Matrix Family Library Version 9.0

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

Matrix Family Library Version 9.0 (August 2012) contains 1381 weight matrices in 411 families classified into the following groups:

Fungi (155 matrices in 67 families)
Insects (91 matrices in 52 families)
Plants (191 matrices in 79 families)
Vertebrates (907 matrices in 186 families)
Miscellaneous (21 matrices in 17 families)
General Core Promoter Elements (16 matrices in 10 families)

The vertebrate group represents binding site descriptions of 7847 transcription factors:

Homo sapiens: 803
Mus musculus: 784
Rattus norvegicus: 749
Bos taurus: 729
Canis familiaris: 719
Pan troglodytes: 699
Danio rerio: 644
Macaca mulatta: 576
Gallus gallus: 574
Sus scrofa: 368
Xenopus tropicalis: 299
Equus caballus: 291
Monodelphis domestica: 213
Oryctolagus cuniculus: 198
Taeniopygia guttata: 38
Ornithorhynchus anatinus: 36

The plant group represents binding site descriptions of 1105 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$AP1R	MAF and AP1 related factors	V$NRL.02	Neural retinal basic leucine zipper factor (bZIP)
V$AP2F	Activator protein 2	V$TCFAP2A.02	Transcription factor AP-2, alpha
V$BRAC	Brachyury gene, mesoderm developmental factor	V$TBX20.01	T-box transcription factor TBX20
V$BRAC	Brachyury gene, mesoderm developmental factor	V$TBX20.01	T-box transcription factor TBX20
V$CEBP	Ccaat/Enhancer Binding Protein	V$CEBPB.02	CCAAT/enhancer binding protein beta
V$CEBP	Ccaat/Enhancer Binding Protein	V$CEBPD.01	CCAAT/enhancer binding protein (C/EBP), delta
V$CTCF	CTCF and BORIS gene family, transcriptional regulators with 11 highly conserved zinc finger domains	V$CTCF.05	Insulator protein CTCF (CCCTC-binding factor)
V$EBOX	E-box binding factors	V$CMYC.02	Myelocytomatosis oncogene (c-myc proto-oncogene)
V$EBOX	E-box binding factors	V$USF1.02	Upstream stimulating factor 1
V$ETSF	Human and murine ETS1 factors	V$ELF1.01	E74-like factor 1
V$ETSF	Human and murine ETS1 factors	V$ERG.02	v-ets erythroblastosis virus E26 oncogene homolog
V$FAST	FAST-1 SMAD interacting proteins	V$FAST1.03	Forkhead box H1 (Foxh1)
V$FKHD	Fork head domain factors	V$FOXP1.01	Forkhead box P1
		V$FOXP1.02	Sites bound by FOXP1 and an alternative splicing variant FOXP1_ES, activated in ESCs
		V$FOXP1_ES.01	Alternative splicing variant of FOXP1, activated in ESCs
V$GATA	GATA binding factors	V$GATA4.01	GATA binding protein 4
V$GRHL	Grainyhead-like transcription factors	V$GRHL2.01	Grainyhead-like 2 (BOM, TFCP2L3)
V$HAML	Human acute myelogenous leukemia factors	V$AML1.02	Acute myeloid leukemia 1 protein, RUNX1 (runt-related transcription factor 1)
		V$AML2.01	RUNX3 (Runt-related transcription factor 3), AML2 (Acute myeloid leukemia 2)
		V$AML3.02	RUNX2 (Runt-related transcription factor 2) / CBFA1 (core-binding factor, runt domain, alpha subunit 1)
V$IRFF	Interferon regulatory factors	V$ISRE.02	Interferon-stimulated response element
V$MIZ1	Myc-interacting Zn finger protein 1	V$MIZ1.01	Myc-interacting Zn finger protein 1, zinc finger and BTB domain containing 17 (ZBTB17)
V$MYOD	Myoblast determining factors	V$TCF12.01	Helix-loop-helix transcription factor 12
V$MYOD	Myoblast determining factors	V$TCFE2A.03	Transcription factor E2a (E12/E47)
V$NDPK	Nucleoside diphosphate kinase	V$NM23.01	NME/NM23 nucleoside diphosphate kinase1 and 2
V$NKXH	NKX homeodomain factors	V$NKX25.05	Homeodomain factor Nkx-2.5/Csx
V$P53F	p53 tumor suppressor	V$P53.08	Tumor suppressor p53
V$PLZF	C2H2 zinc finger protein PLZF	V$PLZF.02	Promyelocytic leukemia zink finger (TF with nine Krueppel-like zink fingers)
V$SAL2	Spalt-like transcription factor 2	V$SALL2.01	Zinc finger protein Spalt-2, sal-like 2, p150(sal2)
V$SMAD	Vertebrate SMAD family of transcription factors	V$GC_SBE.01	GC-rich Smad1/5 binding element
V$SORY	SOX/SRY-sex/testis determinig and related HMG box factors	V$SOX3.01	SRY-box containing gene 3
V$SORY	SOX/SRY-sex/testis determinig and related HMG box factors	V$SOX6.01	SRY (sex determining region Y)-box 6
V$SRFF	Serum response element binding factor	V$SRF.05	Serum response factor
V$STAF	Selenocysteine tRNA activating factor	V$ZNF143.01	Zinc finger protein 143
V$STAT	Signal transducer and activator of transcription	V$STAT5A.01	Signal transducer and activator of transcription 5A
V$STAT	Signal transducer and activator of transcription	V$STAT5B.01	Signal transducer and activator of transcription 5B
V$YY1F	Activator/repressor binding to transcription initiation site	V$YY1.03	Transcription factor yin yang 1
V$ZF02	C2H2 zinc finger transcription factors 2	V$ZBTB7.03	Zinc finger and BTB domain containing 7A, pokemon
V$ZF57	KRAB domain zinc finger protein 57	V$ZFP57.01	Krüppel-associated box-containing zinc-finger protein 57 (KRAB-ZFP 57)
V$ZFHX	Two-handed zinc finger homeodomain transcription factors	V$ZEB1.01	Zinc finger E-box binding homeobox 1 (AREB6, DELTAEF1)

Plants

Family	Family Information	Matrix Name	Matrix Information
P$DREB	Dehydration responsive element binding factors	P$RAP2.1.01	Ethylene-responsive transcription factor RAP2.1
P$MADS	MADS box proteins	P$FLC.01	Flowering locus C
P$MYBL	MYB-like proteins	P$MYB96.01	Myb domain protein 96 (MYBCOV1)
P$MYBS	MYB proteins with single DNA binding repeat	P$PHR1.02	P1BS, PHR1 binding sequences
P$MYCL	Myc-like basic helix-loop-helix binding factors	P$NTMYC2.01	Tobacco bHLH transcription factor MYC2
P$MYCS	Cis-regulatory elements involved in the transcriptional activation of the arbuscular mycorrhizal (AM)-mediated inorganic phosphate transporter genes	P$MYCS.01	Mycorrhiza transcription factor
P$NACF	Plant specific NAC [NAM (no apical meristem), ATAF172, CUC2 (cup-shaped cotyledons 2)] transcription factors	P$ORS1.01	NAC domain containing protein 3 (ORE1 SISTER1)
		P$TANAC69.02	Wheat NAC-domain DNA binding factor (DNA binding site I)
		P$TANAC69.03	Wheat NAC-domain DNA binding factor (DNA binding site II)

Fungi

Family	Family Information	Matrix Name	Matrix Information
F$PHD1	Pseudoh yphal determinant 1	F$PHD1.02	Transcription factor involved in regulation of filamentous growth
F$PHD1.03	Pseudoh yphal determinant 1	Transcription factor involved in regulation of filamentous growth
F$RDNA	RDNA binding factor	F$REB1.03	Yeast transcription factor REB1
F$YRAP	Yeast activator of glycolyse genes / repressor of mating type l	F$RAP1.04	RAP1 telomeric binding sites
		F$RAP1.05	RAP1 (TUF1), activator or repressor depending on context
		F$RAP1.06	RAP1 (TUF1), activator or repressor depending on context

Weight matrices moved to other families

P$IDEF2.01 moved from P$WNAC to P$NACF
P$ANAC019.01 moved from P$WNAC to P$NACF
P$ANAC092.01 moved from P$WNAC to P$NACF
P$ANAC078.01 moved from P$WNAC to P$NACF

Weight matrices modified

The following weight matrices have been replaced by better matrices:

P$NRE.01

Matrix families renamed

The following matrix families have been renamed:

V$SALL renamed to V$SAL1