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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:

The vertebrate group represents binding site descriptions of 7847 transcription factors: 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$TBX20.01 T-box transcription factor TBX20
V$CEBP Ccaat/Enhancer Binding Protein V$CEBPB.02 CCAAT/enhancer binding protein beta
V$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$USF1.02 Upstream stimulating factor 1
V$ETSF Human and murine ETS1 factors V$ELF1.01 E74-like factor 1
V$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$TCFE2A.03 Transcription factor E2a (E12/E47)
V$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$SOX3.01 SRY-box containing gene 3
V$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$STAT5B.01 Signal transducer and activator of transcription 5B
V$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$PHD1.03 Transcription factor involved in regulation of filamentous growth
F$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


Weight matrices modified

The following weight matrices have been replaced by better matrices:

Matrix families renamed

The following matrix families have been renamed: