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PAnDA (Protein And DNA Associations)

PAnDA (Protein And DNA Associations)

PAnDA is an algorithm for the prediction of direct and indirect TF binding events.



 

Submission reference: 815375


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Run mode
Default mode is recommended for majority of users. The expert mode enables the selection of specific motifs databases and expression level thresholds in cell lines of interest. Please see Tutorial for detailed description.

Default mode
Expert mode


Human cell lines

A549 (lung carcinoma epithelial cell)
AG04450 (fetal lung fibroblast)
BJ (skin fibroblast)
GM12878 (B-lymphocyte, lymphoblastoid)
H1-hESC (embryonic stem cells)
HUVEC (umbilical vein endothelial cells)
HeLa-S3 (cervical carcinoma)
HepG2 (hepatocellular carcinoma)
K562 (leukemia)
MCF-7 (mammary gland, adenocarcinoma)
NHEK (epidermal keratinocytes)
SK-N-SH_RA (neuroblastoma cell line differentiated w/ retinoic acid)


Motifs databases

JASPAR CORE (2014)
Jolma (2013)
Uniprobe (2011)
Wang (2012)
SeAMotE (2014)
All


Cofactors expression threshold (quantiles)

0.1
0.2
0.3
0.4
0.5


Mediated Cofactors expression threshold (quantiles)

0.1
0.2
0.3
0.4
0.5


Machine learning method

Support Vector Machine (linear function)
Support Vector Machine (radial based function)
Random Forest
K-nearest neighbors
Adaptive Boosting


Interaction databases (STRING)

STRING (confidence score: 0.7)
STRING (confidence score: 0.8)
STRING (confidence score: 0.9)
none


Interaction databases (BioGRID)

BioGRID (co-localization, co-purification, FRET, Two-hydrid)
BioGRID (FRET, Two-hydrid)
none


Upload protein sequence(s) (FASTA format)

 uploaded - prot.fa delete

Upload DNA sequence(s) (FASTA format)

 uploaded - bot.dna.fa delete


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Sample data

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SP1 tethering to HNF4 in HepG2 cells - (Kardassis et al. Biochemistry 2002, 41:1217–1228)
NANOG binding modes in H1-hESC cells (high affinity peaks) - (ENCODE Project Consortium et al. Nature 2012, 489:57–74)
NANOG binding modes in H1-hESC cells (low affinity peaks) - (ENCODE Project Consortium et al. Nature 2012, 489:57–74)