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Matrix Family Library Version 8.0

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

Matrix Family Library Version 8.0 (November 2008) contains 974 weight matrices in 325 families classified into the following groups:

The vertebrate group represents binding site descriptions of 5287 transcription factors: The plant group represents binding site descriptions of 680 transcription factors from several plant species.

New weight matrices


Family Family Information Matrix Name Matrix Information
V$ABDB Abdominal-B type homeodomain transcription factors V$HOXA9.02 Homeobox A9 / Hox1-gamma
V$HOXA10.01 Homeobox A10 / Hox1.8
V$HOXA11.01 Homeobox A11
V$HOXA13.01 Homeobox A13
V$HOXB9.02 Homeobox B9
V$HOXB13.01 Homeobox B13
V$HOXC9.01 Homeobox C9 / Hox-3beta
V$HOXC10.01 Homeobox C10/ Hox-3iota
V$HOXC11.01 Homeobox C11/ Hox-3H
V$HOXC12.01 Homeobox C12/ Hox-3phi
V$HOXC13.02 Homeobox C13 / Hox-3gamma
V$HOXD10.01 Homeobox D10
V$HOXD11.01 Homeobox D11 / Hox-4phi
V$HOXD12.01 Homeobox D12 / Hox-4H
V$HOXD13.01 Homeobox D13 / Hox-4I
V$BCDF Bicoid-like homeodomain transcription factors V$CRX.02 Cone-rod homeobox-containing transcription factor
V$DMBX1.01 Diencephalon/mesencephalon homeobox 1
V$GSC.02 Vertebrate bicoid-type homeodomain protein Goosecoid
V$OBOX1.01 Oocyte specific homeobox 1
V$OBOX2.01 Oocyte specific homeobox 2
V$OBOX3.01 Oocyte specific homeobox 3
V$OBOX5.01 Oocyte specific homeobox 5
V$OBOX6.01 Oocyte specific homeobox 6
V$OTX1.01 Orthodenticle homeobox 1
V$OTX2.02 Orthodenticle homeobox 2
V$PITX2.01 Pituitary homeo box 2, Ptx2, paired-like homeodomain 2
V$PITX3.01 Paired-like homeodomain 3, CTPP 4, Ptx3
V$PTX1.02 Pituitary homeo box 1 (Pitx1), paired-like homeodomain 1
V$BRN5 Brn-5 POU domain factors V$BRN5.04 POU class 6 homeobox 1 (POU6F1)
V$BRNF Brn POU domain factors V$BRN2.04 POU class 3 homeobox 2 (POU3F2), OTF7
V$BRN3.03 POU class 4 homeobox 3 (POU4F3), BRN3C
V$BRN4.02 POU class 3 homeobox 4 (POU3F4)
V$TST1.02 POU class 3 homeobox 1 (POU3F1), OCT6
V$CART Cart-1 (cartilage homeoprotein 1) V$ALX3.01 Aristaless-like homeobox 3
V$ALX4.01 Aristaless-like homeobox 4
V$ARX.01 Aristaless related homeobox
V$CART1.02 Cartilage homeo protein 1
V$ESX1.01 ESX homeobox 1
V$ISX.01 Intestine-specific homeobox
V$OTP.01 Orthopedia homeobox
V$PHOX2A.01 Paired-like homeobox 2a (Arix)
V$PHOX2B.01 Paired-like homeobox 2b, PMX2 B
V$PROP1.01 Prophet of Pit 1, PROP paired-like homeobox 1
V$PRRX1.01 Paired related homeobox 1, paired mesoderm homeo box 1 (PMX1)
V$PRRX2.01 Paired related homeobox 2, paired mesoderm homeo box 1 (PMX1), S8
V$RAX.01 Retina and anterior neural fold homeobox
V$RHOX6.01 Reproductive homeobox 6, placenta specific homeobox 1
V$SHOX2.01 Short stature homeobox 2
V$UNCX4.01 UNC homeobox (UNCX)
V$VSX1.01 Visual system homeobox 1
V$CDXF Vertebrate caudal related homeodomain protein V$CDX1.02 Caudal type homeo box 1
V$CDX2.02 Caudal type homeobox transcription factor 2
V$CLOX CLOX and CLOX homology (CDP) factors V$CPHX.01 Cytoplasmic polyadenylated homeobox
V$CP2F CP2-erythrocyte Factor related to drosophila Elf1 V$TCFCP2L1.01 Transcription factor CP2-like 1 (LBP-9)
V$CTCF CTCF and BORIS gene family, transcriptional regulators with 11 highly conserved zinc finger domains V$CTCF.02 Insulator protein CTCF (CCCTC-binding factor)
V$CTCF.03 Insulator protein CTCF (CCCTC-binding factor)
V$CTCF.04 Insulator protein CTCF (CCCTC-binding factor)
V$DLXF Distal-less homeodomain transcription factors V$DLX1.02 Distal-less homeobox 1
V$DLX2.01 Distal-less homeobox 2
V$DLX3.03 Distal-less homeobox 3
V$DLX4.01 Distal-less homeobox 4
V$DLX5.01 Distal-less homeobox 5
V$EBOX E-box binding factors V$CMYC.01 Myelocytomatosis oncogene (c-myc proto-oncogene)
V$NMYC.02 v-myc myelocytomatosis viral related oncogene, neuroblastoma derived
V$USF1.01 Upstream stimulating factor 1
V$EREF Estrogen response elements V$ESRRB.01 Estrogen-related receptor beta
V$FKHD Fork head domain factors V$HNF3.01 Hepatocyte nuclear factor 3 (alpha, beta) (FOXA1, FOXA2)
V$HNF3B.02 Hepatic nuclear factor 3beta (FOXA2)
V$HBOX Homeobox transcription factors V$EMX2.01 Empty spiracles homeobox 2
V$EN1.02 Engrailed homeobox 1
V$EN2.01 Engrailed homeobox 2
V$EVX1.01 Even-skipped homeobox 1
V$EVX2.01 Even-skipped homeobox 2
V$GBX1.01 Gastrulation brain homeobox 1
V$GBX2.01 Gastrulation brain homeobox 2
V$GSH2.02 Homeodomain transcription factor Gsh-2
V$HLXB9.01 Motor neuron and pancreas homeobox 1 (Mnx1)
V$MEOX1.01 Mesenchyme homeobox 1
V$VAX1.01 Ventral anterior homeobox 1
V$VAX2.01 Ventral anterior homeobox 2
V$HNF1 Hepatic Nuclear Factor 1 V$HMBOX.01 Homeobox containing 1
V$HNF1.04 Hepatocyte nuclear factor 1 alpha (Tcf-1)
V$TCF2.01 Hepatocyte nuclear factor 1 beta (HNF1B)
V$HOMF Homeodomain transcription factors V$BARHL1.01 BarH-like homeobox 1
V$BARHL2.01 BarH-like homeobox 2
V$BARX1.01 BARX homeobox 1
V$BARX2.02 BARX homeobox 2
V$BSX.01 Brain specific homeobox
V$HMX1.01 H6 family homeobox 1 / NKX5-3
V$HMX2.03 Hmx2/Nkx5-2 homeodomain transcription factor
V$HMX3.03 H6 homeodomain HMX3/Nkx5.1 transcription factor
V$LBX2.01 Ladybird homeobox 2
V$MSX1.01 Muscle-segment homeobox 1, msh homeobox 1
V$MSX2.02 Muscle-segment homeobox 2, msh homeobox 2
V$MSX3.01 Homeobox, msh-like 3
V$NOBOX.02 NOBOX oogenesis homeobox
V$TLX2.01 T-cell leukemia, homeobox 2
V$HOXF Paralog hox genes 1-8 from the four hox clusters A, B, C, D V$HOXA1.01 Homeobox A1
V$HOXA2.01 Homeobox A2
V$HOXA3.01 Homeobox A3
V$HOXA4.01 Homeobox A4
V$HOXA5.01 Homeobox A5 / Hox-1.3
V$HOXA6.01 Homeobox A6 / Hox 1beta
V$HOXB3.01 Homeobox B3 / Hox 2-gamma
V$HOXB4.01 Homeobox B4 / Hox-2phi
V$HOXB5.01 Homeobox B5 / Hox-2alpha
V$HOXB6.01 Homeobox B6 / Hox2-beta
V$HOXB7.01 Homeobox B7 / Hox2c
V$HOXB8.01 Homeobox B8 / Hox-2delta
V$HOXC4.01 Homeobox C4 / Hox-3epsilon
V$HOXC5.01 Homeobox C5 / Hox-3delta
V$HOXC6.01 Homeobox C6 / Hox-3C
V$HOXC8.01 Homeobox C8 / Hox-3alpha
V$HOXD1.01 Homeobox D1 / Hox-4gamma
V$HOXD3.01 Homeobox D3 / Hox-4alpha
V$HOXD8.01 Homeobox D8
V$HZIP Homeodomain-leucine zipper transcription factors V$HOMEZ.01 Homeobox and leucine zipper encoding transcription factor
V$IRXF Iroquois homeobox transcription factors V$IRX2.01 Iroquois homeobox 2
V$IRX3.01 Iroquois homeobox 3
V$IRX4.01 Iroquois homeobox 4
V$IRX5.01 Iroquois homeobox 5
V$IRX6.01 Iroquois homeobox 6
V$KLFS Krueppel like transcription factors V$GKLF.03 Gut-enriched Krueppel-like factor / KLF4
V$LHXF Lim homeodomain factors V$ISL2.01 ISL LIM homeobox 2
V$LHX1.01 LIM homeobox 1
V$LHX2.01 LIM homeobox 2
V$LHX3.03 LIM homeobox 3
V$LHX4.01 LIM homeobox 4, Gsh4
V$LHX5.01 LIM homeobox 5
V$LHX6.01 LIM homeobox 6
V$LHX8.01 LIM homeobox 8
V$LHX9.01 LIM homeobox 9
V$LMX1A.01 LIM homeobox transcription factor 1, alpha
V$LMX1B.02 LIM homeobox transcription factor 1, beta
V$NKX1 NK1 homeobox transcription factors V$NKX11.01 NK1 homeobox 1, SAX2
V$NKX12.01 NK1 homeobox 2, Sax1-like
V$NKX6 NK6 homeobox transcription factors V$NKX61.03 NK6 homeobox 1, NKX6 ALPHA
V$NKX61.03 NK6 homeobox 3
V$NKXH NKX homeodomain factors V$BAPX1.01 Bagpipe homeobox homolog 1 (homeodomain protein Nkx-3.2)
V$NKX22.01 NK2 homeobox 2, NKX2BETA
V$NKX23.01 NK2 homeobox 3, CSX 3
V$NKX24.01 NK2 homeobox 4, NKX 2 DELTA
V$NKX25.04 NK2 homeobox 5, cardiac-specific homeo box 1 (Csx1)
V$NKX26.01 NK2 homeobox 6, Csx2
V$NKX29.01 NK2 homeobox 9, NKX2H
V$NKX31.02 NK3 homeobox 1, NKX-3 ALPHA, BAPX2
V$TTF1.02 Thyroid transcription factor-1, NK2 homeobox 1 (Nkx2-1)
V$NR2F Nuclear receptor subfamily 2 factors V$HNF4A.01 Hepatic nuclear factor 4alpha, DR1 sites
V$NRSF Neuron-restrictive silencer factor V$NRSF.02 Neuron-restrictive silencer factor (11 bp spacer between half sites)
V$NRSF.03 Neuron-restrictive silencer factor (17 bp spacer between half sites)
V$OCT1 Octamer binding protein V$OCT1.03 Octamer-binding transcription factor-1, POU class 2 homeobox 1 (POU2F1)
V$OCT2.01 Octamer-binding transcription factor-2, POU class 2 homeobox 2 (POU2F2)
V$OCT3_4.02 POU domain, class 5, transcription factor 1
V$POU2F3.01 POU class 2 homeobox 3 (POU2F3)
V$POU3F3.01 POU class 3 homeobox 3 (POU3F3), OTF8
V$OVOL OVO homolog-like transcription factors V$OVOL1.01 Zinc finger transcription factor OVO homolog-like 1
V$PAXH PAX homeodomain binding sites V$PAX4.02 Paired box 4, homeodomain binding site
V$PAX6_HD.01 Paired box 6, homeodomain binding site
V$PDX1 Pancreatic and intestinal homeodomain transcription factor V$IPF1.01 Insulin promoter factor 1, pancreatic and duodenal homeobox 1 (Pdx1)
V$PIT1 GHF-1 pituitary specific pou domain transcription factor V$PIT1.02 POU domain, class 1, transcription factor 1 (POU1F1) / Pituitary transcription factor-1
V$SIXF Sine oculis (SIX) homeodomain factors V$SIX1.01 (Sine oculis homeobox homolog 1
V$SIX2.01 Sine oculis homeobox homolog 2
V$SIX4.01 Sine oculis homeobox homolog 4
V$SIX6.01 Sine oculis homeobox homolog 6, optic homeobox 2 (OPTX2)
V$SORY SOX/SRY-sex/testis determinig and related HMG box factors V$SOX2.01 SRY-box containing gene 2
V$STAT Signal transducer and activator of transcription V$STAT3.02 Signal transducer and activator of transcription 3
V$TALE TALE homeodomain class recognizing TG motifs V$MEIS1.02 Meis homeobox 1
V$MRG1.01 Meis homeobox 2 (Meis2)
V$MRG2.01 Meis homeobox 3 (Meis3)
V$PKNOX1.01 PBX/knotted 1 homeobox 1
V$PKNOX2.01 PBX/knotted 1 homeobox 2
V$TGIF1.01 TGFB-induced factor homeobox 1, TALE homeobox TG-interacting factor 1
V$TGIF2.01 TGFB-induced factor homeobox 2, TALE homeobox TG-interacting factor 2
V$ZFXY Zfx and Zfy - transcription factors implicated in mammalian sex determination V$ZFX.01 X-linked zinc finger protein


Family Family Information Matrix Name Matrix Information
P$ASRC AS1/AS2 repressor complex P$AS1_AS2_II.01 AS1/AS2 repressor complex binding motif II
P$MYBL MYB-like proteins P$AS1_AS2_I.01 AS1/AS2 repressor complex binding motif I
P$NACF Plant specific NAC [NAM (no apical meristem), ATAF172, CUC2 (cup-shaped cotyledons 2)] transcription factors P$IDEF2.01 Transcription factor of rice and barley binding to the iron deficiency-responsive cis-acting element 2 (IDE2)


Family Family Information Matrix Name Matrix Information
F$PRES Pheromone response elements F$STE12.01 Transcription factor activated by a MAP kinase signaling cascade, activates genes involved in mating or pseudohyphal/invasive growth pathways

Weight matrices moved to other families

Weight matrices modified

The following weight matrices have been replaced by better matrices:

Weight matrices removed

The following weight matrices have been removed: These matrices represent individual CUT repeats that do not bind as monomers to DNA.

Matrix families renamed

The following matrix families have been renamed:

Matrix families merged

The following matrix families have been merged:

Matrix families removed

The following matrix families have been removed: