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Matrix Family Library Version 8.3

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

Matrix Family Library Version 8.3 (October 2010) contains 1283 weight matrices in 398 families classified into the following groups:

The vertebrate group represents binding site descriptions of 6126 transcription factors: The plant group represents binding site descriptions of 995 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


Family Family Information Matrix Name Matrix Information
V$AP1F AP1, Activating protein 1 V$JUNDM2.02 Jun dimerization protein 2 (secondary DNA binding preference)
V$AP1R MAF and AP1 related factors V$MAFB.01 MAFB/Kreisler basic region/leucine zipper transcription factor (half site)
V$MAFK.01 V-maf musculoaponeurotic fibrosarcoma oncogene homolog K (half site)
V$AP2F Activator protein 2 V$TCFAP2A.01 Transcription factor AP-2, alpha
V$TCFAP2B.01 Transcription factor AP-2, beta
V$TCFAP2C.01 Transcription factor AP-2, gamma
V$TCFAP2E.01 Transcription factor AP-2, epsilon
V$ARID AT rich interactive domain factor V$ARID5A.01 AT rich interactive domain 5A (MRF1-like)
V$BCL6 POZ domain zinc finger expressed in B-Cells V$BCL6.03 B-cell CLL/lymphoma 6, member B (BCL6B)
V$BRAC Brachyury gene, mesoderm developmental factor V$EOMES.01 Eomesodermin, TBR-2 (T-box, brain, 2)
V$EOMES.02 Eomesodermin, TBR-2 (secondary DNA binding preference)
V$CARE Calcium-response elements V$CARF.01 Calcium-reponse factor
V$CART Cart-1 (cartilage homeoprotein 1) V$MIXL1.01 Mix1 homeobox-like 1
V$CREB cAMP-responsive element binding proteins V$ATF1.01 Activating transcription factor 1
V$JUNDM2.01 Jun dimerization protein 2
V$E2FF E2F-myc activator/cell cycle regulator V$E2F2.01 E2F transcription factor 2
V$E2F3.01 E2F transcription factor 3
V$E2F3.02 E2F transcription factor 3 (secondary DNA binding preference)
V$EBOX E-box binding factors V$MAX.02 MYC associated factor X
V$EGRF EGR/nerve growth factor induced protein C & related factors V$EGR1.03 EGR1, early growth response 1
V$ZBTB7.01 Zinc finger and BTB domain containing 7, Proto-oncogene FBI-1, Pokemon
V$ZBTB7.02 Zinc finger and BTB domain containing 7, Proto-oncogene FBI-1, Pokemon (secondary DNA binding preference)
V$EREF Estrogen response elements V$ESRRA.01 Estrogen-related receptor alpha
V$ESRRA.02 Estrogen-related receptor alpha (secondary DNA binding preference)
V$ETSF Human and murine ETS1 factors V$EHF.01 Ets homologous factor
V$ELF3.01 E74-like factor 3 (epithelial-specific ets domain transcription factor)
V$GABPA.01 GA binding protein transcription factor, alpha
V$SPDEF.01 SAM pointed domain containing ets transcription factor
V$SPI1_PU1.03 Spleen focus forming virus (SFFV) proviral integration oncogene Spi1/transcription factor PU.1
V$FKHD Fork head domain factors V$HNF3B.03 Hepatic nuclear factor 3 beta (FOXA2)
V$FOXJ1.01 Forkhead box J1
V$FOXJ3.01 Forkhead box J3
V$FOXK1.01 Forkhead box K1, myocyte nuclear factor
V$FOXL1.01 Forkhead box L1
V$GATA GATA binding factors V$GATA1.07 GATA-binding factor 1
V$GATA2.03 GATA-binding factor 2
V$GATA3.03 GATA-binding protein 3
V$GATA5.01 GATA-binding protein 5
V$GATA6.01 GATA-binding protein 6
V$GCMF Chorion-specific transcription factors with a GCM DNA binding domain V$GCM1.02 Glial cells missing homolog 1
V$GCM1.03 Glial cells missing homolog 1 (secondary DNA binding preference)
V$GLIF GLI zinc finger family V$GLIS2.01 GLIS family zinc finger 2
V$HAND Twist subfamily of class B bHLH transcription factors V$TAL1_E2A.02 T-cell acute lymphocytic leukemia 1, SCL
V$HASF HIF-1 ancillary sequence family V$HAS.01 HIF-1 ancillary sequence
V$HESF Vertebrate homologues of enhancer of split complex V$BHLHB2.01 Basic helix-loop-helix domain containing, class B, 2
V$BHLHB2.02 Basic helix-loop-helix domain containing, class B, 2 (secondary DNA binding preference)
V$HICF Krueppel-like C2H2 zinc finger factors hypermethylated in cancer V$HIC1.02 Hypermethylated in cancer 1 (secondary DNA binding preference)
V$HIFF Hypoxia inducible factor, bHLH/PAS protein family V$HRE.02 Hypoxia-response elements
V$HOXF Paralog hox genes 1-8 from the four hox clusters A, B, C, D V$HOXA3.02 Homeobox A3
V$IRFF Interferon regulatory factors V$IRF4.03 Interferon regulatory factor 4
V$IRF5.01 Interferon regulatory factor 5
V$IRF6.01 Interferon regulatory factor 6
V$ISGF3G.01 Interferon-stimulated transcription factor 3, gamma (IRF9)
V$KLFS Krueppel like transcription factors V$EKLF.02 Erythroid krueppel like factor (EKLF, KLF1)
V$KLF7.01 Kruppel-like factor 7 (ubiquitous, UKLF)
V$KLF7.02 Kruppel-like factor 7 (ubiquitous, UKLF) (secondary DNA binding preference)
V$LEF1.04 TCF/LEF-1 (secondary DNA binding preference)
V$TCF7L1.01 HMG box transcription factor Tcf7l1 (TCF3)
V$TCF7L2.01 HMG box transcription factor Tcf7l2 (TCF4)
V$TCF7.01 T-cell specific HMG-box transcription factor 7
V$LTFM Lactotransferrin motif V$LACTOFERRIN.01 Lactotransferrin and delta-lactoferrin, growth-inhibiting protein 12
V$MTF1 Metal induced transcription factor V$MTF-1.02 Metal-regulatory transcription factor 1
V$MYBL Cellular and viral myb-like transcriptional regulators V$MYBL1.01 V-myb avian myeloblastosis viral oncogene homolog-like 1 (AMYB)
V$MYBL1.02 V-myb avian myeloblastosis viral oncogene homolog-like 1 (AMYB) (secondary DNA binding preference)
V$MYOD Myoblast determining factors V$MYF6.01 Myogenic factor 6 (herculin)
V$SGN1.01 bHLH transcription factor Sgn-1 (Salivary Glands 1), achaete-scute complex homolog 3 (Ascl3)
V$TCFE2A.01 Transcription factor E2a (E12/E47)
V$TCFE2A.02 Transcription factor E2a (E12/E47) (secondary DNA binding preference)
V$NEUR NeuroD, Beta2, HLH domain V$ASCL2.01 Achaete-scute complex homolog-like 2
V$NF1F Nuclear factor 1 V$NF1.04 Nuclear factor 1
V$NFKB Nuclear factor kappa B/c-rel V$NFKAPPAB65.02 NF-kappaB (p65)
V$NKXH NKX homeodomain factors V$NKX31.03 NK3 homeobox 1
V$NOLF Neuron-specific olfactory factor V$EBF1.01 Early B-cell factor 1
V$OSRF Odd-skipped related factors V$OSR1.01 Odd-skipped related 1
V$OSR2.01 Odd-skipped related 2
V$PLAG Pleomorphic adenoma gene V$PLAG1.02 Pleomorphic adenoma gene 1
V$PLAGL1.01 Pleiomorphic adenoma gene-like 1
V$PLAGL1.02 Pleiomorphic adenoma gene-like 1 (secondary DNA binding preference)
V$SF1F Vertebrate steroidogenic factor V$FTF.02 Alpha (1)-fetoprotein transcription factor (FTF), liver receptor homologue-1 (LRH-1), Nr5a2
V$SMAD Vertebrate SMAD family of transcription factors V$SMAD3.02 Smad3 transcription factor involved in TGF-beta signaling factor PU.1
V$SORY SOX/SRY-sex/testis determinig and related HMG box factors V$HBP1.02 HMG box-containing protein 1
V$SOX11.01 SRY-related HMG-box gene 11
V$SOX12.01 SRY-related HMG-box gene 12
V$SOX13.01 SRY-related HMG-box gene 13
V$SOX15.01 SRY-related HMG-box gene 15
V$SOX30.01 SRY-related HMG-box gene 30
V$SOX4.01 SRY-related HMG-box gene 4
V$SOX5.02 SRY-related HMG-box gene 5
V$SOX7.01 SRY-related HMG-box gene 7
V$SRY.02 Sex determining region Y
V$SP1F GC-Box factors SP1/GC V$SP4.01 Sp4 transcription factor
V$SP4.02 Sp4 transcription factor (secondary DNA binding preference)
V$XBBF X-box binding factors V$RFX3.01 Regulatory factor X, 3
V$RFX3.02 Regulatory factor X, 3 (secondary DNA binding preference)
V$RFX4.01 Regulatory factor X, 4
V$RFX4.02 Regulatory factor X, 4 (secondary DNA binding preference)
V$RFXDC2.01 Regulatory factor X domain containing 2 (RFX7)
V$ZF05 C2H2 zinc finger transcription factors 5 V$ZFP410.01 Zinc finger protein 410, APA-1
V$ZF07 C2H2 zinc finger transcription factors 7 V$ZNF263.01 Zinc finger protein 263, ZKSCAN12 (zinc finger protein with KRAB and SCAN domains 12)
V$ZF08 C2H2 zinc finger transcription factors 8 V$ZNF354C.01 KRAB-zinc finger protein synten (KID3)
V$ZF5F ZF5 POZ domain zinc finger V$ZF5.02 ZF5 POZ domain zinc finger, zinc finger protein 161
V$ZF5.03 ZF5 POZ domain zinc finger, zinc finger protein 161 (secondary DNA binding preference)
V$ZICF Members of ZIC-family, zinc finger protein of the cerebellum V$ZIC1.01 Zic family member 1 (odd-paired Drosophila homolog) (secondary DNA binding preference)
V$ZIC2.02 Zic family member 2 (odd-paired Drosophila homolog) (secondary DNA binding preference)
V$ZIC3.01 Zic family member 3 (odd-paired Drosophila homolog) (secondary DNA binding preference)


Family Family Information Matrix Name Matrix Information
P$MADS MADS box proteins P$AGL15.02 AGL15, Arabidopsis MADS-domain protein AGAMOUS-like 15
P$AP1.01 Floral homeotic protein APETALA1
P$SEP3.01 SEPALLATA3, transcription factor AGL9
P$MYCL Myc-like basic helix-loop-helix binding factors P$AMS.01 ABORTED MICROSPORES
P$CCAF Circadian control factors P$EE.01 Evening element
P$IDRS Iron-dependent regulatory sequences P$IDRS.01 Iron-dependent regulatory sequence
P$MYBS MYB proteins with single DNA binding repeat P$PHR1.01 Phosphate starvation response 1
P$EREF ER stress-response elements P$WRI1.01 WRINKLED 1


Family Family Information Matrix Name Matrix Information
I$DDVL Drosophila Dorsal Ventral Factor I$DL.04 Dorsal
I$DODD Drosophila odd-skipped I$ODD.01 Odd-skipped
I$RUNT Runt-domain transcription factors I$RUNT_BGB.01 Runt/BigBrother heterodimeric complex

Weight matrices modified

The following weight matrices have been replaced by better matrices:

Matrix families renamed

The following matrix families have been renamed: