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Matrix Family Library Version 2.4

[New weight matrices] [Matrix families moved to a new group] [Matrix families renamed]
[Weight matrices renamed] [Weight matrices moved to other families]
[Changes in previous release]


Changes from Family Library Version 2.2 to Version 2.4


New weight matrices

Miscellaneous

Family Family Information Matrix Name Matrix Information
B$SIGF Bacterial promoters for a different sigma factor B$SIGMAP54.01 Subgroup of bacterial promoters specifically recognized by sigma p54 Polymerase subunit

Plants

Family Family Information Matrix Name Matrix Information
P$AREF Auxin response element P$ARE.01 Auxin Response Element
P$GCCF GCC Box family P$GCC-BOX.01 GCC-box, ethylene-responsive element (ERE)
P$HOCT Octamer motif of Histone H3, H4 promoters P$HOCT.01 Octamer motif found in plant histone H3 and H4 genes
P$LEGB Legumin Box family P$LEGB.01 Legumin box, highly conserved sequence element about 100 bp upstream of the TSS in legumin genes
P$PBOX Plant P-Box binding sites P$PBOX.01 Prolamin box, conserved in cereal seed storage protein gene promoter s
P$PGCN Plant GCN4 homolog P$GCN4.01 GCN4, conserved in cereal seed storage protein gene promoters, simil ar to yeast GCN4 and vertebrate AP-1
P$WBXF W Box family P$WRKY.01 WRKY plant specific zinc-finger-type factor associated with pathogen defence, W box
P$ZAPF Zinc-dependent Activator Protein P$ZAP1.01 Arabidopsis thaliana Zinc-dependent Activator Protein-1 (ZAP1)

Vertebrates

Family Family Information Matrix Name Matrix Information
V$BCL6 POZ domain zinc finger expressed in B-Cells V$BCL6.01 POZ/zinc finger protein, transcriptional repressor, translocations observed in diffuse large cell lymphoma
V$BCL6.02 POZ/zinc finger protein, transcriptional repressor, translocations observed in diffuse large cell lymphoma
V$BRNF Brn POU domain factors V$BRN3.01 POU transcription factor Brn-3
V$CABL C-abl DNA binding sites V$CABL.01 Multifunctional c-Abl src type tyrosine kinase
V$CART Cart-1 (cartilage homeoprotein 1) V$XVENT2.01 Xenopus homeodomain factor Xvent-2; early BMP signaling response
V$EBOX E-BOX binding factors V$ATF6.01 Member of b-zip family, induced by ER damage/stress
V$EKLF Erythroid krueppel like factor V$EKLF.01 Erythroid krueppel like factor (EKLF)
V$ETSF Human and murine ETS1 Factors V$FLI.01 ETS family member FLI
V$HOXF Factors with moderate activity to homeodomain consensus sequence V$HOXA9.01 Member of the vertebrate HOX - cluster of homeobox factors
V$LEFF LEF1/TCF V$LEF1.01 TCF/LEF-1, involved in the Wnt signal transduction pathway
V$MEIS Homeodomain factor aberrantly expressed in myeloid leukemia V$MEIS1.01 Homeobox protein MEIS1 binding site
V$MOKF Mouse Krueppel like factor V$MOK2.01 Ribonucleoprotein associated zinc finger protein MOK-2
V$PDX1 Pancreatic and intestinal homeodomain transcr. factor V$ISL1.01 Pancreatic and intestinal lim-homeodomain factor
V$RARF Nuclear receptor for retinoic acid V$RTR.01 Retinoid receptor-related testis-associated receptor (GCNF/RTR)
V$RBPF RBPJ - kappa V$RBPJK.01 Mammalian transcriptional repressor RBP-Jkappa/CBF1
V$RXRF RXR heterodimer binding sites V$FXRE.01 Farnesoid X - activated receptor (RXR/FXR dimer)
V$LXRE.01 Nuclear receptor involved in the regulation lipid homeostasis
V$SATB Special AT-rich sequence binding protein V$SATB1.01 Special AT-rich sequence-binding protein 1, predominantly expressed in thymocytes, binds to matrix attachment regions (MARs)
V$SMAD Vertebrate SMAD family of transcription factors V$FAST1.01 FAST-1 SMAD interacting protein
V$SORY SOx/sRY-sex/testis determining and related HMG Box factors V$HMGIY.01 (HMGI(Y) high-mobility-group protein I (Y), architectural transcription factor organizing the framework of a nuclear protein-DNA transcriptional complex
V$STAT Signal Transducer and Activator of Transcript. factors V$STAT5.01 STAT5: signal transducer and activator of transcription 5
V$STAT6.01 STAT6: signal transducer and activator of transcription 6
V$ZBPF Zinc binding protein factor V$ZBP89.01 Zinc finger transcription factor ZBP-89


Matrix families moved to a new group

The following matrix families have been moved to the group "Other functional elements" as they do not describe transcription factor binding sites:


Matrix families renamed

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


Weight matrices renamed

The following weight matrices have been renamed:


Weight matrices moved to other families