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GSE102086



Basic Information
Study GSE102086
Organism Mus musculus (mm10)
Tissue Embryonic skin
Protocol 10X
Reference Fan, X., et al. (2018). Single Cell and Open Chromatin Analysis Reveals Molecular Origin of Epidermal Cells of the Skin. Developmental Cell 47(1): 21-37.e25.
Experiments 8 GSM2723623GSM2723624GSM2723625GSM2723626GSM2723627GSM2723628GSM2723629GSM2723630

Gene# 24894 Cell# 1578
PolyA site# Gene with polyA site#
APA event# Gene with APA event#
Cell types 10

Single Nucleotide Profile

Endothelial_cells
Erythroid-like_and_erythroid_precursor_cells
Fibroblasts
Keratinocytes
Macrophages
Mast_cells
Melanocytes
Peri-islet_Schwann_cells
Pericytes
Unknown

Single Nucleotide Profile: 5000 poly(A) sites
0501001502000.10.20.30.40.5
ATCGSingle nucleotide profile of 200nt around the poly(A) site in the 3' UTR of the Endothelial_cells of GSE102086PositionFraction of each base
Motifs
Endothelial_cells
Erythroid-like_and_erythroid_precursor_cells
Fibroblasts
Keratinocytes
Macrophages
Mast_cells
Melanocytes
Peri-islet_Schwann_cells
Pericytes
Unknown
FUE (-100 to -50)
NUE (-50 to 0)
DE (0 to +50)
Motif Logo
DREME Results

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DREME results in plain text format.

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The name of the motif uses the IUPAC codes for nucleotides which has a different letter to represent each of the 15 possible combinations.

The name is itself a representation of the motif though the position weight matrix is not directly equivalent as it is generated from the sites found that matched the letters given in the name.

Read more about the MEME suite's use of the IUPAC alphabets.

The E-value is the enrichment p-value times the number of candidate motifs tested.

The enrichment p-value is calculated using Fisher's Exact Test for enrichment of the motif in the positive sequences.

Note that the counts used in Fisher's Exact Test are made after erasing sites that match previously found motifs.

The E-value of the motif calculated without erasing the sites of previously found motifs.

Show more information on the motif.

Submit your motif to another MEME Suite program or download your motif.

Supported Programs
Tomtom
Tomtom is a tool for searching for similar known motifs.
MAST
MAST is a tool for searching biological sequence databases for sequences that contain one or more of a group of known motifs.
FIMO
FIMO is a tool for searching biological sequence databases for sequences that contain one or more known motifs.
GOMo
GOMo is a tool for identifying possible roles (Gene Ontology terms) for DNA binding motifs.
SpaMo
SpaMo is a tool for inferring possible transcription factor complexes by finding motifs with enriched spacings.

# positive sequences matching the motif / # positive sequences.

Note these counts are made after erasing sites that match previously found motifs.

# negative sequences matching the motif / # negative sequences.

Note these counts are made after erasing sites that match previously found motifs.

The p-value of Fisher's Exact Test for enrichment of the motif in the positive sequences.

Note that the counts used in Fisher's Exact Test are made after erasing sites that match previously found motifs.

The E-value is the motif p-value times the number of candidate motifs tested.

Note that the p-value was calculated with counts made after erasing sites that match previously found motifs.

The E-value of the motif calculated without erasing the sites of previously found motifs.

All words matching the motif whose uncorrected p-value is less than 0.01.

# positive sequences with matches to the word / # positive sequences.

Note these counts are made after erasing sites that match previously found motifs.

# negative sequences with matches to the word / # negative sequences.

Note these counts are made after erasing sites that match previously found motifs.

The p-value of Fisher's Exact Test for enrichment of the word in the positive sequences.

Note that the counts used in Fisher's Exact Test are made after erasing sites that match previously found motifs.

The word p-value times the number of candidates tested.

Note that the p-value was calculated with counts made after erasing sites that match previously found motifs.

The sequence file used by DREME to find the motifs.

The alphabet of the sequences.

The count of the sequences.

The name of the alphabet symbol.

The frequency of the alphabet symbol in the control dataset.

Details

Positives
Negatives
P-value
E-value
Unerased E-value
/ /

Enriched Matching Words

For further information on how to interpret these results please access https://meme-suite.org/meme/doc/dreme.html.
To get a copy of the MEME software please access https://meme-suite.org.

If you use DREME in your research please cite the following paper:
Timothy L. Bailey, "DREME: Motif discovery in transcription factor ChIP-seq data", Bioinformatics, 27(12):1653-1659, 2011. [full text]

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Discovered Motifs

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Inputs & Settings

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Sequences

Source
Alphabet
Sequence Count
./fasta/GSE102086_Endothelial_cells.up50nt.fa DNA 5000

Control Sequences

Source
Sequence Count
Shuffled Sequences 5000

Background

Name 
Bg. 
Bg. 
Name 
Adenine0.354A~T0.309Thymine
Cytosine0.171C~G0.166Guanine

Other Settings

Strand Handling This alphabet only has one strand Only the given strand is processed Both the given and reverse complement strands are processed
# REs to Generalize100
Shuffle Seed1
E-value Threshold0.05
Max Motif CountNo maximum motif count.
Max Run TimeNo maximum running time.
DREME version
5.3.3 (Release date: Sun Feb 7 15:39:52 2021 -0800)
Reference
Timothy L. Bailey, "DREME: Motif discovery in transcription factor ChIP-seq data", Bioinformatics, 27(12):1653-1659, 2011. [full text]
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