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Matrix Family Library Version 9.2

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

Matrix Family Library Version 9.2 (October 2014) contains 1574 weight matrices in 440 families classified into the following groups:

The vertebrate group represents binding site descriptions of 8419 transcription factors: The plant group represents binding site descriptions of 936 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$AP1F AP1, Activating protein 1 V$FOSL2.01 FOS-like antigen 2 (FRA2)
V$JUNB.01 Transcription factor Jun-B
V$AP1R MAF and AP1 related factors V$MAFF.01 Transcription factor MafF
V$NFE2L2.01 Nuclear factor, erythroid 2-like 2 (NFE2L2)
V$BEDF BED subclass of zinc-finger proteins V$ZBED4.01 Zinc finger, BED-type containing 4; GC-box binding sites
V$ZBED4.02 Zinc finger, BED-type containing 4; polyG binding sites
V$BHLH bHLH transcription factors expressed in muscle, intestine and stomach V$BHLHA15.01 Muscle, intestine and stomach expression 1 (MIST1)
V$BRAC Brachyury gene, mesoderm developmental factor V$MGA.01 MAX gene associated, dimeric binding site
V$TBR1.01 T-box brain protein 1
V$TBX15.01 T-box transcription factor TBX15, dimeric binding site
V$TBX15.02 T-box transcription factor TBX15, dimeric binding site
V$TBX21.01 T-box transcription factor TBX21, dimeric binding site
V$BRN5 Brn-5 POU domain factors V$POU6F2.01 Retina-derived POU-domain factor-1, dimeric binding site
V$BZIP Heterodimers between bZIP family members V$CEBPE_ATF4.01 Heterodimer of CEBP epsilon and ATF4
V$CEBPE_ATF4.02 Heterodimer of CEBP epsilon and ATF4
V$CART Cart-1 (cartilage homeoprotein 1) V$HESX1.01 HESX homeobox 1, dimeric binding site
V$PROP1.02 Prophet of Pit 1, PROP paired-like homeobox 1, dimeric binding site
V$CEBP Ccaat/Enhancer Binding Protein V$CEBPE.01 CCAAT/enhancer binding protein (C/EBP), epsilon
V$CEBPE.02 CCAAT/enhancer binding protein (C/EBP), epsilon
V$CEBPG.01 CCAAT/enhancer binding protein (C/EBP), gamma
V$CLOX CLOX and CLOX homology (CDP) factors V$CUX1.01 Cut-like homeobox 1, dimeric binding site
V$CUX2.01 Cut-like homeobox 2, dimeric binding site
V$CREB cAMP-responsive element binding proteins V$BATF3.01 Basic leucine zipper transcription factor, ATF-like 3
V$CREB3.01 cAMP responsive element binding protein 3, dimeric binding site
V$CREB3L2.01 cAMP responsive element binding protein 3-like 2, BBF2H7, dimeric binding site
V$CTCF CTCF and BORIS gene family, transcriptional regulators with 11 highly conserved zinc finger domains V$CTCFL.01 CCCTC-binding factor (zinc finger protein)-like (BORIS)
V$DMTF Cyclin D binding myb-like transcription factor V$DMP1.02 Cyclin D binding myb-like transcription factor
V$E2FF E2F-myc activator/cell cycle regulator V$E2F7.01 E2F transcription factor 7
V$E2F7.02 E2F transcription factor 7
V$EBOX E-box binding factors V$MNT.01 MAX binding protein
V$EGRF EGR/nerve growth factor induced protein C & related factors V$EGR2.02 Egr-2/Krox-20 early growth response gene product
V$EREF Estrogen response elements V$ESR2.01 Estrogen receptor 2 (ER beta)
V$ESRR Estrogen-related receptors V$ESRRA.04 Estrogen-related receptor alpha, homodimer DR4 binding site
V$ESRRA.05 Estrogen-related receptor alpha, homodimer DR5 binding site
V$ESRRG.01 Estrogen-related receptor gamma, homodimer DR4 binding site
V$ETSF Human and murine ETS1 factors V$ETV3.02 Ets variant 3
V$GABPA.02 GA binding protein transcription factor, alpha
V$FKHD Fork head domain factors V$FOXO1.01 Forkhead box protein O1
V$GLIF GLI zinc finger family V$GLIS1.01 GLIS family zinc finger 1
V$ZIC3.02 Zic family member 3 (odd-paired Drosophila homolog)
V$GMEB Glucocorticoid modulatory element binding proteins V$GMEB2.01 Glucocorticoid modulatory element binding protein 2
V$HESF Vertebrate homologues of enhancer of split complex V$HES7.01 Hairy and enhancer of split 7
V$HIFF Hypoxia inducible factor, bHLH/PAS protein family V$ARNTL.01 Aryl hydrocarbon receptor nuclear translocator-like, homodimer
V$HRE.03 Hypoxia response elements, binding sites for HIF1alpha/ARNT heterodimers
V$HNF6 Onecut homeodomain factor HNF6 V$HNF6.02 Liver enriched Cut - Homeodomain transcription factor HNF6 (ONECUT1)
V$HNFP Histone nuclear factor P V$HINFP.01 Histone H4 transcription factor, MIZF, dimeric binding site
V$HOXC HOX - PBX complexes V$HOXB4.02 Homeobox B4
V$HUB1 HTLV-I U5 repressive element-binding protein 1 V$ZNF282.01 Zinc finger protein 282 (HTLV-I U5 repressive element-binding protein 1)
V$IRFF Interferon regulatory factors V$IRF2.02 Interferon regulatory factor 2
V$IRF8.01 Interferon consensus sequence binding protein 1, interferon regulatory factor 8, dimeric binding site
V$KLFS Krueppel like transcription factors V$KLF12.01 Krueppel-like factor 12 (AP-2rep)
V$KLF2.01 Krueppel-like factor 2 (lung) (LKLF)
V$LTSM Localized tandem sequence motif V$LTSM.01 LTSM elements with 7 bp spacer
V$LTSM.02 LTSM elements with 6 bp spacer
V$LTSM.03 LTSM elements with 8 bp spacer
V$MEF3 MEF3 binding sites V$SIX2.02 Sine oculis homeobox homolog 2
V$MITF Microphthalmia transcription factor V$CLEAR.01 Coordinated Lysosomal Expression and Regulation (CLEAR) elements bound by TFEB
V$MYBL Cellular and viral myb-like transcriptional regulators V$MYBL2.01 v-myb myeloblastosis viral oncogene homolog (avian)-like 2 (BMYB), dimeric binding site
V$MYOD Myoblast determining factors V$MYOD.02 Myogenic regulatory factor MyoD (myf3)
V$MYOGENIN.03 Myogenic bHLH protein myogenin (myf4)
V$TCF21.01 Podocyte-expressed 1 (POD1)
V$NACA Nascent polypeptide associated complex and coactivator alpha V$NACA1.01 Nascent polypeptide-associated complex subunit alpha 1
V$NEUR NeuroD, Beta2, HLH domain V$OLIG2.01 Oligodendrocyte lineage transcription factor 2
V$NFAT Nuclear factor of activated T-cells V$NFATC1.01 Nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 1, dimeric binding site
V$NKXH NKX homeodomain factors V$NKX21.01 NK2 homeobox 1 (Thyroid transcription factor 1)
V$NKX31.04 NK3 homeobox 1
V$NR2F Nuclear receptor subfamily 2 factors V$NR2F6.01 ERBA-related gene-2, homodimer DR1 binding site
V$P53F p53 tumor suppressor V$TP63.01 Tumor protein p63
V$PAX7 Paired box 7 V$PAX7.01 Paired box 7 homeodomain-binding motif
V$PAX9 PAX-9 binding sites V$PAX9.02 Paired box protein Pax-9
V$PEG3 Imprinted transcription factor PEG3 V$PEG3.01 Paternally expressed 3
V$PRDM PR (PRDI-BF1-RIZ1 homologous) domain transcription factor V$PRDM4.01 PR domain zinc finger protein 4 (PFM1)
V$PROX Prospero-related homeobox V$PROX1.01 Prospero homeobox protein 1, dimeric binding site
V$RORA v-ERB and RAR-related orphan receptor alpha V$RORA.02 RAR-related orphan receptor alpha, homodimer DR5 binding site
V$RORA.03 RAR-related orphan receptor alpha, homodimer DR2 binding site
V$RXRF RXR heterodimer binding sites V$RARA.01 Retinoic acid receptor alpha, homodimer DR4 binding site
V$RARG.01 Retinoic acid receptor gamma, homodimer DR2 binding site
V$THRA.01 Thyroid hormone receptor, alpha (ER4 - everted repeat, spacer 4)
V$THRB.01 Thyroid hormone receptor, beta (ER4 - everted repeat, spacer 4)
V$THRB.02 Thyroid hormone receptor, beta (ER5 - everted repeat, spacer 5)
V$THRB.03 Thyroid hormone receptor, beta (ER6 - everted repeat, spacer 6)
V$SNAI Snail family of zinc finger transcription factors binding to E-box motifs V$SCRT2.01 Scratch homolog 2, zinc finger protein, transcriptional repressor scratch 2
V$SORY SOX/SRY-sex/testis determinig and related HMG box factors V$SOX10.01 SRY (sex determining region Y)-box 10, dimeric binding sites
V$SOX10.02 SRY (sex determining region Y)-box 10, dimeric binding sites
V$SOX10.03 SRY (sex determining region Y)-box 10, dimeric binding sites
V$SOX1.01 SRY (sex determining region Y)-box 1, dimeric binding sites
V$SOX1.02 SRY (sex determining region Y)-box 1, dimeric binding sites
V$SOX1.03 SRY (sex determining region Y)-box 1, dimeric binding sites
V$SOX1.04 SRY (sex determining region Y)-box 1, dimeric binding sites
V$SOX14.01 SRY (sex determining region Y)-box 14, dimeric binding sites
V$SOX15.02 SRY-related HMG-box gene 15, dimeric binding sites
V$SOX15.03 SRY-related HMG-box gene 15, dimeric binding sites
V$SOX15.04 SRY-related HMG-box gene 15, dimeric binding sites
V$SOX17.01 SRY (sex determining region Y)-box 17, dimeric binding sites
V$SOX17.02 SRY (sex determining region Y)-box 17, dimeric binding sites
V$SOX18.01 SRY (sex determining region Y)-box 18, dimeric binding sites
V$SOX18.02 SRY (sex determining region Y)-box 18, dimeric binding sites
V$SOX18.03 SRY (sex determining region Y)-box 18, dimeric binding sites
V$SOX2.02 SRY-box containing gene 2, dimeric binding sites
V$SOX2.03 SRY-box containing gene 2, dimeric binding sites
V$SOX21.01 SRY (sex determining region Y)-box 21, dimeric binding sites
V$SOX21.02 SRY (sex determining region Y)-box 21, dimeric binding sites
V$SOX21.03 SRY (sex determining region Y)-box 21, dimeric binding sites
V$SOX3.02 SRY-box containing gene 3, dimeric binding sites
V$SOX3.03 SRY-box containing gene 3, dimeric binding sites
V$SOX3.04 SRY-box containing gene 3, dimeric binding sites
V$SOX4.02 SRY-related HMG-box gene 4, dimeric binding sites
V$SOX7.02 SRY-related HMG-box gene 7, dimeric binding sites
V$SOX7.03 SRY-related HMG-box gene 7, dimeric binding sites
V$SOX7.04 SRY-related HMG-box gene 7, dimeric binding sites
V$SOX8.01 SRY (sex determining region Y)-box 8, dimeric binding sites
V$SOX8.02 SRY (sex determining region Y)-box 8, dimeric binding sites
V$SOX8.03 SRY (sex determining region Y)-box 8, dimeric binding sites
V$SOX9.04 SRY (sex-determining region Y) box 9, dimeric binding sites
V$SOX9.05 SRY (sex-determining region Y) box 9, dimeric binding sites
V$SOX9.06 SRY (sex-determining region Y) box 9, dimeric binding sites
V$SOX9.07 SRY (sex-determining region Y) box 9, dimeric binding sites
V$SOX9.08 SRY (sex-determining region Y) box 9, dimeric binding sites
V$SOX9.09 SRY (sex-determining region Y) box 9, dimeric binding sites
V$SRY.03 Sex determining region Y, dimeric binding sites
V$SRY.04 Sex determining region Y, dimeric binding sites
V$SRY.05 Sex determining region Y, dimeric binding sites
V$SREB Sterol regulatory element binding proteins V$SREBP.04 Sterol regulatory element binding transcription factor
V$TAIP TGF-beta induced apoptosis proteins V$CSRNP1.01 Cysteine-serine-rich nuclear protein 1 (AXUD1, AXIN1 up-regulated 1)
V$CSRNP3.01 Cysteine-serine-rich nuclear protein 3
V$TALE TALE homeodomain class recognizing TG motifs V$MRG1.02 TALE homeobox protein Meis 2, dimeric binding site
V$TGIF2LX.01 TGFB-induced factor homeobox 2-like, X-linked, dimeric binding site
V$XBBF X-box binding factors V$RFX2.01 Regulatory factor X 2
V$RFX3.03 Regulatory factor X 3
V$RFX4.03 Regulatory factor X 4
V$RFX5.02 Regulatory factor X 5
V$ZBED Zinc finger BED domain-containing protein V$ZBED1.01 Zinc finger, BED-type containing 1
V$ZBED1.02 Zinc finger, BED-type containing 1
V$ZF05 C2H2 zinc finger transcription factors 5 V$ZNF410.02 Zinc finger protein 410
V$ZF12 C2H2 zinc finger transcription factors 12 V$ZFP652.01 Zinc finger protein 652 (ZNF652)
V$ZFP652.02 Zinc finger protein 652 (ZNF652)
V$ZF13 C2H2 zinc finger transcription factors 13 V$ZNF435.01 Zinc finger and SCAN domain containing 16
V$ZF14 C2H2 zinc finger transcription factors 14 V$ZNF232.01 Zinc finger protein 232 (ZSCAN11)
V$ZICF Members of ZIC-family, zinc finger protein of the cerebellum V$ZIC3.03 Zinc finger protein of the cerebellum (Zic3)


Plants

Family Family Information Matrix Name Matrix Information
P$CCAF Circadian control factors P$LHY.01 LATE ELONGATED HYPOCOTYL
P$KAN1 Transcription repressor KANADI1 P$KBX.01 KANADI box
P$LICM Leaf and tiller angle increased controller (LIC) binding motif P$OSLIC.01 Oriza sativa leaf and tiller angle increased controller
P$MIIG MYB IIG-type binding sites P$ATMYB61.01 Myb domain protein 61)
P$PCDR Factors involved in programmed cell death response P$GMNAC30_81.01 Heterodimer of NAC-domain transcription factors GmNAC30 and GmNAC81
P$PNRE Plant nitrate-responsive cis-elements P$NRE43-D8.01 Motif similar to the conserved 8 bp distal element of the 43 bp pseudo-palindromic nitrogen response element (NRE)
P$SWNS Secondary wall NACS P$MDM.01 Mitochondrial dysfunction motif
P$WTBX WT-Box P$WRKY70.01.seq WRKY DNA-binding protein 70


Insects

Family Family Information Matrix Name Matrix Information
I$DHUB Drosophila gap gene hunchback I$CAS.01 Zinc finger transcription factor castor


General Core Promoter Elements

Family Family Information Matrix Name Matrix Information
O$TELO Protein involved in telomere maintenance O$ZSCAN4.01 Zinc finger and SCAN domain containing 4



Weight matrices modified

The following weight matrices have been replaced by better matrices:

Weight matrices moved to other families