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Matrix Family Library Version 9.1

[New weight matrices] [Matrices modified] [Matrices removed]
[Changes in previous release] [View all matrices]

Matrix Family Library Version 9.1 (September 2013) contains 1424 weight matrices in 418 families classified into the following groups:

The vertebrate group represents binding site descriptions of 8403 transcription factors: The plant group represents binding site descriptions of 1160 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$AP1F AP1, Activating protein 1 V$FOSL1.01 FOS-like antigen-1 (FRA1)
V$JUND.01 Transcription factor jun-D
V$AP1R MAF and AP1 related factors V$NFE2.02 Leucine zipper protein NF-E2 (nuclear factor, erythroid-derived
V$CAAT CCAAT binding factors V$NFY.05 Nuclear factor Y (Y-box binding factor)
V$CREB cAMP-responsive element binding proteins V$CREB1.02 cAMP-responsive element binding protein 1
V$E2FF E2F-myc activator/cell cycle regulator V$E2F1.01 E2F transcription factor 1
V$E2F6.01 E2F transcription factor 6
V$EBOX E-box binding factors V$MAX.03 MYC associated factor X
V$EGRF EGR/nerve growth factor induced protein C & related factors V$EGR1.04 EGR1, early growth response 1
V$EREF Estrogen response elements V$ESRRA.03 Estrogen-related receptor alpha
V$FKHD Fork head domain factors V$FOXA1.01 Forkhead box protein A1, hepatocyte nuclear factor 3-alpha (HNF-3-alpha)
V$FOXP2.01 Forkhead box protein P2
V$HNF3B.04 HNF-3-beta, Forkhead box protein A2 (FOXA2)
V$HESF Vertebrate homologues of enhancer of split complex V$DEC1.02 Basic helix-loop-helix protein known as Dec1, Stra13, Sharp2 or BHLHE40
V$IKZF Ikaros family zinc finger 5 V$PEGASUS.01 IKAROS family zinc finger 5 (Pegasus)
V$MEF2 MEF2, myocyte-specific enhancer binding factor V$MEF2A.01 Myocyte enhancer factor 2A
V$MEF2C.01 Myocyte enhancer factor 2C
V$NR2F Nuclear receptor subfamily 2 factors V$HNF4A.02 Hepatic nuclear factor 4 alpha, DR1 sites
V$HNF4G.01 Hepatocyte nuclear factor 4 gamma (NR2A2), DR1 sites
V$NRF1 Nuclear respiratory factor 1 V$NRF1.02 Nuclear respiratory factor 1 (NRF1)
V$PBXC PBX - MEIS complexes V$PBX3.01 Pre-B-cell leukemia homeobox 3
V$PRDF Positive regulatory domain I binding factor V$PRDM1.02 PRDI (positive regulatory domain I element) binding factor 1
V$TEAF TEA/ATTS DNA binding domain factors V$TEAD4.01 TEA domain family member 4, TEF-3
V$XBBF X-box binding factors V$RFX5.01 Regulatory factor X, 5 (influences HLA class II expression)
V$ZF07 C2H2 zinc finger transcription factors 7 V$ZNF263.02 Zinc finger protein 263, ZKSCAN12 (zinc finger protein with KRAB and SCAN domains 12)
V$ZF11 C2H2 zinc finger transcription factors 11 V$ZBTB3.01 Zinc finger and BTB domain containing 3


Plants

Family Family Information Matrix Name Matrix Information
P$AHBP Arabidopsis homeobox protein P$REVOLUTA.01 Homeobox-leucine zipper protein REVOLUTA (REV, IFL1)
P$ATAF ATAF-like NAC domain containing proteins P$ATAF2.01 Arabidopsis NAC domain containing protein 81; ATAF2
P$FLO2 Floral homeotic protein APETALA 2 P$AP2.01 APETALA2
P$GTBX GT-box elements P$GT2_GT3.01 GT2-box and GT3-box motifs
P$JARE Jasmonate response element P$JARE.01 Jasmonate response element
P$LBDF LOB domain factors P$LOB.01 Lateral organ boundaries
P$LEGB Legumin Box family P$FUSCA3.01 B3 domain-containing transcription factor FUS3
P$MADS MADS box proteins P$SOC1.01 Suppressor of overexpression of CO 1 (AGL20)
P$MIIG MYB IIG-type binding sites P$SMRE.01 Secondary wall MYB-responsive element, MYB46 and MYB83 binding sites
P$MYBL MYB-like proteins P$MYBR1.01 Myb domain protein r1 (ATMYB44)
P$MYCL Myc-like basic helix-loop-helix binding factors P$DYT1.01 Transcription factor DYSFUNCTIONAL TAPETUM 1
P$DYT1.02 Transcription factor DYSFUNCTIONAL TAPETUM 1
P$HUD.01 Hormone up-regulated at dawn element
P$PIF3.02 Phytochrome B-regulated transcription factor PIF3 (nuclear-localized bHLH-protein)
P$PIF4.01 Phytochrome interacting factor 4
P$TDTF Transposase-derived transcription factors P$FHY3.01 Far-red elongated hypocotyls 3 protein
P$TCPF DNA-binding proteins with the plant specific TCP-domain P$TCP16.01 TCP domain protein 16
P$TODS Time-of-day-specific cis regulatory elements P$ME.01 Morning element (sequence motifs enriched in morning-phased genes)



Weight matrices modified

The following weight matrices have been replaced by better matrices:

Weight matrices removed

The following weight matrices have been removed: