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Matrix Family Library Version 6.1

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

Matrix Family Library Version 6.1 (June 2006) contains 705 weight matrices in 294 families classified into the following groups:

The vertebrate group represents binding site descriptions of 2675 transcription factors: The plant group represents binding site descriptions of 558 transcription factors from several plant species.


New weight matrices

Vertebrates

Family Family Information Matrix Name Matrix Information
V$ARID AT rich interactive domain factor V$MRF2.01 Modulator recognition factor 2 (MRF2, ARID5B)
V$E2FF E2F-myc activator/cell cycle regulator V$E2F1_DP1.01 E2F-1/DP-1 heterodimeric complex
V$E2F1_DP2.01 E2F-1/DP-2 heterodimeric complex
V$E2F4_DP1.01 E2F-4/DP-1 heterodimeric complex
V$E2F4_DP2.01 E2F-4/DP-2 heterodimeric complex
V$RB_E2F1_DP1.01 RB/E2F-1/DP-1 heterotrimeric complex
V$EBOX E-box binding factors V$USF.04 Upstream stimulating factor 1/2
V$ETSF Human and murine ETS1 factors V$GABPB1.01 GA repeat binding protein, beta 1)
V$SPI1_PU1.01 Spleen focus forming virus (SFFV) proviral integration oncogene Spi1/transcription factor PU.1
V$SPI1_PU1.02 Spleen focus forming virus (SFFV) proviral integration oncogene Spi1/transcription factor PU.1
V$SPIB.01 Spi-B transcription factor (Spi-1/PU.1 related)
V$FKHD Fork head domain factors V$FHXA.01 Fork head homologous X binds DNA with a dual sequence specificity (FHXA and FHXB)
V$FHXB.01 Fork head homologous X binds DNA with a dual sequence specificity (FHXA and FHXB)
V$GCMF Chorion-specific transcription factors with a GCM DNA binding domain V$GCM1.01 Glial cells missing homolog 1, chorion-specific transcription factor GCMa
V$GFI1 Growth factor independence transcriptional repressor V$GFI1.02 Growth factor independence 1
V$GREF Glucocorticoid responsive and related elements V$ARE.02 Androgene receptor binding site
V$HOXF Factors with moderate activity to homeo domain consensus sequence V$NANOG.01 Homeobox transcription factor Nanog
V$IRFF Interferon regulatory factors V$IRF4.02 Interferon regulatory factor 4
V$NFAT Nuclear factor of activated T-cells V$NFAT5.01 Nuclear factor of activated T-cells 5
V$PERO Peroxisome proliferator-activated receptor V$PPAR_RXR.01 PPAR/RXR heterodimers
V$PPAR_RXR.02 PPAR/RXR heterodimers
V$PPAR Peroxisome proliferative activated receptor homodimers V$PPARG.01 Pal3 motif, bound by a PPAR-gamma homodimer
V$PRDF Positive regulatory domain I binding factor V$BLIMP1.01 Transcriptional repressor B lymphocyte-induced maturation protein-1 (Blimp-1, prdm1)
V$PTF1 Pancreas transcription factor 1, heterotrimeric transcription factor V$PTF1.01 PTF1 binding sites are bipartite with an E-box and a TC-box (RBP-J/L) spaced one helical turn apart
V$PURA Pur-alpha binds both single-stranded and douple-stranded DNA in a sequence-specific manner V$PURALPHA.01 Purine-rich element binding protein A
V$RU49 Zinc finger transcription factor RU49, zinc finger proliferation 1 - Zipro1 V$RU49.01 Zinc finger transcription factor RU49 (zinc finger proliferation 1 - Zipro 1). RU49 exhibits a strong preference for binding to tandem repeats of the minimal RU49 consensus binding site.
V$RUSH RING finger motifs that bind to the uteroglobin promoter. RUSH nucleophosphoproteins contain regions of homology with members of the SWI/SNF superfamily of DNA-dependent helicases/ATPases V$SMARCA3.01 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 3
V$SMARCA3.02 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 3
V$SORY SOx/sRY-sex/testis determinig and related HMG box factors V$HMGA.01 HMGA family of architectural transcription factors (HMGA1, HMGA2)
V$TEAF TEA/ATTS DNA binding domain factors V$TEAD.01 TEA domain-containing factors, transcriptional enhancer factors 1,3,4,5
V$TFII GTF2I repeat domain-containing factors V$GTF3R4.01 GTF2I-like repeat 4 of GTF3
V$TFII-IR4.01 GTF2I repeat 4 of the general transcription factor II, i (GTF2I)
V$THAP THAP domain containing protein V$THAP1.01 THAP domain containing, apoptosis associated protein


Plants

Family Family Information Matrix Name Matrix Information
P$CGCG Calmodulin binding / CGCG box binding proteins P$OSCBT.01 Oryza sativa CaM-binding transcription factor
P$GAGA GAGA elements P$BPC.01 (GA)n/(CT)n binding proteins (GBP, soybean; BBR, barley)
P$HMGF High mobility group factors P$HMG_IY.02 High mobility group I/Y-like protein isolated from pea
P$MYBL MYB-like proteins P$NTMYBAS1.01 Anther-specific myb gene from tobacco
P$MYBS MYB proteins with single DNA binding repeat P$HVMCB1.01 Hordeum vulgare Myb-related CAB-promoter-binding protein 1


Insects

Family Family Information Matrix Name Matrix Information
I$DELF Drosophila neuronal cis element binding factor I$GRH.01 Grainyhead transcription factor
I$DESG Drosophila escargot factor I$ESG.01 C2H2-type zinc finger protein escargot
I$DRIF Dead ringer factor I$DRI.01 Dead ringer gene of Drosophila melanogaster



Weight matrices moved to other families


Matrix families renamed


Matrix families moved to other groups

The following matrix families have been moved to the group "Other Functional Elements" as they do not describe transcription factor binding sites: The following viral matrix families have been moved to the group "Miscellaneous":