Matrix Family Library Version 2.2

[New weight matrices] [Matrix family changes]
[Matrix families renamed] [Weight matrices renamed]
[Changes in previous release]

Changes from Family Library Version 2.0 to Version 2.2

Contains 20 new weight matrices.
Matrix family classification is revised.
All matrix descriptions are revised.
References are available for each matrix.
Consistent nomenclature of matrix identifiers (matrices for the same factor are consecutively numbered).

New weight matrices

Fungi

Family	Family Information	Matrix Name	Matrix Information
F$MADS	Yeast MADS-Box factors	F$RLM1.01	Yeast MADS-Box RLM1 transcription factor
F$MADS	Yeast MADS-Box factors	F$SMP1.01	Yeast MADS-Box SMP1 transcription factor

Insects

Family	Family Information	Matrix Name	Matrix Information
I$DCAD	Drosophila homeodomain protein caudal	I$CAD.01	Drosophila homeodomain protein caudal, vertebrate homolog cdx
I$DHOM	Drosophila HOMeoproteins	I$K50_HD.01	K50 type homeodomain site selected with drosophila orthodenticle (OTD) homeodomain
I$DHUB	Drosophila gap gene hunchback	I$HB.02	Hunchback, early maternal and zygotic zinc finger gene, activated by bicoid
I$DKNI	Drosophila segmentation gene knirps	I$KNI.01	Drosophila gap gene knirps, involved in embryonic segmentation
I$DTLL	Drosophila segmentation gene tailless	I$TLL.01	Drosophila gap gene tailless, involved in embryonic segmentation
I$PRDH	Paired homeodomain factors	I$PAX6_HD.01	Drosophila PAX6 P3 homeodomain binding site
I$PRDH	Paired homeodomain factors	I$PRD_HD.01	Drosophila paired homeodomain

Plants

Family	Family Information	Matrix Name	Matrix Information
P$IBOX	Plant I-Box sites	P$IBOX.01	I-Box in rbcS genes and other light regulated genes

Vertebrates

Family	Family Information	Matrix Name	Matrix Information
V$BRAC	Brachyury gene, mesoderm developmental factor	V$TBX5.01	T-Box factor 5 site (TBX5), mutations related to Holt-Oram syndrome
V$GREF	Glucocorticoid responsive and related elements	V$ARE.01	Androgene receptor binding site
V$GREF	Glucocorticoid responsive and related elements	V$PRE.01	Progesterone receptor binding site
V$MYOD	MYOblast Determining factor	V$MYF5.01	Myf5 myogenic bHLH protein
V$NKXH	NKX - Homeodomain sites	V$NKX31.01	prostate-specific homeodomain protein NKX3.1
V$OAZF	Olfactory associated zinc finger protein	V$ROAZ.01	Rat C2H2 Zn finger protein involved in olfactory neuronal differentiation
V$PAX8	PAX-2/5/8 binding sites	V$PAX8.01	PAX 2/5/8 binding site
V$RBIT	Regulator of B-Cell IgH transcription	V$BRIGHT.01	Bright, B cell regulator of IgH transcription
V$TEAF	TEA/ATTS DNA binding domain factors	V$TEF1.01	TEF-1 related muscle factor
V$TTFF	Thyroid transcription factor-1	V$TTF1.01	Thyroid transcription factor-1 (TTF1) binding site

Matrix family changes

The following matrix families have been merged because they did contain matrices for functionally similar transcription factors:
- V$CRBP merged with V$CREB
- V$HEPA merged with V$FKHD
- V$AHR2 merged with V$AHRR
- V$CDCR merged with V$CLOX
- V$CAAT merged with V$PCAT
The following matrices were moved to another family:
- V$AHRARNT.01 was moved from family V$EBOR to family V$AHRR
- V$NKX25.01 was moved from family V$EBOR to the new family V$NKXH
- V$NKX25.02 moved from family V$HMYO to the new family V$NKXH

Matrix families renamed

The following matrix families have been renamed because of previously misleading family names:

V$OCTR renamed to V$OCTP
I$DUBX renamed to I$DSNA

Weight matrices renamed

Fungi

Old name	Renamed to	Old name	Renamed to
F$FACBCA_Q2	F$FACBCA.01	F$FACBCB_Q2	F$FACBCB.01
F$ABAA_01	F$ABAA.01	F$STUAP_01	F$STUAP.01
F$UAY_01	F$UAY.01	F$HAP1_B	F$HAP1.01
F$LEU3_B	F$LEU3.01	F$LAC9_C	F$LAC9.01
F$MAT1MC_02	F$MAT1MC.01	F$DDE1_B	F$DDE1.01
F$REB1_B	F$REB1.01	F$XBP1_B	F$XBP1.01
F$MAT1MC_01	F$STE11.02	F$STE11_01	F$STE11.01
F$ABF_C	F$ABF1.01	F$ABF1_01	F$ABF1.02
F$ADR1_01	F$ADR1.01	F$HAP234_01	F$HAP234.01
F$CBF1_B3	F$CBF1.01	F$GAL4_C	F$GAL4.01
F$GAL4_01	F$GAL4.02	F$GCN4	F$GCN4.01
F$GCN4_C	F$GCN4.02	F$GCR1_01	F$GCR1.01
F$GCR1_B	F$GCR1.02	F$HSF_02	F$HSF.01
F$HSF_03	F$HSF.02	F$HSF_04	F$HSF.03
F$HSF_05	F$HSF.04	F$MATA1_01	F$MATA1.01
F$MCM1_01	F$MCM1.01	F$MIG1_01	F$MIG1.01
F$NIT2_01	F$NIT2.01	F$PACC_01	F$PACC.01
F$PHO4_01	F$PHO4.01	F$QA1F_01	F$QA1F.01
F$RAP1_C	F$RAP1.01	F$REPCAR1_01	F$REPCAR1.01
F$STRE_B	F$STRE.01	F$STRE_01	F$STRE.02

Insects

Old name	Renamed to	Old name	Renamed to
I$ADF1_Q6	I$ADF1.01	I$BRCZ4_01	I$BRCZ4.01
I$BRCZ2_01	I$BRCZ2.01	I$BRCZ1_01	I$BRCZ1.01
I$CF1_02	I$CF1.01	I$CF2II_01	I$CF2II.01
I$CF2II_02	I$CF2II.02	I$CROC_01	I$CROC.01
I$DL_01	I$DL.01	I$DL_02	I$DL.02
I$E74A_01	I$E74A.01	I$ELF1_01	I$ELF1.01
I$GCM_01	I$GCM.01	I$HAIRY_01	I$HAIRY.01
I$BCD_01	I$BCD.01	I$FTZ_01	I$FTZ.01
I$DFD_01	I$DFD.01	I$HSF_02	I$HSF.01
I$HSF_03	I$HSF.02	I$HSF_04	I$HSF.03
I$HSF_05	I$HSF.04	I$HB_01	I$HB.01
I$KR_01	I$KR.01	I$STAT_01	I$STAT.01
I$SUH_01	I$SUH.01	I$dTCF_1	I$DTCF.01
I$TTK69_01	I$TTK.01	I$SN_01	I$SN.01
I$SN_02	I$SN.02	I$ZESTE_Q2	I$ZESTE.01

Miscellaneous

Old name	Renamed to		Old name	Renamed to
B$CRP_C	B$CRP.01		N$CES2_01	N$CES2.01
N$SKN1_01	N$SKN1.01		N$SKN1_02	N$SKN1.02

Plants

Old name	Renamed to	Old name	Renamed to
P$ABF1_01	P$ABF1.01	P$ABF1_02	P$ABF1.02
P$ABF1_03	P$ABF1.03	P$DOF1_01	P$DOF1.01
P$DOF2_01	P$DOF2.01	P$DOF3_01	P$DOF3.01
P$PBF_01	P$PBF.01	P$AG_01	P$AG.01
P$AGL3_01	P$AGL3.01	P$AGL3_02	P$AGL3.02
P$ATHB1_01	P$ATHB1.01	P$CPRF_Q2	P$CPRF.01
P$CPRF2_Q2	P$CPRF2.01	P$EMBP1A_Q2	P$EMBP1A.01
P$HBP1A_Q2	P$HBP1A.01	P$CPRF3_Q2	P$CPRF3.01
P$TAF1_Q2	P$TAF1.01	P$TGA1A_Q2	P$TGA1A.01
P$TGA1B_Q2	P$TGA1B.01	P$CDC5_01	P$CDC5.01
P$GBP_Q6	P$GBP.01	P$BZIP910_01	P$BZIP910.01
P$BZIP910_02	P$BZIP910.02	P$BZIP911_01	P$BZIP911.01
P$BZIP911_02	P$BZIP911.02	P$MADSA_Q2	P$MADSA.01
P$MADSB_Q2	P$MADSB.01	P$P_01	P$P_ACT.01
P$GAMYB_01	P$GAMYB.01	P$MYBPH3_01	P$MYBPH3.01
P$MYBPH3_02	P$MYBPH3.02	P$O2_02	P$O2.02
P$O2_03	P$O2.03	P$O2_01	P$O2.01
P$SBF1_01	P$SBF1.01	P$RAV1_02	P$RAV1-3.01
P$RAV1_01	P$RAV1-5.01

Vertebrates

Old name	Renamed to	Old name	Renamed to
V$AHRARNT_01	V$AHRARNT.01	V$AHR_01	V$AHR.01
V$AHRARNT_02	V$AHRARNT.02	V$AP1_C	V$AP1.01
V$AP1_Q2	V$AP1.02	V$AP1_Q4	V$AP1.03
V$AP1FJ_Q2	V$AP1FJ.01	V$NFE2_01	V$NFE2.01
V$VMAF_01	V$VMAF.01	V$TCF11MAFG_01	V$TCF11MAFG.01
V$BEL1_B	V$BEL1.01	V$AP2_Q6	V$AP2.01
V$AP4_Q5	V$AP4.01	V$AP4_Q6	V$AP4.02
V$TAL1ALPHAE47_01	V$TAL1ALPHAE47.01	V$TAL1BETAE47_01	V$TAL1BETAE47.01
V$TAL1BETAITF2_01	V$TAL1BETAITF2.01	V$AP4_01	V$AP4.03
V$AREB6_04	V$AREB6.04	V$AREB6_02	V$AREB6.02
V$AREB6_03	V$AREB6.03	V$AREB6_01	V$AREB6.01
V$ARP1_01	V$ARP1.01	V$BARBIE_01	V$BARBIE.01
V$BRACH_01	V$BRACH.01	V$BRN2_01	V$BRN2.01
V$CAAT_C	V$CLTR_CAAT.01	V$CART1_01	V$CART1.01
V$CDPCR3HD_01	V$CDPCR3HD.01	V$CDX2_B	V$CDX2.01
V$CEBPB_01	V$CEBPB.01	V$CEBP_C	V$CEBP.02
V$CHOP_01	V$CHOP.01	V$CDP_01	V$CDP.01
V$CDP_02	V$CDP.02	V$CDPCR3_01	V$CDPCR3.01
V$CLOX_01	V$CLOX.01	V$CMYB_01	V$CMYB.01
V$COMP1_01	V$COMP1.01	V$COUP_01	V$COUP.01
V$CP2_01	V$CP2.01	V$CREBP1_01	V$CREBP1.01
V$CREBP1CJUN_01	V$CREBP1CJUN.01	V$CREB_01	V$CREB.01
V$HLF_01	V$HLF.01	V$E4BP4_01	V$E4BP4.01
V$CREB_02	V$CREB.02	V$CREB_Q2	V$CREB.03
V$CREB_Q4	V$CREB.04	V$CREBP1_Q2	V$CREBP1.02
V$ATF_B	V$ATF.02	V$ATF_01	V$ATF.01
V$TAXCREB_01	V$TAXCREB.01	V$TAXCREB_02	V$TAXCREB.02
V$VJUN_01	V$VJUN.01	V$E2F_02	V$E2F.02
V$E2F_Q6	V$E2F.03	V$E2F_01	V$E2F.01
V$E2_01	V$E2.01	V$E2_Q6	V$E2.02
V$NKX25_01	V$NKX25.01	V$DELTAEF1_01	V$DELTAEF1.01
V$XBP1_01	V$XBP1.01	V$USF_C	V$USF.02
V$USF_Q6	V$USF.03	V$MYCMAX_B	V$MYCMAX.03
V$SREBP1_01	V$SREBP1.01	V$SREBP1_02	V$SREBP1.02
V$MYCMAX_02	V$MYCMAX.02	V$NMYC_01	V$NMYC.01
V$USF_01	V$USF.01	V$MYCMAX_01	V$MYCMAX.01
V$MAX_01	V$MAX.01	V$ARNT_01	V$ARNT.01
V$SRE_B	V$SREBP.01	V$NFY_Q6	V$NFY.02
V$NFY_C	V$NFY.03	V$NFY_01	V$NFY.01
V$EGR1_01	V$EGR1.01	V$EGR2_01	V$EGR2.01
V$EGR3_01	V$EGR3.01	V$NGFIC_01	V$NGFIC.01
V$WT1_B	V$WT1.01	V$CETS1P54_01	V$CETS1P54.01
V$NRF2_01	V$NRF2.01	V$GABP_B	V$GABP.01
V$ELK1_02	V$ELK1.02	V$ETS2_B	V$ETS2.01
V$ETS1_B	V$ETS1.01	V$ELK1_01	V$ELK1.01
V$PU1_B	V$PU1.01	V$EVI1_06	V$EVI1.06
V$EVI1_02	V$EVI1.02	V$EVI1_03	V$EVI1.03
V$EVI1_05	V$EVI1.05	V$EVI1_04	V$EVI1.04
V$EVI1_01	V$EVI1.01	V$HNF3B_01	V$HNF3B.01
V$HFH1_01	V$HFH1.01	V$HFH2_01	V$HFH2.01
V$HFH3_01	V$HFH3.01	V$HFH8_01	V$HFH8.01
V$XFD1_01	V$XFD1.01	V$XFD2_01	V$XFD2.01
V$XFD3_01	V$XFD3.01	V$FREAC2_01	V$FREAC2.01
V$FREAC3_01	V$FREAC3.01	V$FREAC4_01	V$FREAC4.01
V$FREAC7_01	V$FREAC7.01	V$LMO2COM_02	V$LMO2COM.02
V$GATA1_05	V$GATA1.04	V$GATA1_06	V$GATA1.05
V$GATA2_02	V$GATA2.01	V$GATA2_03	V$GATA2.02
V$GATA3_02	V$GATA3.01	V$GATA3_03	V$GATA3.02
V$GATA_C	V$GATA.01	V$GATA1_04	V$GATA1.03
V$GATA1_02	V$GATA1.01	V$GATA1_03	V$GATA1.02
V$GFI1_01	V$GFI1.01	V$GKLF_01	V$GKLF.01
V$GRE_C	V$GRE.01	V$AML1_01	V$AML1.01
V$HSF1_01	V$HSF1.01	V$HEN1_01	V$HEN1.01
V$HEN1_02	V$HEN1.02	V$MTBF_B	V$MTBF.01
V$NKX25_02	V$NKX25.02	V$S8_01	V$S8.01
V$HNF1_01	V$HNF1.01	V$HNF1_C	V$HNF1.02
V$HNF4_01_B	V$HNF4.01	V$HNF4_02_B	V$HNF4.02
V$HOGNESS_B	V$HOGNESS.01	V$HOX13_01	V$HOX1-3.01
V$IK2_01	V$IK2.01	V$IK1_01	V$IK1.01
V$IK3_01	V$IK3.01	V$IRF1_01	V$IRF1.01
V$IRF2_01	V$IRF2.01	V$ISRE_01	V$ISRE.01
V$LDSPOLYA_B	V$LDSPOLYA.01	V$TAACC_B	V$TAACC.01
V$LYF1_01	V$LYF1.01	V$TH1E47_01	V$TH1E47.01
V$MEF2_Q6	V$MEF2.05	V$MEF2_01	V$MEF2.01
V$HMEF2_Q6	V$HMEF2.01	V$MMEF2_Q6	V$MMEF2.01
V$RSRFC4_01	V$RSRFC4.01	V$RSRFC4_Q2	V$RSRFC4.02
V$AMEF2_Q6	V$AMEF2.01	V$MEF2_02	V$MEF2.02
V$MEF2_03	V$MEF2.03	V$MEF2_04	V$MEF2.04
V$MEF3_B	V$MEF3.01	V$MINI20_B	V$MUSCLE_INI.01
V$MINI19_B	V$MUSCLE_INI.02	V$MUSCLE_INI_B	V$MUSCLE_INI.03
V$MTF-1_B	V$MTF-1.01	V$MYOD_Q6	V$MYOD.02
V$MYOD_01	V$MYOD.01	V$LMO2COM_01	V$LMO2COM.01
V$E47_01	V$E47.01	V$E47_02	V$E47.02
V$MYOGNF1_01	V$MYOGNF1.01	V$NF1_Q6	V$NF1.01
V$MYT1_02_B	V$MYT1.02	V$MYT1_01_B	V$MYT1.01
V$MZF1_01	V$MZF1.01	V$NFAT_Q6	V$NFAT.01
V$CREL_01	V$CREL.01	V$NFKAPPAB_01	V$NFKAPPAB.01
V$NFKAPPAB65_01	V$NFKAPPAB65.01	V$NFKAPPAB50_01	V$NFKAPPAB50.01
V$NFKB_C	V$NFKAPPAB.02	V$NFKB_Q6	V$NFKAPPAB.03
V$OLF1_01	V$OLF1.01	V$NRSF_01	V$NRSF.01
V$NRSE_B	V$NRSE.01	V$OCT1_B	V$OCT1.02
V$OCT1_07	V$OCT1.06	V$OCT_C	V$OCT.01
V$OCT1_06	V$OCT1.05	V$OCT1_05	V$OCT1.04
V$OCT1_Q6	V$OCT1.03	V$OCT1_01	V$OCT1.01
V$TST1_01	V$TST1.01	V$OCT1_02	V$OCT1P.01
V$P53_01	V$P53.01	V$PAX1_01	V$PAX1.01
V$PAX3	V$PAX3.01	V$PAX4_02	V$PAX4.01
V$PAX9_B	V$PAX9.01	V$PAX5_01	V$PAX5.01
V$PAX5_02	V$PAX5.02	V$PAX6_01	V$PAX6.01
V$PBX1_02	V$PBX1.01	V$ACAAT_B	V$ACAAT.01
V$CAAT_01	V$CAAT.01	V$PDX1_B	V$PDX1.01
V$PPARA_01	V$PPARA.01	V$PIT1_B	V$PIT1.01
V$RAR_B	V$RAR.01	V$R_01	V$EBVR.01
V$RORA1_01	V$RORA1.01	V$RORA2_01	V$RORA2.01
V$ER_Q6	V$ER.01	V$PADS_C	V$PADS.01
V$LPOLYA_B	V$LPOLYA.01	V$DTYPEPA_B	V$DTYPEPA.01
V$APOLYA_B	V$APOLYA.01	V$POLY_C	V$POLYA.01
V$RREB1_01	V$RREB1.01	V$SEF1_C	V$SEF1.01
V$SF1_B	V$SF1.01	V$SMAD3_B	V$SMAD3.01
V$SMAD4_B	V$SMAD4.01	V$SOX5_01	V$SOX5.01
V$SRY_02	V$SRY.01	V$SOX9_B1	V$SOX9.01
V$SP1_Q6	V$SP1.01	V$GC_01	V$GC.01
V$SRF_Q6	V$SRF.02	V$SRF_C	V$SRF.03
V$SRF_01	V$SRF.01	V$STAT_01	V$STAT.01
V$STAT1_01	V$STAT1.01	V$STAT3_01	V$STAT3.01
V$T3R_01	V$T3R.01	V$TANTIGEN_B	V$TANTIGEN.01
V$TATA_C	V$TATA.02	V$ATATA_B	V$ATATA.01
V$TATA_01	V$TATA.01	V$MTATA_B	V$MTATA.01
V$TCF11_01	V$TCF11.01	V$VBP_01	V$VBP.01
V$VDR_RXR_B	V$VDR_RXR.01	V$VDR_RXR2_B	V$VDR_RXR.02
V$VMYB_02	V$VMYB.02	V$VMYB_01	V$VMYB.01
V$WHN_B	V$WHN.01	V$RFX1_01	V$RFX1.01
V$RFX1_02	V$RFX1.02	V$MIF1_01	V$MIF1.01
V$STAF_02	V$STAF.02	V$STAF_01	V$STAF.01
V$YY1_02	V$YY1.01	V$ZID_01	V$ZID.01