Table 1 List of the top and bottom most regulated genes for each cell line in the C vs H and C’ vs H’ comparisons
Gene symbol | Gene name | Accession number | MCF-10A | MCF-7 | MDA-231 | MDA-468 |
|---|---|---|---|---|---|---|
MCF10A | ||||||
XAGE1A | X antigen family, member 1A, TV3 | NM_001097593.1 | 64.0 | 1.2 | 1.0 | 122.0 |
XAGE1B | X antigen family, member 1B, TV1 | NM_001097595.1 | 60.3 | 1.2 | 1.1 | 131.6 |
SRGN | Serglycin, TV1 | NM_002727.2 | 58.1 | 1.1 | -1.5 | 65.8 |
SRGN | Serglycin, TV1 | NM_002727.2 | 56.5 | 1.2 | -1.5 | 67.7 |
LOC652683 | Similar to sperm protein associated with the nucleus, X chromosome, family member B1 | XM_942283.2 | 50.0 | 1.2 | -1.0 | 71.5 |
SPANXA2 | SPANX family, member A2 | NM_145662.2 | 49.3 | 1.2 | -1.1 | 67.7 |
SPANXB1 | SPANX family, member B1 | NM_032461.2 | 48.7 | 1.2 | -1.0 | 70.0 |
TOP2A | Topoisomerase (DNA) II alpha 170 kDa | NM_001067.2 | 39.0 | -2.0 | -3.7 | 1.1 |
LOC653219 | Similar to G antigen, family D, 2 isoform 1a, TV1 | XM_927237.1 | 37.0 | 1.2 | 1.1 | 71.8 |
LOC100133171 | Hypothetical protein LOC100133171 | XM_001713741.1 | 34.8 | 1.3 | -1.1 | 52.7 |
RN5S9 | RNA, 5S ribosomal 9 | NR_023371.1 | -48.2 | 11.5 | 59.7 | 11.5 |
RN7SK | RNA, 7SK small nuclear | NR_001445.1 | -55.1 | 13.1 | 45.4 | 38.6 |
SERPINB5 | Serpin peptidase inhibitor, clade B (ovalbumin), member 5 | NM_002639.3 | -65.8 | 1.2 | 7.6 | -3.8 |
KIAA1666 | KIAA1666 protein | XM_942124.2 | -72.9 | 17.9 | 33.4 | 35.3 |
AKR1C2 | Aldo-keto reductase family 1, member C2, TV1 | NM_001354.4 | -82.3 | 1.4 | 24.4 | -9.6 |
LOC650517 | Hypothetical LOC650517 | XR_019109.1 | -90.0 | 1.2 | 1.7 | -2.0 |
RN7SK | RNA, 7SK small nuclear | NR_001445.1 | -109.9 | 20.2 | 62.1 | 45.2 |
KRT17P3 | Predicted misc_RNA KRT17P3 | XR_015626.2 | -133.2 | 1.5 | 2.6 | -4.5 |
LOC651397 | Predicted misc_RNA LOC651397 | XR_037048.1 | -141.4 | 1.2 | 5.1 | -4.1 |
KRT6A | Keratin 6A | NM_005554.3 | -242.8 | 1.2 | 116.7 | -11.7 |
MCF7 | ||||||
RNY5 | RNA, Ro-associated Y5 | NR_001571.2 | -17.4 | 22.6 | 4.6 | 4.3 |
RN7SK | RNA, 7SK small nuclear | NR_001445.1 | -109.9 | 20.2 | 62.1 | 45.2 |
KIAA1666 | KIAA1666 protein | XM_942124.2 | -72.9 | 17.9 | 33.4 | 35.3 |
MIR1974 | MicroRNA 1974 | NR_031738.1 | -9.4 | 14.2 | 20.8 | 133.3 |
LOC100008589 | 28S ribosomal RNA | NR_003287.1 | -26.8 | 13.8 | 26.4 | 113.8 |
RN7SK | RNA, 7SK small nuclear | NR_001445.1 | -55.1 | 13.1 | 45.4 | 38.6 |
LOC100132394 | Hypothetical protein LOC100132394 | XM_001713809.1 | -19.4 | 12.3 | 22.2 | 105.0 |
RNU4-1 | RNA, U4 small nuclear 1 | NR_003925.1 | -7.7 | 11.5 | 11.4 | 13.2 |
RN5S9 | RNA, 5S ribosomal 9 | NR_023371.1 | -48.2 | 11.5 | 59.7 | 11.5 |
SNORD3C | Small nucleolar RNA, C/D box 3C | NR_006881.1 | -34.9 | 11.1 | 30.5 | 11.8 |
CCDC117 | Coiled-coil domain containing 117 | NM_173510.1 | 3.2 | -3.3 | -1.7 | -1.8 |
LOC730432 | Hypothetical protein LOC730432 | XM_001125680.1 | 3.7 | -3.3 | -1.3 | -4.7 |
LOC644799 | Hypothetical protein LOC644799, TV1 | XM_934554.1 | 2.5 | -3.3 | -2.1 | 1.1 |
RPS6KB1 | Ribosomal protein S6 kinase, 70 kDa, polypeptide 1 | NM_003161.2 | 2.9 | -3.4 | -1.8 | -3.7 |
NRIP1 | Nuclear receptor interacting protein 1 | NM_003489.2 | 1.1 | -3.4 | -1.8 | -4.2 |
AP4E1 | Adaptor-related protein complex 4, epsilon 1 subunit | NM_007347.3 | 2.3 | -3.4 | -2.1 | -2.2 |
DCP2 | DCP2 decapping enzyme homolog (S. cerevisiae), TV1 | NM_152624.4 | 3.1 | -3.4 | -2.4 | -6.8 |
TROVE2 | TROVE domain family, member 2, TV1 | NM_001042369.1 | 2.0 | -3.8 | -1.2 | -8.2 |
PURB | Purine-rich element binding protein B | NM_033224.3 | 3.2 | -3.8 | -2.6 | -7.1 |
ZNF217 | Zinc finger protein 217 | NM_006526.2 | 3.2 | -3.9 | -1.7 | -2.5 |
MDA231 | ||||||
KRT6A | Keratin 6A | NM_005554.3 | -242.8 | 1.2 | 116.7 | -11.7 |
RN7SK | RNA, 7SK small nuclear | NR_001445.1 | -109.9 | 20.2 | 62.1 | 45.2 |
RN5S9 | RNA, 5S ribosomal 9 | NR_023371.1 | -48.2 | 11.5 | 59.7 | 11.5 |
RN7SK | RNA, 7SK small nuclear | NR_001445.1 | -55.1 | 13.1 | 45.4 | 38.6 |
SNORD3D | Small nucleolar RNA, C/D box 3D | NR_006882.1 | -47.2 | 11.1 | 36.8 | 9.4 |
SNORD3A | Small nucleolar RNA, C/D box 3A | NR_006880.1 | -46.0 | 11.1 | 36.5 | 9.0 |
KIAA1666 | KIAA1666 protein | XM_942124.2 | -72.9 | 17.9 | 33.4 | 35.3 |
SNORD3C | Small nucleolar RNA, C/D box 3C | NR_006881.1 | -34.9 | 11.1 | 30.5 | 11.8 |
LOC100008589 | 28S ribosomal RNA | NR_003287.1 | -26.8 | 13.8 | 26.4 | 113.8 |
LOC100132564 | Hypothetical protein LOC100132564 | XM_001713808.1 | -21.6 | 8.4 | 25.3 | 13.3 |
PAK2 | p21 protein (Cdc42/Rac)-activated kinase 2 | NM_002577.3 | 5.9 | -2.9 | -3.1 | -1.3 |
CEP55 | Centrosomal protein 55 kDa, TV1 | NM_018131.3 | 19.2 | -1.7 | -3.2 | -1.2 |
RHOBTB3 | Rho-related BTB domain containing 3 | NM_014899.3 | 14.0 | -1.1 | -3.2 | 2.5 |
ZAK | Sterile alpha motif and leucine zipper containing kinase AZK, V2 | NM_133646.2 | 2.8 | -2.6 | -3.2 | -4.0 |
KATNAL1 | Katanin p60 subunit A-like 1, TV2 | NM_001014380.1 | 3.6 | -1.4 | -3.2 | -1.3 |
PBK | PDZ binding kinase | NM_018492.2 | 10.5 | -1.9 | -3.3 | -1.0 |
PAFAH1B1 | Platelet-activating factor acetylhydrolase, isoform Ib, alpha subunit | NM_000430.2 | 4.5 | -2.6 | -3.5 | 1.2 |
TOP2A | Topoisomerase (DNA) II alpha 170 kDa | NM_001067.2 | 39.0 | -2.0 | -3.7 | 1.1 |
FAM83D | Family with sequence similarity 83, member D | NM_030919.2 | 15.4 | -1.8 | -4.0 | -1.7 |
BCAT1 | Branched chain aminotransferase 1, cytosolic | NM_005504.4 | 8.9 | 1.1 | -4.9 | 2.9 |
MDA468 | ||||||
MIR1974 | microRNA 1974 | NR_031738.1 | -9.4 | 14.2 | 20.8 | 133.3 |
XAGE1B | X antigen family, member 1B, TV1 | NM_001097595.1 | 60.3 | 1.2 | 1.1 | 131.6 |
XAGE1A | X antigen family, member 1A, TV3 | NM_001097593.1 | 64.0 | 1.2 | 1.0 | 122.0 |
LOC100008589 | 28S ribosomal RNA | NR_003287.1 | -26.8 | 13.8 | 26.4 | 113.8 |
LOC100132394 | Hypothetical protein LOC100132394 | XM_001713809.1 | -19.4 | 12.3 | 22.2 | 105.0 |
CST3 | Cystatin C | NM_000099.2 | -1.8 | 1.2 | 1.7 | 103.9 |
ACTG1 | Actin, gamma 1 | NM_001614.2 | 1.1 | 1.5 | 1.5 | 75.2 |
LOC653219 | Similar to G antigen, family D, 2 isoform 1a, | XM_927237.1 | 37.0 | 1.2 | 1.1 | 71.8 |
LOC652683 | Similar to sperm protein associated with the nucleus, X chromosome, family member B1 | XM_942283.2 | 50.0 | 1.2 | -1.0 | 71.5 |
SPANXB1 | SPANX family, member B1 | NM_032461.2 | 48.7 | 1.2 | -1.0 | 70.0 |
CSAG1 | Chondrosarcoma associated gene 1, TVb | NM_153479.1 | 1.7 | 1.2 | -1.0 | -27.4 |
SERPINA3 | Serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3 | NM_001085.4 | -8.5 | 1.1 | 2.0 | -30.5 |
ALDH1A3 | Aldehyde dehydrogenase 1 family, member A3 | NM_000693.1 | -1.5 | -1.0 | 2.0 | -34.0 |
EPCAM | Epithelial cell adhesion molecule | NM_002354.2 | 1.6 | -1.2 | -1.2 | -36.1 |
LAD1 | Ladinin 1 | NM_005558.3 | -47.9 | 1.2 | 13.5 | -37.5 |
OLFML3 | Olfactomedin-like 3 | NM_020190.2 | -1.2 | 1.2 | 1.2 | -39.0 |
TACSTD1 | Tumor-associated calcium signal transducer 1 | NM_002354.1 | 2.1 | -1.1 | -1.4 | -47.5 |
RARRES1 | Retinoic acid receptor responder (tazarotene induced) 1, TV1 | NM_206963.1 | -1.3 | 1.3 | -1.1 | -49.9 |
MGP | Matrix Gla protein | NM_000900.2 | -18.6 | 1.0 | 2.4 | -51.1 |
KLK5 | Kallikrein-related peptidase 5, TV1 | NM_012427.4 | -1.3 | 1.1 | 1.1 | -56.3 |