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Plants and Fungi
- Saccharomyces cerevisiae
- person_outline Zhu J.
Publication for SCPD
MIP diversity from Trichoderma: Structural considerations and transcriptional modulation during mycoparasitic association with Fusarium solani olive trees
[…] 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/). […]
Role of MAPK Signaling Pathways in Regulating the Hydrophobin Cryparin in the Chestnut Blight Fungus Cryphonectria parasitica
[…] 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 […]
Evaluation of single cell genomics to address evolutionary questions using three SAGs of the choanoflagellate Monosiga brevicollis
[…] 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 […]
Drug Repositioning for Cancer Therapy Based on Large Scale Drug Induced Transcriptional Signatures
[…] 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 […]
Molecular mechanisms of system responses to novel stimuli are predictable from public data
[…] 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 […]
Genomic clustering and co regulation of transcriptional networks in the pathogenic fungus Fusarium graminearum
[…] 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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