Matrix Family Library Version 6.3

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

Matrix Family Library Version 6.3 (March 2007) contains 737 weight matrices in 301 families classified into the following groups:

Fungi (47 matrices in 35 families)
Insects (43 matrices in 30 families)
Plants (142 matrices in 66 families)
Vertebrates (482 matrices in 152 families)
Miscellaneous (12 matrices in 11 families)
Other Functional Elements (11 matrices in 7 families)

The vertebrate group represents binding site descriptions of 3113 transcription factors:

Homo sapiens: 671
Mus musculus: 655
Rattus norvegicus: 555
Pan troglodytes: 393
Gallus gallus: 279
Macaca mulatta: 221
Danio rerio: 160
Bos taurus: 113
Canis familiaris: 65
Monodelphis domestica: 1

The plant group represents binding site descriptions of 573 transcription factors from several plant species.

New weight matrices

Vertebrates

Family	Family Information	Matrix Name	Matrix Information
V$HOMF	Homeodomain transcription factors	V$NOBOX.01	Homeobox containing germ cell-specific transcription factor NOBOX
V$NR2F	Nuclear receptor subfamily 2 factors	V$HNF4.03	Hepatic nuclear factor 4, DR1 sites
		V$TR2_TR4.01	DR1 binding sites for TR2 homodimers or TR2/TR4 heterodimers
		V$TR4.01	TR4 homodimer, DR1 site
V$P53F	p53 tumor suppressor	V$P53.04	Tumor suppressor p53
		V$P53.05	Tumor suppressor p53
		V$P53.06	Tumor suppressor p53
V$PAX6	PAX-4/PAX-6 paired domain binding sites	V$PAX6.03	PAX6 paired domain binding site
V$PAX6	PAX-4/PAX-6 paired domain binding sites	V$PAX6.04	PAX6 paired domain binding site
V$RORA	v-ERB and RAR-related orphan receptor alpha	V$REV-ERBA.01	Orphan nuclear receptor rev-erb alpha (NR1D1)
		V$REV-ERBA.02	Orphan nuclear receptor rev-erb alpha (NR1D1), homodimer DR2 binding site
		V$REV-ERBA.03	Orphan nuclear receptor rev-erb alpha (NR1D1), homodimer DR2 binding site
		V$RORA.01	RAR-related orphan receptor alpha
		V$RORGAMMA.01	RAR-related orphan receptor gamma
V$RXRF	RXR heterodimer binding sites	V$CAR_RXR.01	Constitutive androstane receptor / retinoid X receptor heterodimer, DR4 sites
		V$PXR_RXR.01	Pregnane X receptor / retinoid X receptor heterodimer, DR4 sites
		V$RAR_RXR.01	Retinoic acid receptor / retinoid X receptor heterodimer, DR1 sites
		V$RAR_RXR.02	Retinoic acid receptor / retinoid X receptor heterodimer, DR2 sites
		V$RAR_RXR.03	Retinoic acid receptor / retinoid X receptor heterodimer, DR5 sites
		V$RXR_RXR.01	Retinoid X receptor homodimer, DR1 sites
		V$THR.01	THR/RXR heterodimer and THR homodimer DR4 binding sites

Plants

Family	Family Information	Matrix Name	Matrix Information
P$CE1F	Coupling element 1 binding factors	P$SBOX.01	Sugar and ABA responsive element conserved in several rbcS promoters
P$IDRE	Iron-deficiency response elements	P$IDE1.01	Iron-deficiency-responsive element 1
P$MYCL	Myc-like basic helix-loop-helix binding factors	P$OSIRO2.01	Rice iron-related transcription factor 2
P$PREM	Motifs of plastid response elements	P$MGPROTORE.01	Promoter elements involved in MgProto (Mg-protoporphyrin IX) and light-mediated induction
P$SBPD	SBP-domain proteins	P$SBP.01	SQUA promoter binding proteins
P$SURE	Sugar response elements, SURE and SURE-like sequences in plant promoters	P$SURE.01	Sugar responsive elements

Weight matrices moved to other families

V$FXRE.01 moved from V$RXRF to V$FXRE
V$RTR.01 moved from V$RARF to V$GCNR
V$NBRE.01 moved from V$RORA to V$NBRE
V$TR2.01 moved from V$RORA to V$NR2F
V$TR4.01 moved from V$RORA to V$NR2F

Weight matrices renamed

The following weight matrices have been renamed because of the previously incorrect naming:

V$T3R.01 renamed to V$VERBA.01

Weight matrices modified

The following weight matrices have been replaced by better matrices:

Weight matrices removed

The following weight matrices have been removed because they describe only half sites to which the corresponding transcription factors do not bind:

V$PXRCAR.01
V$RAR.01
V$RAR.02