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READMEFILE.txt
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#READMEFILE.TXT CONTENTS TABLE# >Osterwalder Lab Bern 2021.09.27<
-------------------------------
1. Provider
2. Softwares
3. Biosample
4. UCSC Tracks Acronyms
5. Attachments List
-------------------------------
1. Provider
Osterwalder Lab, University of Bern (https://www.osterwalderlab.com)
Iros Barozzi, Medical University of Vienna (https://krebsforschung.meduniwien.ac.at/en/research/research-focus/tumor-progression-and-metastasis/iros-barozzi/)
2. Softwares
Motifs Annotations by Position Weight Matrices (PWMs) sequence probability match -> MEME-suite package FIMO tool (https://anaconda.org/bioconda/meme)
Average Conservation Score by phyloP (phylogenetic p-value) -> Bwtool (https://github.com/CRG-Barcelona/bwtool)
3. Biosample
Assay : polyA plus RNA-seq
Replicates : 2
Biosample summary : Mus musculus strain B6NCrl heart tissue embryo (11.5 days)
Biosample Type : tissue
Replication type : isogenic
Description : PolyA RNA-Seq from oligo-dT primed Total RNA on embryonic 11.5 day (e11.5) mouse heart
Sample provider : Lab Barbara Wold, Caltech
Award : U54HG006998 (Richard Myers, HAIB)
Project : ENCODE
URLLinks : https://www.encodeproject.org/experiments/ENCSR691OPQ/
https://doi.org/doi:10.17989%2FENCSR691OPQ
4. UCSC Tracks Acronyms
CLS = TF Motif Class
FAM = TF Motif Family
PWM = TF Motif's Position Weight Matrix ID
STR = TF Motif's Strand localisation
SEQ = TF Motif's sequence
SCR = TF Motif's "Identity" Score (MEME-suite-FIMO tool; TF Motif's matrix match probability)
PVL = TF Motif's "Identity" p-value (MEME-suite-FIMO tool; TF Motif's matrix match probability)
ACS = Average Conservation Score (Bwtool; TFs Motifs sequences conservation scoring – By phyloP [phylogenetic p-value])
5. Attachments List
ATTACHMENT 1 = Motif's relative TPM / FPKM scores (FPKM threshold : >= 2) : AnnotatedTFsMotifsTPMFPKM.txt
ATTACHMENT 2 = PWM / Mouse_Gene_Name / Name_Human / ID / Superclass / Class / Family / Subfamily / References : AnnotatedTFsMotifsList.txt