanger Cancer Gene Census: http://www.sanger.ac.uk/genetics/CGP/Census/
             HuGe Breast Cancer: http://hugenavigator.net/HuGENavigator/geneProspectorStartPage.do, Sea
             Cancer Candidate Genes (CAN): Wood et al. Science. 2007 Nov 16;318(5853):1108-13.
Description: Gene list comparisons with curated external databases showed that 80 (17%) of the potential RF
             Morbid Map [1], or are listed in cancer candidate databases such as the Sanger Gene Census [2],
             disease “breast cancer” [4]. 1.6% of protein-coding genes in the human genome are reported to
             contribute to cancer development [2]; therefore, the potential RFX1/SRC-3 target genes with dise
          1   Amberger, J., et al., McKusick's Online Mendelian Inheritance in Man (OMIM). Nucleic Acids Res, 2
          2   Futreal, P.A., et al., A census of human cancer genes. Nat Rev Cancer, 2004. 4(3): p. 177-83.
          3   Wood, L.D., et al., The genomic landscapes of human breast and colorectal cancers. Science, 2007. 3
          4   Yu, W., et al., A navigator for human genome epidemiology. Nat Genet, 2008. 40(2): p. 124-5.

              Abbreviations used for Sanger Cancer Genes entries: E: epithelial, L: leukaemia/lymphoma, M: m
              Numbers in HuGe Breast Cancer column represent rank positions in the top 500 genes related to


SRC3/RFX1 Targets
  GeneID  GeneSymbol


        21    ABCA3
        81    ACTN4
      3899    AFF3
       267    AMFR
     10159    ATP6AP2
     64919    BCL11B
       652    BMP4
     83990    BRIP1
     55799    CACNA2D3
       863    CBFA2T3
       595    CCND1
      1236    CCR7
      1604    CD55
      1001    CDH3
      1021    CDK6
      1289    COL5A1
      1384    CRAT
      1523    CUX1
      1591    CYP24A1
      9231    DLG5
     26298    EHF
      8891    EIF2B3
    157697    ERICH1
      2099    ESR1
     51466    EVL
  2194   FASN
  2263   FGFR2
  2324   FLT4
  8456   FOXN1
  9568   GABBR2
  2771   GNAI2
  9289   GPR56
 83872   HMCN1
  3227   HOXC11
  3315   HSPB1
  3425   IDUA
  3480   IGF1R
  3630   INS
  3708   ITPR1
  3778   KCNMA1
  3860   KRT13
  3856   KRT8
  3912   LAMB1
  4010   LMX1B
  4197   MDS1
145873   MESP2
 79083   MLPH
124540   MSI2
  4477   MSMB
  4602   MYB
  9612   NCOR2
  9722   NOS1AP
  8622   PDE8B
  5339   PLEC1
 51422   PRKAG2
  5583   PRKCH
  5618   PRLR
  5890   RAD51L1
 10743   RAI1
  5914   RARA
  5979   RET
 92304   SCGB3A1
  6338   SCNN1B
  6505   SLC1A1
  9368   SLC9A3R1
  6709   SPTAN1
  6753   SSTR3
  6901   TAZ
  7054   TH
 64699   TMPRSS3
 23495   TNFRSF13B
  7139   TNNT2
  8626   TP63
  6955   TRA@
      6957   TRB@
     25828   TXN2
      7466   WFS1
     23286   WWC1
     51741   WWOX
     64131   XYLT1
   Counts:           80




rbl 4/2009
 SRC-3/RFX1 Target Genes with Human Disease Associations

  orbidMap: http://www.ncbi.nlm.nih.gov/Omim/getmorbid.cgi
 anger Cancer Gene Census: http://www.sanger.ac.uk/genetics/CGP/Census/
 uGe Breast Cancer: http://hugenavigator.net/HuGENavigator/geneProspectorStartPage.do, Searched for "Breast Cancer"
 ancer Candidate Genes (CAN): Wood et al. Science. 2007 Nov 16;318(5853):1108-13.
 ene list comparisons with curated external databases showed that 80 (17%) of the potential RFX1/SRC-3 target genes hav
  orbid Map [1], or are listed in cancer candidate databases such as the Sanger Gene Census [2], CAN [3], or the human ge
  sease “breast cancer” [4]. 1.6% of protein-coding genes in the human genome are reported to show recurrent somatic m
 ontribute to cancer development [2]; therefore, the potential RFX1/SRC-3 target genes with disease associations represent
 mberger, J., et al., McKusick's Online Mendelian Inheritance in Man (OMIM). Nucleic Acids Res, 2009. 37(Database issue): p.
 utreal, P.A., et al., A census of human cancer genes. Nat Rev Cancer, 2004. 4(3): p. 177-83.
Wood, L.D., et al., The genomic landscapes of human breast and colorectal cancers. Science, 2007. 318(5853): p. 1108-13.
 u, W., et al., A navigator for human genome epidemiology. Nat Genet, 2008. 40(2): p. 124-5.

 bbreviations used for Sanger Cancer Genes entries: E: epithelial, L: leukaemia/lymphoma, M: mesenchymal, O: other
 umbers in HuGe Breast Cancer column represent rank positions in the top 500 genes related to human breast cancer


                                                          Human Disease Databases
                                            MorbidMap Pathology                                  SangerCance
                                                                                                    rGene

             Surfactant metabolism dysfunction, pulmonary, 3, 610921 (3)
             Glomerulosclerosis, focal segmental, 1, 603278 (3)
                                                                                                 L

             Mental retardation, X-linked, with epilepsy, 300423 (3)
                                                                                                 L
             Microphthalmia, syndromic 6, 607932 (3)
             Breast cancer, early-onset, 114480 (3)                                              L, E

                                                                                                 L
             Centrocytic lymphoma (2)                                                            L, E

             [Blood group Cromer] (3)
             Hypotrichosis, congential, with juvenile macular dystrophy, 601553 (3)
             {Stature QTL 11}, 612223 (3)                                                        L
             Ehlers-Danlos syndrome, type I, 130000 (3)
             Carnitine acetyltransferase deficiency (1) (?)


             {Crohn disease, susceptibility to}, 266600 (3)

             Leukoencephalopathy with vanishing white matter, 603896 (3)

             Breast cancer (1)
Antley-Bixler syndrome, 207410 (                                               E
Hemangioma, capillary infantile, somatic, 602089 (3)
T-cell immunodeficiency, congenital alopecia, and nail dystrophy, 601705 (3)
{Nicotine dependence, protection against}, 188890 (3)
Pituitary ACTH-secreting adenoma (3)
Polymicrogyria, bilateral frontoparietal, 606854 (3)
{Macular degeneration, age-related, 1}, 603075 (3)
                                                                               L
Charcot-Marie-Tooth disease, axonal, type 2F, 606595 (3)
Mucopolysaccharidosis Ih, 607014 (3)
Intrauterine and postnatal growth retardation (3)
Diabetes mellitus, rare form (1)
Spinocerebellar ataxia 15, 606658 (3)
Generalized epilepsy and paroxysmal dyskinesia, 609446 (3)
White sponge nevus, 193900 (3)
Cirrhosis, cryptogenic (3)
Cutis laxa, marfanoid neonatal type (1) (?)
Nail-patella syndrome with open-angle glaucoma, 137750 (3)
Myelodysplasia syndrome-1 (3)                                                  L
Spondylocostal dysostosis, autosomal recessive 2, 608681 (3)
Griscelli syndrome, type 3, 609227 (3)
                                                                               L
{Prostate cancer, hereditary, 13}, 611928 (3)
{T-cell acute lymphoblastic leukemia} (3)

QT interval, modifier of, 610141 (3)
Pigmented nodular adrenocortical disease, primary, 3 (3)
Epidermolysis bullosa simplex with pyloric atresia, 612138 (3)
Cardiomyopathy, hypertrophic 6, with WPW, 600858 (3)
{Cerebral infarction, susceptibility to}, 601367 (3)

                                                                               M
Smith-Magenis syndrome, 182290 (3)
Leukemia, acute promyelocytic (1)                                              L
Central hypoventilation syndrome, congenital, 209880 (3)                       E, O

Liddle syndrome, 177200 (3)
Dicarboxylicaminoaciduria, 222730 (1) (?)
Nephrolithiasis/osteoporosis, hypophosphatemic, 2, 612287 (3)


Barth syndrome, 302060 (3)
Segawa syndrome, recessive (3)
Deafness, autosomal recessive 10, congenital, 605316 (3)
Common variable immunodeficiency, 240500 (3)
Cardiomyopathy, dilated, 1D, 601494 (3)
ADULT syndrome, 103285 (3)
                                                                               L
                                                                       L

Hearing loss, low-frequency sensorineural, 600965 (3)
[Memory, enhanced, association with] (3)
Esophageal squamous cell carcinoma, 133239 (3)
{Pseudoxanthoma elasticum, modifier of severity of}, 264800 (3)
                                                                  57       15
hed for "Breast Cancer"

1/SRC-3 target genes have one or more human disease associations in
CAN [3], or the human genome epidemiology HuGE database for the
 how recurrent somatic mutations in cancer with strong evidence that these
 se associations represent a 2.7 fold over-representation.
09. 37(Database issue): p. D793-6.

8(5853): p. 1108-13.


senchymal, O: other
uman breast cancer


                                                               Binding Site Profile by ChIP Analyses
            HuGE Breast    CAN gene       RFX1      SRC3_veh      SRC3_E2      Tx_veh       Tx_E2
              Cancer

                          CAN         RFX1                      SRC3_E2      Tx_veh     Tx_E2
                                      RFX1         SRC3_veh     SRC3_E2      Tx_veh     Tx_E2
                                      RFX1         SRC3_veh     SRC3_E2                 Tx_E2
                          CAN         RFX1         SRC3_veh     SRC3_E2                 Tx_E2
                                      RFX1         SRC3_veh     SRC3_E2      Tx_veh     Tx_E2
                                      RFX1                      SRC3_E2      Tx_veh     Tx_E2
                                      RFX1         SRC3_veh     SRC3_E2      Tx_veh     Tx_E2
            63                        RFX1         SRC3_veh     SRC3_E2      Tx_veh     Tx_E2
                          CAN         RFX1         SRC3_veh     SRC3_E2      Tx_veh     Tx_E2
                                      RFX1         SRC3_veh     SRC3_E2      Tx_veh     Tx_E2
            60                        RFX1         SRC3_veh     SRC3_E2      Tx_veh     Tx_E2
            365                       RFX1         SRC3_veh     SRC3_E2                 Tx_E2
                                      RFX1         SRC3_veh     SRC3_E2      Tx_veh     Tx_E2
                                      RFX1         SRC3_veh     SRC3_E2      Tx_veh     Tx_E2
            219                       RFX1                      SRC3_E2      Tx_veh     Tx_E2
                                      RFX1         SRC3_veh     SRC3_E2      Tx_veh     Tx_E2
                                      RFX1         SRC3_veh     SRC3_E2      Tx_veh     Tx_E2
                          CAN         RFX1         SRC3_veh     SRC3_E2      Tx_veh     Tx_E2
            376                       RFX1                      SRC3_E2
                                      RFX1                      SRC3_E2      Tx_veh     Tx_E2
            416                       RFX1         SRC3_veh     SRC3_E2
                                      RFX1         SRC3_veh     SRC3_E2      Tx_veh     Tx_E2
                          CAN         RFX1         SRC3_veh     SRC3_E2      Tx_veh
            8                         RFX1         SRC3_veh     SRC3_E2      Tx_veh     Tx_E2
                          CAN         RFX1         SRC3_veh     SRC3_E2      Tx_veh     Tx_E2
397         RFX1              SRC3_E2   Tx_veh   Tx_E2
11          RFX1   SRC3_veh   SRC3_E2   Tx_veh
405         RFX1   SRC3_veh   SRC3_E2            Tx_E2
            RFX1   SRC3_veh   SRC3_E2            Tx_E2
            RFX1   SRC3_veh   SRC3_E2
            RFX1   SRC3_veh   SRC3_E2   Tx_veh   Tx_E2
            RFX1              SRC3_E2   Tx_veh   Tx_E2
            RFX1   SRC3_veh   SRC3_E2   Tx_veh   Tx_E2
            RFX1   SRC3_veh   SRC3_E2   Tx_veh   Tx_E2
            RFX1   SRC3_veh   SRC3_E2   Tx_veh   Tx_E2
            RFX1   SRC3_veh   SRC3_E2   Tx_veh   Tx_E2
285         RFX1   SRC3_veh   SRC3_E2   Tx_veh   Tx_E2
457         RFX1              SRC3_E2
            RFX1   SRC3_veh   SRC3_E2   Tx_veh   Tx_E2
            RFX1   SRC3_veh   SRC3_E2
            RFX1              SRC3_E2            Tx_E2
            RFX1   SRC3_veh   SRC3_E2   Tx_veh   Tx_E2
            RFX1   SRC3_veh   SRC3_E2   Tx_veh   Tx_E2
            RFX1   SRC3_veh   SRC3_E2   Tx_veh   Tx_E2
            RFX1   SRC3_veh   SRC3_E2   Tx_veh   Tx_E2
            RFX1   SRC3_veh   SRC3_E2
            RFX1   SRC3_veh   SRC3_E2   Tx_veh   Tx_E2
            RFX1   SRC3_veh   SRC3_E2   Tx_veh   Tx_E2
            RFX1   SRC3_veh   SRC3_E2   Tx_veh   Tx_E2
            RFX1   SRC3_veh   SRC3_E2   Tx_veh   Tx_E2
335         RFX1   SRC3_veh   SRC3_E2   Tx_veh   Tx_E2
            RFX1   SRC3_veh   SRC3_E2   Tx_veh   Tx_E2
            RFX1   SRC3_veh   SRC3_E2   Tx_veh   Tx_E2
            RFX1   SRC3_veh   SRC3_E2   Tx_veh   Tx_E2
            RFX1   SRC3_veh   SRC3_E2   Tx_veh   Tx_E2
            RFX1   SRC3_veh   SRC3_E2   Tx_veh   Tx_E2
207         RFX1   SRC3_veh   SRC3_E2   Tx_veh   Tx_E2
164         RFX1   SRC3_veh   SRC3_E2   Tx_veh   Tx_E2
352         RFX1   SRC3_veh   SRC3_E2   Tx_veh   Tx_E2
            RFX1   SRC3_veh   SRC3_E2   Tx_veh   Tx_E2
      CAN   RFX1   SRC3_veh   SRC3_E2   Tx_veh   Tx_E2
644         RFX1   SRC3_veh   SRC3_E2            Tx_E2
      CAN   RFX1              SRC3_E2
            RFX1   SRC3_veh   SRC3_E2
            RFX1   SRC3_veh   SRC3_E2   Tx_veh   Tx_E2
      CAN   RFX1   SRC3_veh   SRC3_E2   Tx_veh   Tx_E2
578         RFX1   SRC3_veh   SRC3_E2            Tx_E2
            RFX1              SRC3_E2   Tx_veh   Tx_E2
            RFX1              SRC3_E2
            RFX1   SRC3_veh   SRC3_E2   Tx_veh   Tx_E2
            RFX1              SRC3_E2
            RFX1              SRC3_E2   Tx_veh   Tx_E2
            RFX1   SRC3_veh   SRC3_E2
            RFX1   SRC3_veh   SRC3_E2   Tx_veh   Tx_E2
               RFX1     SRC3_veh      SRC3_E2
194            RFX1     SRC3_veh      SRC3_E2        Tx_veh        Tx_E2
               RFX1                   SRC3_E2                      Tx_E2
               RFX1      SRC3_veh     SRC3_E2        Tx_veh        Tx_E2
               RFX1      SRC3_veh     SRC3_E2        Tx_veh
               RFX1      SRC3_veh     SRC3_E2
      19   9          80         65             80            58           64
P Analyses
                  ER     FoxA1


             ER
             ER        FoxA1
             ER        FoxA1
             ER
             ER
             ER        FoxA1
             ER        FoxA1
             ER        FoxA1
                       FoxA1
             ER        FoxA1
             ER        FoxA1
             ER        FoxA1
             ER        FoxA1
             ER        FoxA1
             ER        FoxA1
             ER        FoxA1
             ER        FoxA1
             ER        FoxA1
             ER        FoxA1
             ER        FoxA1
             ER        FoxA1

             ER        FoxA1
             ER        FoxA1
             ER        FoxA1
ER
ER   FoxA1
     FoxA1
ER
ER   FoxA1
ER
ER
ER   FoxA1
ER
ER   FoxA1
ER
ER   FoxA1
ER
ER   FoxA1
ER   FoxA1
ER
ER   FoxA1
ER   FoxA1
ER   FoxA1
ER   FoxA1

ER   FoxA1
ER   FoxA1
ER   FoxA1
ER   FoxA1
ER
ER   FoxA1

ER
ER   FoxA1
ER   FoxA1
     FoxA1
ER   FoxA1
ER   FoxA1
ER   FoxA1
ER
     FoxA1
ER   FoxA1
ER   FoxA1
ER   FoxA1
ER
ER
ER
ER
ER   FoxA1

ER
ER   FoxA1
ER   FoxA1
ER        FoxA1

ER
ER        FoxA1
ER        FoxA1
ER        FoxA1
     71           55
Notable Potential SRC3/RFX1 Target Genes:
Gene Symbol            Gene ID     GEMS
TFF1 (pS2)                7031    early up      trefoil factor 1
GREB1                     9687    early up      GREB1 protein
IGFBP4                    3487    early up      insulin-like growth factor binding protein 4
WISP2                     8839    early up      WNT1 inducible signaling pathway protein 2
RARA                      5914    early up      retinoic acid receptor, alpha
FAM102A (EEIG1)         399665    early up      early estrogen-induced gene 1
PTPRG (PTPgamma)          5793    early up      protein tyrosine phosphatase, receptor type, G
CCND1                      595    early up      cyclin D1
ESR1                      2099early/late down   estrogen receptor 1
RXRA                      6256early/late down   retinoid X receptor, alpha
ing protein 4
 way protein 2


receptor type, G

				
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