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Matrix Family Library Version 8.1

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

Matrix Family Library Version 8.1 (June 2009) contains 1106 weight matrices in 364 families classified into the following groups:

The vertebrate group represents binding site descriptions of 5621 transcription factors: The plant group represents binding site descriptions of 687 transcription factors from several plant species.

The fungi group represents binding site descriptions of 140 transcription factors from Saccharomyces cerevisiae and Schizosaccharomyces pombe.


New weight matrices

Vertebrates

Family Family Information Matrix Name Matrix Information
V$ARID AT rich interactive domain factor V$JARID2.01 Jumonji, AT rich interactive domain 2 (JMJ)
V$CAAT CCAAT binding factors V$NFY.04 Nuclear factor Y (Y-box binding factor
V$GLIF GLI zinc finger family V$GLI3.02 GLI-Kruppel family member GLI3
V$GREF Glucocorticoid responsive and related elements V$ARE.03 Androgene receptor binding site, IR3 sites
V$GRHL Grainyhead-like transcription factors V$GRHL1.01 Grainyhead-like 1 (LBP32, MGR, TFCP2L2)
V$GTBX GT box V$ZEC.01 Zinc finger protein ZEC (ZFP628)
V$HAND Twist subfamily of class B bHLH transcription factors V$MESP1_2.01 Mesoderm posterior 1 and 2
V$TWIST.01 TWIST homolog of drosophila
V$HDGF Hepatoma-derived growth factor V$HDGF.01 Hepatoma-derived growth factor
V$HNFP Histone nuclear factor P V$MIZF.01 MBD2 (methyl-CpG-binding protein)-interacting zinc finger protein, histone nuclear factor P (HiNF-P)
V$HOMF Homeodomain transcription factors V$TLX1.01 T-cell leukemia homeobox 1
V$MEF3 MEF3 binding sites V$SIX.01 Binding sites for Six1, Six4 and Six5
V$NEUR NeuroD, Beta2, HLH domain V$MASH1.01 Mammalian achaete scute homolog 1 (Ascl1)
V$NFAT Nuclear factor of activated T-cells V$NFAT5.02 Nuclear factor of activated T-cells 5
V$PAX8 PAX-2/5/8 binding sites V$PAX2.02 Paired box protein 2
V$PCBE PREB core-binding element V$PREB.01 Prolactin regulatory element-binding protein
V$PRDM PRDI-BF1 and RIZ homologous (PR) domain proteins (PRDM) V$PRDM5.01 PR domain containing 5
V$SIX3 Sine oculis homeobox homolog 3 V$SIX3.02 SIX3 / SIXdomain (SD) and Homeodomain (HD) transcription factor
V$SIX3.03 SIX3 / SIXdomain (SD) and Homeodomain (HD) transcription factor
V$SORY SOX/SRY-sex/testis determinig and related HMG box factors V$SOX9.03 SRY (sex determining region Y)-box 9 homodimer
V$SP1F (GC-Box factors SP1/GC V$SP1.03 Stimulating protein 1, ubiquitous zinc finger transcription factor
V$STAT Signal transducer and activator of transcription V$STAT1.02 Signal transducer and activator of transcription 1
V$YY1F Y-box binding transcription factors, multifunctional proteins involved in transcriptional and translational regulation, mRNA splicing, DNA replication and repair V$REX1.01 REX1 transcription factor; zinc finger protein 42
V$YY2.01 Transcription factor yin yang 2
V$YY2.02 Transcription factor yin yang 2
V$ZBPF Zinc binding protein factors V$ZNF300.01 KRAB-containing zinc finger protein 300
V$ZFTR Zinc finger transcriptional repressor V$ZNF217.01 Zinc finger protein 217


Plants

Family Family Information Matrix Name Matrix Information
P$NACF Plant specific NAC [NAM (no apical meristem), ATAF172, CUC2 (cup-shaped cotyledons 2)] transcription factors P$ANAC019.01 Arabidopsis NAC domain containing protein 19
P$ANAC092.01 Arabidopsis NAC domain containing protein 92 (ATNAC2/ATNAC6)


Fungi

Family Family Information Matrix Name Matrix Information
F$ASG1 Activator of stress genes F$ASG1.01 Fungal zinc cluster transcription factor Asg1
F$AZF1 Asparagine-rich zinc finger 1 F$AZF1.01 Glucose-dependent zinc finger transcriptional activator
F$BAS1 Myb-related transcription factor Bas1 F$BAS1.01 Transcription factor involved in the expression of genes encoding enzymes acting in histidine, purine, and pyrimidine biosynthetic pathways
F$BZIP Fungal basic leucine zipper family F$CIN5.01 bZIP transcriptional factor of the yAP-1 family that mediates pleiotropic drug resistance and salt tolerance
F$CST6.01 Chromosome stability, bZIP transcription factor of the ATF/CREB family (ACA2)
F$HAC1.01 bZIP transcription factor (ATF/CREB1 homolog) that regulates the unfolded protein response
F$HAC1.02 bZIP transcription factor (ATF/CREB1 homolog) that regulates the unfolded protein response
F$YAP1.01 Yeast activator protein of the basic leucine zipper (bZIP) family
F$YAP1.02 Yeast activator protein of the basic leucine zipper (bZIP) family
F$CDTF Calcineurin-dependent transcription factor F$CRZ1.01 Calcineurin-responsive zinc finger 1
F$CSRE Carbon source-responsive elements F$CAT8.01 Zinc cluster transcriptional activator binding to carbon source responsive elements (CSRE)
F$RDS2.01 Regulator of drug sensitivity 2, zinc cluster transcriptional activator involved in conferring resistance to ketoconazole
F$SIP4.01 Zinc cluster transcriptional activator, binds to the carbon source-responsive element (CSRE) of gluconeogenic genes
F$DUIS DAL upstream induction sequence F$DAL82.01 Transcriptional activator for allantoin catabolic genes
F$FBAS Fungi branched amino acid biosynthesis F$LEU3.02 LEU3, S. cerevisiae, zinc cluster protein
F$FKHD Fungal fork head transcription factors F$FKH1.01 Fork head transcription factor Fkh1
F$FKH2.01 Fork head transcription factor Fkh2
F$G1TF G1 specifc transcription factors F$ACE2.01 Transcription factor that activates expression of early G1-specific genes
F$SWI5.01 SWI5, activates transcription of genes expressed at the M/G1 boundary and in G1 phase of the cell cycle
F$GATA Fungal GATA binding factors F$DAL80.01 Degradation of allantoin, negative regulator of genes in multiple nitrogen degradation pathways
F$GAT1.01 GATA-type Zn finger protein Gat1
F$GLN3.01 Transcriptional regulator of nitrogen metabolism
F$GZF3.01 GATA zinc finger protein Gzf3
F$GATC GATA-class proteins binding to GATC motifs F$GAT3.01 (GATA-type Zn finger protein Gat3
F$GAT4.01 GATA-type Zn finger protein Gat4
F$SRD1.01 Protein involved in the processing of pre-rRNA to mature rRNA
F$HAL9 Halotolerance 9 F$HAL9.01 Zinc cluster transcription factor HAL9, involved in salt tolerance
F$HOMD Homeodomain-containing transcriptional regulators F$YOX1.01 Yeast homeobox 1, homeodomain-containing transcriptional repressor
F$YOX1.02 Yeast homeobox 1, homeodomain-containing transcriptional repressor
F$ICGG Inverted CGG triplets spaced preferentially by 10 bp F$CHA4.01 Fungal zinc cluster transcription factor Cha4, single triplet
F$CHA4.02 Fungal zinc cluster transcription factor Cha4, single triplet
F$ICGG_N10.01 Inverted CGG motifs separated by a spacer of 10 bp; Put3, Tea1 and Cha4 binding sites
F$TEA1.01 Ty1 enhancer activator, zinc cluster DNA-binding protein
F$IRTF Iron-responsive transcriptional activators F$AFT1.01 Transcription factor involved in iron utilization and homeostasis (iron-sensing transcription factor AFT1)
F$AFT2.01 Activator of Fe (iron) transcription 2, iron-regulated transcriptional activator
F$MGCM Monomeric Gal4-class motifs F$ARO80.01 Aromatic amino acid requiring (activates transcription of aromatic amino acid catabolic genes in the presence of aromatic amino acids)
F$CEP3.01 Essential kinetochore protein, component of the CBF3 complex that binds the CDEIII region of the centromere
F$LYS14.01 Transcriptional activator involved in regulation of genes of the lysine biosynthesis pathway
F$RGT1.01 Glucose-responsive transcription factor involved in regulation of glucose transporters
F$RGT1.02 Glucose-responsive transcription factor involved in regulation of glucose transporters
F$YRR1.01 Zinc cluster transcription factor, activates genes involved in multidrug resistance (PDR2)
F$MOT3 Modifier of transcription 3 F$MOT3.01 Modifier of transcription 3, zinc finger transcription factor involved in repression of a subset of hypoxic genes
F$NRGF NRG zinc finger factors F$NRG1.01 Transcriptional repressor Nrg1
F$PACE Proteasome-associated control elements F$RPN4.01 Transcriptional activator of proteasomal genes
F$PDRE Pleiotropic drug resistance responsive elements F$PDR1.01 Zinc cluster protein, master regulator involved in recruiting other zinc cluster proteins to pleiotropic drug response elements (PDREs)
F$PHD1 Pseudoh yphal determinant 1 F$PHD1.01 Transcription factor involved in regulation of filamentous growth
F$PHRR pH responsive regulators F$RIM101.01 Transcriptional repressor involved in response to pH and in cell wall construction
F$RDNA RDNA binding factor F$REB1.02 rDNA enhancer binding protein 1, termination factor for RNA polymerase I and transcription factor for RNA polymerase II
F$RDR1 Repressor of Drug Resistance 1 F$RDR1.01 Repressor of Drug Resistance 1 (transcriptional repressor involved in the control of multidrug resistance
F$RDS1 Regulator of Drug Sensitivity 1 F$RDS1.01 Regulator of Drug Sensitivity 1, zinc cluster transcription factor involved in conferring resistance to cycloheximide
F$RFXP Regulatory factor X protein, homologous to mammalian RFX1-5 F$RFX1.01 RFX1 (CRT1) is a DNA-binding protein that acts by recruiting Ssn6 and Tup1, general repressors to the promoters of damage-inducible genes
F$RFX1.02 RFX1 (CRT1) is a DNA-binding protein that acts by recruiting Ssn6 and Tup1, general repressors to the promoters of damage-inducible genes
F$ROX1 Repressor of hypoxic genes F$ROX1.01 Heme-dependent transcriptional repressor of hypoxic genes
F$RRPE Ribosomal RNA processing element F$STB3.01 Ribosomal RNA processing element (RRPE)-binding protein
F$SKN7 Skn7 response regulator of Saccharomyces cerevisiae F$SKN7.01 SKN7, a transcription factor contributing to the oxidative stress response
F$SREB Sterol regulatory element binding F$ECM22_UPC2.01 Sterol regulatory element binding proteins Ecm22 and Upc2
F$STPF STP gene family F$STP2.01 Proteolytically activated transcription factor
F$STP4.01 Krueppel-type zinc finger protein
F$SXBP S.cerevisiae, XhoI site-binding protein I F$XBP1.02 Stress-induced transcriptional repressor
F$TALE Fungal TALE homeodomain class F$CUP9.01 Homeodomain transcriptional repressor Cup9
F$TOS8.01 Homeodomain-containing transcription factor
F$TEAF TEA/ATTS DNA binding domain factors F$TEC1.01 Transposon enhancement control 1, required for full Ty1 epxression, Ty1-mediated gene activation, and haploid invasive and diploid pseudohyphal growth
F$TGRF Telobox-containing general regulatory factor F$TBF1.01 TTAGGG repeat binding factor 1
F$TBF1.02 TTAGGG repeat binding factor 1
F$TRMM Transcriptonal regulator of methionine metabolism F$MET31.01 Zinc-finger DNA-binding protein, involved in transcriptional regulation of the methionine biosynthetic genes
F$MET32.01 Zinc-finger DNA-binding protein, involved in transcriptional regulation of the methionine biosynthetic genes
F$URS1 Sequence element located upstream of early meiosis-specific genes F$UME6.01 UME6, key regulator of nitrogen repression and meiotic development
F$WHBS Winged helix binding sites F$FHL1.01 Fork head transcription factor Fhl1
F$YABF Yeast ABF factors F$ABF1.03 ARS (autonomously replicating sequence)-binding factor I
F$ABF1.04 ARS (autonomously replicating sequence)-binding factor I
F$YGAL Yeast GAL4 factor F$GAL4.03 DNA-binding zinc cluster transcription factor required for activation of GAL genes
F$YGCN Yeast GCN4 factor F$GCN4.03 Leucine zipper transcription factor Gcn4
F$YHLH Yeast helix-loop-helix F$CBF1.02 Helix-loop-helix DNA-binding factor Cbf1 (centromere binding factor)
F$PHO4.02 bHLH transcription factor involved in the transcriptional control of the phosphatase regulon
F$RTG3.01 bHLH/Zip transcription factor that forms a complex with Rtg1p, to activate the retrograde (RTG) and TOR pathways
F$TYE7.01 bHLH transcription factor involved in transcriptional activation of glycolytic genes
F$YHSF Yeast heat shock factors F$HSF1.01 Trimeric heat shock transcription factor
F$HSF1.02 Trimeric heat shock transcription factor
F$MGA1.01 Heat shock transcription factor Mga1
F$YMAT Yeast mating factors F$HMRA2.01 Hidden Mat Right A2, a2 is one of two genes encoded by the a mating type cassette in S. cerevisiae
F$MATALPHA2.02 Homeodomain transcriptional repressor Matalpha2
F$YMCB Yeast Mlu I cell cycle box F$MBP1.01 Transcription factor binding to the MluI cell cycle box (MCB)
F$SWI4.01 DNA binding component of the SBF(SCB binding factor) complex (Swi4p-Swi6p)
F$YMCM Yeast cell cycle and metabolic regulator F$MCM1.02 Yeast factor MCM1 cooperating with MATalpha factors
F$YMIG Yeast GC-Box Proteins F$MIG1.02 MIG1, zinc finger protein mediates glucose repression
F$MIG2.01 MIG2, zinc finger protein mediates glucose repression
F$MIG3.01 Zinc finger transcriptional repressor MIG3
F$YMSE Yeast middle sporulation elements F$MSE.01 Middle sporulation element (MSE)
F$NDT80.01 Meiosis-specific transcription factor, binds to promoters containing middle sporulation elements (MSE)
F$SUM1.01 Transcriptional repressor required for mitotic repression of middle sporulation-specific genes
F$YORE Yeast oleate response elements F$OAF1.01 Oleate-activated transcription factor, acts alone and as a heterodimer with Pip2p
F$ORE.01 Oleate response element, binding motif of Oaf1 homodimers or Oaf1/Pip2 heterodimers
F$YRAP Yeast activator of glycolyse genes / repressor of mating type l F$RAP1.02 RAP1 (TUF1), activator or repressor depending on context
F$RAP1.03 RAP1 (TUF1), activator or repressor depending on context
F$YRSC Yeast transcription factors remodeling chromatin structure F$RSC30.01 Component of the RSC chromatin remodeling complex
F$RSC3.01 Component of the RSC chromatin remodeling complex
F$YSTR Yeast stress response elements F$GIS1.01 GIg1-2 suppressor, involved in the expression of genes during nutrient limitation, JmjC domain-containing histone demethylase
F$MSN2.01 Transcriptional activator for genes in multistress response
F$MSN4.01 Transcriptional activator related to Msn2p, activated in stress conditions
F$RPH1.01 Jumonji-like transcription factor
F$USV1.01 (Usv (Up in StarVation), Nsf1 (nutrient and stress factor 1)


Insects

Family Family Information Matrix Name Matrix Information
I$PPRE Proximal proneural response elements I$AC_SC.01 Achaete (ac) - scute (sc) complex binding sites


General Core Promoter Elements

Family Family Information Matrix Name Matrix Information
O$YTBP Yeast TATA binding protein factor O$SPT15.01 TATA-binding protein, general transcription factor that interacts with other factors to form the preinitiation complex at promoters



Weight matrices moved to other families


Weight matrices modified

The following weight matrices have been replaced by better matrices:

Matrix families renamed

The following matrix families have been renamed:

Matrix families removed

The following matrix families have been removed: