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Matrix Family Library Version 5.0

[New weight matrices] [Weight matrices moved to other families]
[Matrix families renamed] [Matrices renamed]
[Changes in previous release] [View all matrices]

Matrix Family Library Version 5.0 (February 2005) contains 634 weight matrices in 279 families classified into the following groups:

The vertebrate group represents binding site descriptions of 1499 transcription factors: The plant group represents binding site descriptions of 519 transcription factors from several plant species.


New weight matrices

Vertebrates

Family Family Information Matrix Name Matrix Information
V$AP4R AP4 and related proteins V$PARAXIS.01 Paraxis (TCF15), member of the Twist subfamily of Class B bHLH factors, forms heterodimers with E12
V$CHRE Carbohydrate response elements, consist of two E box motifs separated by 5 bp V$CHREBP_MLX.01 Carbohydrate response element binding protein (CHREBP) and Max-like protein X (Mlx) bind as heterodimers to glucose-responsive promoters
V$DICE Downstream Immunoglobulin Control Element, critical for B cell activity and specificity V$DICE.01 Downstream Immunoglobulin Control Element, interacting factor: BEN (also termed Mus-TRD1 and WBSCR11)
V$EGRF EGR/nerve growth factor induced protein C & related factors V$CKROX.01 Collagen krox protein (zinc finger protein 67 - zfp67)
V$EREF Estrogen Response Elements V$ERR.01 Estrogen related receptor
V$ETSF Human and murine ETS1 factors V$PDEF.01 Prostate-derived Ets factor
V$EVI1 EVI1-myleoid transforming protein V$MEL1.01 MEL1 (MDS1/EVI1-like gene 1) DNA-binding domain 1
V$MEL1.02 MEL1 (MDS1/EVI1-like gene 1) DNA-binding domain 2
V$MEL1.03 MEL1 (MDS1/EVI1-like gene 1) DNA-binding domain 2
V$FKHD Fork Head Domain factors V$ILF1.01 Winged-helix transcription factor IL-2 enhancer binding factor (ILF), forkhead box K2 (FOXK2)
V$GKLF Gut-enriched Krueppel like binding factor V$GKLF.02 Gut-enriched Krueppel-like factor
V$GLIF GLI zinc finger family V$ZIC2.01 Zinc finger transcription factor, Zic family member 2 (odd-paired homolog, Drosophila)
V$HICF Krueppel-like C2H2 zinc finger factors hypermethylated in cancer V$HIC1.01 Hypermethylated in cancer 1, transcriptional repressor containing five Krüppel-like C2H2 zinc fingers, for optimal binding multiple binding sites are required.
V$HNF4 Hepatic Nuclear Factor 4 V$HPF1.01 HepG2-specific P450 2C factor-1 (ZNF83)
V$HOXC HOX - PBX complexes V$HOX_PBX.01 HOX/PBX binding sites
V$HOXF Factors with moderate activity to homeo domain consensus sequence V$BARX2.01 Barx2, homeobox transcription factor that preferentially binds to paired TAAT motifs
V$GSH2.01 Homeodomain transcription factor Gsh-2
V$HOXB9.01 Abd-B-like homeodomain protein Hoxb-9
V$HOXC13.01 Homeodomain transcription factor HOXC13
V$PHOX2.01 Phox2a (ARIX) and Phox2b
V$HOXH HOX - MEIS1 heterodimers V$MEIS1A_HOXA9.01 Meis1a and Hoxa9 form heterodimeric binding complexes on target DNA
V$MEIS1B_HOXA9.01 Meis1b and Hoxa9 form heterodimeric binding complexes on target DNA
V$INSM Insulinoma associated factors V$INSM1.01 Zinc finger protein insulinoma-associated 1 (IA-1) functions as a transcriptional repressor
V$NFKB Nuclear Factor Kappa B/c-rel V$HIVEP1.01 ZAS domain transcription factor: human immunodeficiency virus type 1 enhancer-binding protein-1 (HIVEP1), major histocompatibility complex-binding protein-1 (MBP-1), positive regulatory domain II-binding factor 1 (PRDII-BF1)
V$NRF1 Nuclear respiratory factor 1 V$NRF1.01 Nuclear respiratory factor 1 (NRF1), bZIP transcription factor that acts on nuclear genes encoding mitochondrial proteins
V$PLAG Pleomorphic adenoma gene V$PLAG1.01 Pleomorphic adenoma gene (PLAG) 1, a developmentally regulated C2H2 zinc finger protein
V$SNAP snRNA-activating protein complex V$PSE.01 Proximal sequence element (PSE) of RNA polymerase II-transcribed snRNA genes
V$PSE.02 Proximal sequence element (PSE) of RNA polymerase III-transcribed genes
V$SORY SOx/sRY-sex/testis determinig and related HMG box factors V$HBP1.01 HMG box-containing protein 1
V$SP1F GC-Box factors SP1/GC V$SP2.01 Sp2, member of the Sp/XKLF transcription factors with three C2H2 zinc fingers in a conserved carboxyl-terminal domain
V$STAF Signal transducer and activator of transcription V$ZNF76_143.01 ZNF143 is the human ortholog of Xenopus Staf, ZNF76 is a DNA binding protein related to ZNF143 and Staf
V$TBPF Tata-binding protein factor V$LTATA.01 Lentivirus LTR TATA box
V$ZF35 Zinc finger protein ZNF35 V$ZNF35.01 Human zinc finger protein ZNF35
V$ZNFP Zinc finger proteins V$SZF1.01 SZF1, hematopoietic progenitor-restricted KRAB-zinc finger protein
V$ZBRK1.01 Transcription factor with 8 central zinc fingers and an N-terminal KRAB domain


Plants

Family Family Information Matrix Name Matrix Information
P$GCCF (GCC Box family P$ERE_JERE.01 Ethylene-responsive elements (ERE) and jasmonate- and elicitor-responsive elements (JERE)
P$MIIG MYB IIG-type binding sites P$MYBC1.01 Maize C1 myb-domain protein
P$MYCL Myc-like binding factors P$MYCRS.01 Myc recognition sequences
P$NCS1 Nodulin consensus sequence 1 P$NCS1.01 Nodulin consensus sequence 1
P$NCS2 Nodulin consensus sequence 2 P$NCS2.01 Nodulin consensus sequence 2
P$NCS3 Nodulin consensus sequence 3 P$NCS3.01 Nodulin consensus sequence 3


Other Functional Elements

Family Family Information Matrix Name Matrix Information
O$RVUP Retroviral upstream element O$LTRUP.01 Upstream element of C-type Long Terminal Repeats



Weight matrices moved to other families


Matrix families renamed


Matrices renamed