Motif | LMX1A.H12CORE.0.SM.B |
Gene (human) | LMX1A (GeneCards) |
Gene synonyms (human) | |
Gene (mouse) | Lmx1a |
Gene synonyms (mouse) | |
LOGO | |
LOGO (reverse complement) | |
Motif subtype | 0 |
Quality | B |
Motif | LMX1A.H12CORE.0.SM.B |
Gene (human) | LMX1A (GeneCards) |
Gene synonyms (human) | |
Gene (mouse) | Lmx1a |
Gene synonyms (mouse) | |
LOGO | |
LOGO (reverse complement) | |
Motif subtype | 0 |
Quality | B |
Motif length | 12 |
Consensus | nnnYTAATTRnn |
GC content | 24.34% |
Information content (bits; total / per base) | 11.496 / 0.958 |
Data sources | HT-SELEX + Methyl-HT-SELEX |
Aligned words | 9172 |
HT-SELEX benchmarking | auROC10 | auPRC10 | auROC25 | auPRC25 | auROC50 | auPRC50 | |
---|---|---|---|---|---|---|---|
Overall, 4 experiments | median | 0.959 | 0.931 | 0.9 | 0.873 | 0.764 | 0.765 |
best | 0.979 | 0.961 | 0.97 | 0.95 | 0.919 | 0.898 | |
Methyl HT-SELEX, 1 experiments | median | 0.952 | 0.917 | 0.909 | 0.874 | 0.821 | 0.795 |
best | 0.952 | 0.917 | 0.909 | 0.874 | 0.821 | 0.795 | |
Non-Methyl HT-SELEX, 3 experiments | median | 0.966 | 0.945 | 0.89 | 0.872 | 0.707 | 0.735 |
best | 0.979 | 0.961 | 0.97 | 0.95 | 0.919 | 0.898 |
rSNP benchmarking, SNP-SELEX | auROC | auPRC | Pearson r | Kendall tau |
---|---|---|---|---|
batch 2 | 0.971 | 0.925 | 0.899 | 0.635 |
TF superclass | Helix-turn-helix domains {3} (TFClass) |
TF class | Homeo domain factors {3.1} (TFClass) |
TF family | HD-LIM {3.1.5} (TFClass) |
TF subfamily | LMX {3.1.5.6} (TFClass) |
TFClass ID | TFClass: 3.1.5.6.1 |
HGNC | HGNC:6653 |
MGI | MGI:1888519 |
EntrezGene (human) | GeneID:4009 (SSTAR profile) |
EntrezGene (mouse) | GeneID:110648 (SSTAR profile) |
UniProt ID (human) | LMX1A_HUMAN |
UniProt ID (mouse) | LMX1A_MOUSE |
UniProt AC (human) | Q8TE12 (TFClass) |
UniProt AC (mouse) | Q9JKU8 (TFClass) |
GRECO-DB-TF | yes |
ChIP-Seq | 0 human, 0 mouse |
HT-SELEX | 3 |
Methyl-HT-SELEX | 1 |
PCM | LMX1A.H12CORE.0.SM.B.pcm |
PWM | LMX1A.H12CORE.0.SM.B.pwm |
PFM | LMX1A.H12CORE.0.SM.B.pfm |
Alignment | LMX1A.H12CORE.0.SM.B.words.tsv |
Threshold to P-value map | LMX1A.H12CORE.0.SM.B.thr |
Motif in other formats | |
JASPAR format | LMX1A.H12CORE.0.SM.B_jaspar_format.txt |
MEME format | LMX1A.H12CORE.0.SM.B_meme_format.meme |
Transfac format | LMX1A.H12CORE.0.SM.B_transfac_format.txt |
Homer format |
A | C | G | T | |
---|---|---|---|---|
01 | 2078.0 | 2208.0 | 1976.0 | 2910.0 |
02 | 2599.5 | 2530.5 | 1802.5 | 2239.5 |
03 | 3197.0 | 2196.0 | 1985.0 | 1794.0 |
04 | 216.0 | 2000.0 | 1172.0 | 5784.0 |
05 | 0.0 | 0.0 | 0.0 | 9172.0 |
06 | 9172.0 | 0.0 | 0.0 | 0.0 |
07 | 9172.0 | 0.0 | 0.0 | 0.0 |
08 | 0.0 | 0.0 | 0.0 | 9172.0 |
09 | 11.0 | 33.0 | 69.0 | 9059.0 |
10 | 6545.0 | 206.0 | 2147.0 | 274.0 |
11 | 2684.75 | 2181.75 | 2612.75 | 1692.75 |
12 | 3006.25 | 1871.25 | 1794.25 | 2500.25 |
A | C | G | T | |
---|---|---|---|---|
01 | 0.227 | 0.241 | 0.215 | 0.317 |
02 | 0.283 | 0.276 | 0.197 | 0.244 |
03 | 0.349 | 0.239 | 0.216 | 0.196 |
04 | 0.024 | 0.218 | 0.128 | 0.631 |
05 | 0.0 | 0.0 | 0.0 | 1.0 |
06 | 1.0 | 0.0 | 0.0 | 0.0 |
07 | 1.0 | 0.0 | 0.0 | 0.0 |
08 | 0.0 | 0.0 | 0.0 | 1.0 |
09 | 0.001 | 0.004 | 0.008 | 0.988 |
10 | 0.714 | 0.022 | 0.234 | 0.03 |
11 | 0.293 | 0.238 | 0.285 | 0.185 |
12 | 0.328 | 0.204 | 0.196 | 0.273 |
A | C | G | T | |
---|---|---|---|---|
01 | -0.098 | -0.038 | -0.149 | 0.238 |
02 | 0.125 | 0.098 | -0.24 | -0.024 |
03 | 0.332 | -0.043 | -0.144 | -0.245 |
04 | -2.353 | -0.137 | -0.67 | 0.925 |
05 | -6.914 | -6.914 | -6.914 | 1.386 |
06 | 1.386 | -6.914 | -6.914 | -6.914 |
07 | 1.386 | -6.914 | -6.914 | -6.914 |
08 | -6.914 | -6.914 | -6.914 | 1.386 |
09 | -5.152 | -4.175 | -3.472 | 1.373 |
10 | 1.048 | -2.4 | -0.066 | -2.117 |
11 | 0.158 | -0.05 | 0.13 | -0.303 |
12 | 0.271 | -0.203 | -0.245 | 0.086 |
P-value | Threshold |
---|---|
0.001 | 3.090715 |
0.0005 | 5.25331 |
0.0001 | 7.93318 |