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SCPD specifications

Information


Unique identifier OMICS_01867
Name SCPD
Restrictions to use None
Community driven No
Data access Browse
User data submission Allowed
Maintained Yes

Taxon


  • Plants and Fungi
    • Saccharomyces cerevisiae

Maintainer


  • person_outline Zhu J.

Publication for SCPD

SCPD citations

 (13)
library_books

MIP diversity from Trichoderma: Structural considerations and transcriptional modulation during mycoparasitic association with Fusarium solani olive trees

2018
PLoS One
PMCID: 5854309
PMID: 29543834
DOI: 10.1371/journal.pone.0193760

[…] m Trichoderma harzianum CBS 226.95 that corresponded to the 1.5Kb of the genomic sequence upstream of the initiation codon. TFBSs were detected with the Promoter Database of Saccharomyces cerevisiae, SCPD (http://rulai.cshl.edu/SCPD/; []), and the putative biological processes (GO) were identified with SCPD and the Universal Protein Resource Uniprot (http://www.uniprot.org/). […]

library_books

Role of MAPK Signaling Pathways in Regulating the Hydrophobin Cryparin in the Chestnut Blight Fungus Cryphonectria parasitica

2017
PMCID: 5780368
PMID: 29371804
DOI: 10.5941/MYCO.2017.45.4.362

[…] ntained three types of binding motifs at a combined p-value of 8.41e-5 (). Motif 1 occurred five times and motifs 2 and 3 each occurred twice in the promoter region (). Using the yeast motif database SCPD, the motif database-scanning algorithm TOMTOM identified regulatory elements corresponding to binding motifs []. The regulatory elements corresponding to motif 1 were stress responsive myocyte en […]

library_books

Evaluation of single cell genomics to address evolutionary questions using three SAGs of the choanoflagellate Monosiga brevicollis

2017
Sci Rep
PMCID: 5591225
PMID: 28887541
DOI: 10.1038/s41598-017-11466-9

[…] For the phylogenomic analyses, we used the dataset of 78 single-copy protein domains (SCPD78) developed in a previous study. For each of our SAGs assemblies, we recovered the gene markers using the ortholog search algorithm developed by Torruella and co-workers which uses tBLASTn to ex […]

library_books

Drug Repositioning for Cancer Therapy Based on Large Scale Drug Induced Transcriptional Signatures

2016
PLoS One
PMCID: 4783079
PMID: 26954019
DOI: 10.1371/journal.pone.0150460

[…] inst any other type of cancer including all the drugs in the KD set.Next, the structural signature was extracted as 1,024 bits of FP2 chemical fingerprints implemented in Open Babel [] for compounds (SCPD) or known drugs (SKD). The target information was collected from 10 public databases comprising 342,311 compound-target interactions among 205,570 unique compounds (Figure A in ). The sets of gen […]

library_books

Molecular mechanisms of system responses to novel stimuli are predictable from public data

2013
Nucleic Acids Res
PMCID: 3919619
PMID: 24185701
DOI: 10.1093/nar/gkt938

[…] ary Table S7.An additional stream of regulatory evidence was determined based on the de novo motifs detected by cMonkey (). Those detected motifs with an e-value were run against the ‘macisaac’ and ‘scpd’ yeast motif databases using TomTom (). The resulting P-values are subjected to a cutoff value of 0.05 to determine regulation. If a TF regulates a cluster, it is considered to regulate all genes […]

library_books

Genomic clustering and co regulation of transcriptional networks in the pathogenic fungus Fusarium graminearum

2013
BMC Syst Biol
PMCID: 3703260
PMID: 23805903
DOI: 10.1186/1752-0509-7-52

[…] e tested for motif enrichment with significance threshold p-value < 10-3 (Additional file : Figure S3B). Tomtom (v4.8.1) [] was used to detect similarity to yeast motifs (databases MacIsaac_v1 [] and SCPD []; E < 1 and motif length ≤ 9) and to identify S. cerevisiae motif-associated proteins (ScAPs). F. graminearum homologues of ScAPs were identified (BLASTp; E < 10-6 and matched regions covering […]

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SCPD institution(s)
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
SCPD funding source(s)
This tool was funded by Public Health Service grant HG01696 from NIH/NIHGR

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