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Matrix Family Library Version 6.0

[New weight matrices] [Weight matrices removed]
[Matrix families merged] [Matrices renamed]
[Changes in previous release] [View all matrices]

Matrix Family Library Version 6.0 (November 2005) contains 664 weight matrices in 284 families classified into the following groups:

The vertebrate group represents binding site descriptions of 1543 transcription factors: The plant group represents binding site descriptions of 526 transcription factors from several plant species.

New weight matrices


Family Family Information Matrix Name Matrix Information
V$AHRR AHR-arnt heterodimers and AHR-related factors V$NXF_ARNT.01 bHLH-PAS type transcription factors NXF/ARNT heterodimer
V$AP2F Activator protein 2 V$AP2.02 Activator protein 2 alpha
V$AP4R AP4 and related proteins V$LYL1_E12.01 LYL1-E12 heterodimeric complex
V$TAL1BETAHEB.01 Tal-1beta/HEB heterodimer
V$BTBF BTB/POZ (broad complex, Trantrach, Bric à brac/pox viruses and zinc fingers) transcription factor V$KAISO.01 Transcription factor Kaiso, ZBTB33
V$CLOX CLOX and CLOX homology (CDP) factors V$CUT2.01 Cut repeat II
V$CREB Camp-responsive element binding proteins V$ATF2.01 Activating transcription factor 2
V$CJUN_ATF2.01 c-Jun/ATF2 heterodimers
V$CSEN Calsenilin, presenilin binding protein, EF hand transcription factor V$DREAM.01 Downstream regulatory element-antagonist modulator, Ca2+-binding protein of the neuronal calcium sensors family that binds DRE (downstream regulatory element) sites as a tetramer
V$EKLF Basic and erythroid krueppel like factors V$KKLF.01 Kidney-enriched kruppel-like factor, KLF15
V$EVI1 EVI1-myleoid transforming protein V$EVI1.07 Evi-1 zinc finger protein, carboxy-terminal zinc finger domain
V$GZF1 GDNF-inducible zinc finger gene 1 V$GZF1.01 GDNF-inducible zinc finger protein 1 (ZNF336)
V$HEAT Heat shock factors V$HSF1.02 Heat shock factor 1
V$HSF1.03 Heat shock factor 1
V$HSF2.01 Heat shock factor 2
V$HSF2.02 Heat shock factor 2
V$HIFF Hypoxia inducible factor, bHLH / PAS protein family V$DEC2.01 Basic helix-loop-helix protein known as Dec2 or Sharp2
V$MEF2 MEF2, myocyte-specific enhancer binding factor V$MEF2.06 Myocyte-specific enhancer factor 2
V$MEF2.07 Myocyte-specific enhancer factor 2
V$SL1.01 Member of the RSRF (related to serum response factor) protein family from Xenopus laevis
V$MYOD Myoblast determining factors V$MYOGENIN.01 Myogenic bHLH protein myogenin (myf4)
V$MZF1 Myeloid zinc finger 1 factors V$MZF1.02 Myeloid zinc finger protein MZF1
V$NKXH NKX homeodomain factors V$HMX2.01 Hmx2/Nkx5-2 homeodomain transcription factor
V$HMX2.02 Hmx2/Nkx5-2 homeodomain transcription factor
V$HMX3.02 Hmx3/Nkx5-1 homeodomain transcription factor
V$NR2F Nuclear receptor subfamily 2 factors V$PNR.01 Photoreceptor-specific nuclear receptor subfamily 2, group E, member 3 (Nr2e3)
V$PAX3 PAX-3 binding sites V$PAX3.02 Pax-3 paired domain protein
V$RARF Nuclear receptor for retinoic acid V$RAR.02 Retinoic acid receptor, member of nuclear receptors, DR5 site
V$RXRF RXR heterodimer binding sites V$VDR_RXR.03 Bipartite binding site of VDR/RXR heterodimers without a spacer between directly repeated motifs
V$VDR_RXR.04 Bipartite binding site of VDR/RXR heterodimers: 2 spacer nucleotides between the two directly repeated motifs
V$VDR_RXR.05 Bipartite binding site of VDR/RXR heterodimers: 3 spacer nucleotides between the two directly repeated motifs
V$VDR_RXR.06 Bipartite binding site of VDR/RXR heterodimers: 4 spacer nucleotides between the two directly repeated motifs
V$SP1F GC-Box factors SP1/GC V$SP1.02 Stimulating protein 1, ubiquitous zinc finger transcription factor
V$YY1F Activator/repressor binding to transcription initiation site V$YY1.02 Yin and Yang 1 repressor sites
V$ZBPF Zinc binding protein factors V$ZNF219.01 Kruppel-like zinc finger protein 219


Family Family Information Matrix Name Matrix Information
P$AGP1 Plant GATA-type zinc finger protein P$AGP1.01 AG-motif binding protein 1
P$AHBP Arabidopsis homeobox protein P$HAHB4.01 Sunflower homeodomain leucine-zipper protein Hahb-4
P$DREB Dehydration responsive element binding factors P$HVDRF1.01 H. vulgare dehydration-response factor 1
P$GBOX Plant G-box/C-box bZIP proteins P$ABZ1.01 Anaerobic basic leucine zipper
P$GBF1.01 bZIP protein G-Box binding factor 1
P$OSBHLH66.01 Rice bHLH protein
P$TGA1.01 Arabidopsis leucine zipper protein TGA1
P$IDDF ID domain factors, the ID domain includes a cluster of three different types of zinc fingers seperated from a fourth C2H2 finger by a long spacer P$ID1.01 Maize INDETERMINATE1 zinc finger protein
P$MADS MADS box proteins P$SQUA.01 MADS-box protein SQUAMOSA
P$MYBS MYB proteins with single DNA binding domains P$TAMYB80.01 MYB protein from wheat
P$NACF Nascent polypeptide-associated complex (NAC) domain-containing factor P$TANAC69.01 Wheat NACdomain DNA binding factor
P$URNA Upstream sequence element of U-snRNA genes P$USE.01 Upstream sequence elements in the promoters of U-snRNA genes of higher plants


Family Family Information Matrix Name Matrix Information
I$DBRC Drosophila Broad-Complex for ecdysone steroid response I$BRCZ3.01 Broad-Complex Z3 Zinc Finger isoform
I$DHOM Drosophila homeoproteins I$FTZ.01 Fushi tarazu, involved in body segmentation of the drosophila embryo


Family Family Information Matrix Name Matrix Information
F$ARPU Regulator of pyrimidine and purine utilization pathway F$PPR1.01 Pyrimidine pathway regulator 1
F$GATA Fungal GATA binding factors F$GATA.01 GATA binding factor (yeast)
F$HPHO Homeodomain protein Pho2 F$PHO2.01 Homeodomain protein Pho2
F$PDRE Pleiotropic drug resistance responsive elements F$PDRE.01 Pleiotropic drug resistance responsive element (yeast)
F$YGCR Yeast activator of glycolytic genes F$CSRE.01 Carbon source-responsive element (yeast)
F$YMAT Yeast mating factors F$MATALPHA2.01 Homeodomain protein mating factor alpha2
F$YMCB Yeast Mlu I cell cycle box F$MCB.01 Mlu I cell cycle box, activates G1/S-specific transcription (yeast)

Weight matrices removed

The following weight matrices (originally based on TRANSFAC) were removed since binding sites used for generation of the matrices are not available:

Matrix families merged

Matrices renamed