LoGo

Description of result pages

For this motif data base, we've slightly changed the typical HOMERv3 layout. Additional description of the typical content
of results pages is provided below. Available information will appear once you point your mouse over column headers.


 

Known motif results will look like this:

Total target sequences = 33960
Total background sequences = 33914
Rank
Motif
Name
P-value
q-value
(Benjamini)
Enrichment
Motif File
PDF
1
AP-1(bZIP)/ThioMac-PU.1-ChIP-Seq/Homer1e-12170.00008524.0 (25.10%) targets
3625.4 (10.69%) backgr.		motif file (matrix) pdf
2
HIF1b(HLH)/O785-HIF1b-ChIP-Seq(GSE34871)/Homer1e-12150.00007492.0 (22.06%) targets
2944.0 (8.68%) backgr.		motif file (matrix) pdf
3
Jun-AP1(bZIP)/K562-cJun-ChIP-Seq/Homer1e-10220.00003843.0 (11.32%) targets
1036.1 (3.06%) backgr.		motif file (matrix) pdf


 

De novo motif results will look like this:

Total target sequences = 33960
Total background sequences = 33914
Rank
Motif
P-value
Enrichment
Best Match and Details
1
1e-1333
7265.0 (21.39%) targets
2647.8 (7.81%) backgr.		HIF1b(HLH)/O785-HIF1b-ChIP-Seq(GSE34871)/Homer (0.99)
More Info/Top 5 Known Motifs
2
1e-840
11031.0 (32.48%) targets
6230.1 (18.38%) backgr.		ATF3_f1_HM09 (0.88)
More Info/Top 5 Known Motifs
3
1e-694
10607.0 (31.24%) targets
6263.0 (18.48%) backgr.		MA0080.2_SPI1 (0.95)
More Info/Top 5 Known Motifs

Additional information and matches to known motifs (will open by clicking the 'More Info/Top 5 motifs' link)

Detailed information for motif1

P-value:1e-1333
ln P-value:-3.070e+03
Information content per bp:1.608
Number of target sequences with motif:7265.0
Percentage of target sequences with motif:21.39%
Number of background sequences with motif:2647.8
Percentage of background sequences with motif:  7.81%
Average position of motif in targets:201.8 +/- 76.8bp
Average position of motif in background:196.8 +/- 116.6bp
Strand bias (log2 ratio + to - strand density):0.0
Multiplicity (# of sites on avg that occur together):  1.17
Motif file:file (matrix)
reverse opposite
PDF format logos:file (matrix)
reverse opposite

Motif logos

Forward:
Reverse:


Conservation across vertebrates

Matches to known motifs

HIF1b(HLH)/O785-HIF1b-ChIP-Seq(GSE34871)/Homer

Match rank:  1
Score:0.99
Offset:0
Orientation:forward strand
Alignment:VTGASTCATNN
VTGASTCABH-
  

Jun-AP1(bZIP)/K562-cJun-ChIP-Seq/Homer

Match rank:  2
Score:0.99
Offset:-2
Orientation:reverse strand
Alignment:--VTGASTCATNN
NNATGAGTCATN-
  

AP-1(bZIP)/ThioMac-PU.1-ChIP-Seq/Homer

Match rank:  3
Score:0.98
Offset:-1
Orientation:reverse strand
Alignment:-VTGASTCATNN
GATGAGTCAT--
  

MA0303.1_GCN4

Match rank:  4
Score:0.95
Offset:-6
Orientation:forward strand
Alignment:------VTGASTCATNN----
CAAGGGATGAGTCATACTTCA
  

MA0099.1_Fos

Match rank:  5
Score:0.95
Offset:0
Orientation:forward strand
Alignment:VTGASTCATNN
GTGAGTCA---
  


 

Back to Index
AG Rehli Lab Page
Sandelin Group Page


 

The plot shows average PhastCons scores (46 vertebrate species) across motif-centered regions. The dotted red lines mark the dimensions of the motif.
The score represents the Pearson's correlation coefficient of the aligned and extended matrices
The position weight matrix and the log of the de novo motif can be downloaded both in forward and reverse directions.
Known motifs include PWMs from HOMER, HOCOMOCOv9, SwissRegulon and JASPAR databases
The best matching known motif is given along with the Pearson's correlation coefficient of the aligned and extended matrices in brackets. The 'More Info/Top 5 Known Motifs' link opens a page containing additional information on the motif as well as a more detailed comparison to known motifs.
Numbers of target and background regions containing the de novo motif are given
Motifs are ranked according to enrichment P-values
These are the total number of target sequences that where searched against the given number of auto- and GC-normalized random background sequences
Known motifs were all generated from published ChIP-seq data. The name of the motif usually contains the transcription factor name , information on its DNA binding domain, as well as details on the ChIP experiment it was derived from.
This is the P-value for motif enrichment using binomial scoring
The position weight matrix of the known motif is available for download
The motif logo can be downloaded as a pdf file
Numbers of target and background regions containing the known motif are given
These are the total number of target sequences that where searched against the given number of auto- and GC-normalized random background sequences
Motifs are ranked according to enrichment P-values