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GSE114374

Basic Information
Study GSE114374
Organism Homo sapiens (GRCh38)
Tissue Colon
Protocol 10X
Reference Kinchen, J., et al. (2018). Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease. Cell 175(2): 372-386 e317.
Experiments 4 GSM3140593GSM3140594GSM3140595GSM3140596
Gene# 19893 Cell# 9271
PolyA site# Gene with polyA site#
APA event# Gene with APA event#
Cell types 4

Single Nucleotide Profile

CD4+_T_cell
Colonic_stem_cell
Colorectal_stem_cell
Intestinal_stem_cell
Sequence

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 CD4+_T_cell of GSE114374PositionFraction of each base
Motifs
CD4+_T_cell
Colonic_stem_cell
Colorectal_stem_cell
Intestinal_stem_cell
FUE (-100 to -50)
NUE (-50 to 0)
DE (0 to +50)
Motif
More Details
Motif Logo
DREME Results

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DREME results in plain text format.

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DREME results in XML 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.

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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.

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

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Show more information on the motif.

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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.
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# positive sequences matching the motif / # positive sequences.

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

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# negative sequences matching the motif / # negative sequences.

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

[close ]

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.

[close ]

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.

[close ]

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

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

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

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

[close ]

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

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

[close ]

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.

[close ]

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.

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The sequence file used by DREME to find the motifs.

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The alphabet of the sequences.

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The count of the sequences.

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The name of the alphabet symbol.

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The frequency of the alphabet symbol in the control dataset.

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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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Inputs & Settings

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Sequences

Source
Alphabet
Sequence Count
./fasta/GSE114374_CD4+_T_cell.up50nt.fa DNA 5000

Control Sequences

Source
Sequence Count
Shuffled Sequences 5000

Background

Name 
Bg. 
Bg. 
Name 
Adenine0.349A~T0.321Thymine
Cytosine0.163C~G0.167Guanine

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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