Matrix Family Library Version 7.1

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

Matrix Family Library Version 7.1 (June 2008) contains 799 weight matrices in 314 families classified into the following groups:

Fungi (47 matrices in 35 families)
Insects (44 matrices in 31 families)
Plants (153 matrices in 68 families)
Vertebrates (519 matrices in 154 families)
Miscellaneous (21 matrices in 17 families)
General Core Promoter Elements (15 matrices in 9 families)

The vertebrate group represents binding site descriptions of 4712 transcription factors:

Homo sapiens: 696
Mus musculus: 682
Rattus norvegicus: 589
Pan troglodytes: 566
Canis familiaris: 554
Gallus gallus: 418
Danio rerio: 321
Macaca mulatta: 242
Bos taurus: 537
Equus caballus: 102
Monodelphis domestica: 5

The plant group represents binding site descriptions of 660 transcription factors from several plant species.

New weight matrices

Vertebrates

Family	Family Information	Matrix Name	Matrix Information
V$AP1R	MAF and AP1 related factors	V$MAFA.01	Lens-specific Maf/MafA-sites
V$BPTF	Bromodomain and PHD domain transcription factors	V$FAC1.01	Fetal Alz-50 clone 1 (FAC1)
V$BRNF	Brn POU domain factors	V$BRN5.02	Brn-5, POU-VI protein class (also known as emb and CNS-1)
V$BRNF	Brn POU domain factors	V$BRN5.03	Brn-5, POU-VI protein class (also known as emb and CNS-1)
V$DMRT	DM domain-containing transcription factors	V$DMRT1.01	Doublesex and mab-3 related transcription factor 1
		V$DMRT2.01	Doublesex and mab-3 related transcription factor 2
		V$DMRT3.01	Doublesex and mab-3 related transcription factor 3
		V$DMRT4.01	Doublesex and mab-3 related transcription factor 4
		V$DMRT5.01	Doublesex and mab-3 related transcription factor 5
		V$DMRT7.01	Doublesex and mab-3 related transcription factor 7
V$EREF	Estrogen response elements	V$ER.03	Estrogen response elements, IR3 sites
V$GLIF	GLI zinc finger family	V$GLIS3.01	GLIS family zinc finger 3, Gli-similar 3
V$GREF	Glucocorticoid responsive and related elements	V$GRE.02	Glucocorticoid receptor, IR3 sites
V$HAND	Twist subfamily of class B bHLH transcription factors	V$SCX.01	Tendon-specific bHLH transcription factor scleraxis
V$NEUR	NeuroD, Beta2, HLH domain	V$NGN_NEUROD.01	Neurogenin and NeuroD binding sites
V$RBP2	Retinoblastoma-binding proteins with demethylase activity	V$PLU1_JARID1B.01	Jumonji, AT rich interactive domain 1B
V$SPZ1	Testis-specific bHLH-Zip transcription factors	V$SPZ1.01	Spermatogenic Zip 1 transcription factor
V$YBXF	Y-box binding transcription factors, multifunctional proteins involved in transcriptional and translational regulation, mRNA splicing, DNA replication and repair	V$YB1.01	Y box binding protein 1, has a preference for binding ssDNA
V$ZBPF	Zinc binding protein factors	V$KLF6.01	Kruppel-like factor 6

Plants

Family	Family Information	Matrix Name	Matrix Information
P$BRRE	Brassinosteroid (BR) response element	P$BZR1.01	Brassinazole-resistant 1
P$BRRE	Brassinosteroid (BR) response element	P$BZR1.02	Brassinazole-resistant 1
P$CNAC	Calcium regulated NAC-factors	P$CBNAC.01	Calmodulin-binding NAC protein
P$CNAC	Calcium regulated NAC-factors	P$CBNAC.02	Calmodulin-binding NAC protein
P$MYBL	MYB-like proteins	P$WER.01	Myb-domain transcription factor werewolf

General Core Promoter Elements

Family	Family Information	Matrix Name	Matrix Information
O$INRE	Core promoter initiator elements	O$DINR.01	Drosophila initiator motifs
O$MTEN	Core promoter motif ten elements	O$DMTE.01	Drosophila motif ten element
O$MTEN	Core promoter motif ten elements	O$HMTE.01	Human motif ten element
O$TF2D	General transcription factor IID, GTF2D	O$INR_DPE.01	Initiator (INR) and downstream promoter element (DPE) with strictly maintained spacing
O$TF3A	General transcription factor IIIA, GTF3A	O$TFIIIA.01	General transcription factor IIIA, GTF3A
O$TF3C	RNA polymerase III transcription initiation factor complex (TFIIIC)	O$TFIIIC.01	RNA polymerase III transcription initiation factor complex (TFIIIC)
O$XCPE	Activator-, mediator- and TBP-dependent core promoter element for RNA polymerase II transcription from TATA-less promoters	O$XCPE1.01	X gene core promoter element 1