Organism : Bacillus subtilis | Module List :
BSU19620 yodJ

D-alanyl-D-alanine carboxypeptidase lipoprotein (RefSeq)

CircVis
Functional Annotations (4)
Function System
D-alanyl-D-alanine carboxypeptidase cog/ cog
proteolysis go/ biological_process
serine-type D-Ala-D-Ala carboxypeptidase activity go/ molecular_function
Peptidoglycan biosynthesis kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU19620
(Mouseover regulator name to see its description)

BSU19620 is regulated by 23 influences and regulates 0 modules.
Regulators for BSU19620 yodJ (23)
Regulator Module Operator
BSU01810 385 tf
BSU05050 385 tf
BSU10560 385 tf
BSU14990 385 tf
BSU23100 385 tf
BSU23210 385 tf
BSU24320 385 tf
BSU29740 385 tf
BSU36020 385 tf
BSU37080 385 tf
BSU37160 385 tf
BSU38600 385 tf
BSU38700 385 tf
BSU38910 385 tf
BSU00470 193 tf
BSU00800 193 tf
BSU04680 193 tf
BSU09520 193 tf
BSU10860 193 tf
BSU16600 193 tf
BSU24220 193 tf
BSU25250 193 tf
BSU36420 193 tf

Warning: BSU19620 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
5332 1.70e-02 CcTCCttT
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5333 3.10e+02 tgaGaaaAaaG
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5682 4.90e+01 gcTTtttTtCt
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5683 5.00e+02 AaAaGGaG
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Motif Help

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.

Functional Enrichment for BSU19620

BSU19620 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
D-alanyl-D-alanine carboxypeptidase cog/ cog
proteolysis go/ biological_process
serine-type D-Ala-D-Ala carboxypeptidase activity go/ molecular_function
Peptidoglycan biosynthesis kegg/ kegg pathway
Module neighborhood information for BSU19620

BSU19620 has total of 46 gene neighbors in modules 193, 385
Gene neighbors (46)
Gene Common Name Description Module membership
BSU00140 dck deoxyadenosine/deoxycytidine kinase (RefSeq) 240, 385
BSU00150 dgk deoxyguanosine kinase (RefSeq) 197, 385
BSU00580 yabN putative fusion methylase and nucleotide pyrophosphohydrolase (RefSeq) 66, 193
BSU00590 yabO putative ribosomal RNA binding protein; heat shock protein (RefSeq) 193, 324
BSU09520 sigM RNA polymerase sigma factor SigM (RefSeq) 38, 193
BSU12840 pit low-affinity inorganic phosphate transporter (RefSeq) 119, 385
BSU14100 ykuJ hypothetical protein (RefSeq) 197, 385
BSU14110 ykuK putative RNAse (RefSeq) 313, 385
BSU14850 ftsW cell-division protein (RefSeq) 187, 193
BSU15010 ylbH putative enzyme with adenosyl binding site (RefSeq) 313, 385
BSU15020 coaD phosphopantetheine adenylyltransferase (RefSeq) 313, 385
BSU15220 murG undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase (RefSeq) 176, 193
BSU15450 lspA lipoprotein signal peptidase (RefSeq) 62, 385
BSU15800 thiN thiamine pyrophosphokinase (RefSeq) 197, 385
BSU16950 pbpX penicillin-binding endopeptidase X (RefSeq) 313, 385
BSU19620 yodJ D-alanyl-D-alanine carboxypeptidase lipoprotein (RefSeq) 193, 385
BSU22190 ypsA hypothetical protein (RefSeq) 382, 385
BSU22370 aspB aspartate aminotransferase (RefSeq) 382, 385
BSU22380 ypmB hypothetical protein (RefSeq) 382, 385
BSU22390 ypmA hypothetical protein (RefSeq) 382, 385
BSU22400 dinG bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon (RefSeq) 227, 385
BSU22440 birA biotin acetyl-CoA-carboxylase ligase and biotin regulon repressor (RefSeq) 382, 385
BSU22600 aroE 3-phosphoshikimate 1-carboxyvinyltransferase (RefSeq) 187, 385
BSU22870 fni isopentenyl pyrophosphate isomerase (RefSeq) 187, 193
BSU22880 rpsA 30S ribosomal protein S1 (RefSeq) 63, 193
BSU22890 cmk cytidylate kinase (RefSeq) 42, 193
BSU22900 ypfB hypothetical protein (RefSeq) 36, 193
BSU24890 yqgN 5-formyltetrahydrofolate cyclo-ligase (RefSeq) 89, 385
BSU25310 dgkA undecaprenol kinase (RefSeq) 170, 193
BSU25320 yqfG putative metalloprotease (RefSeq) 193, 221
BSU27620 recJ putative single-strand DNA-specific exonuclease (RefSeq) 193, 234
BSU28240 ysoA putative hydrolase (RefSeq) 162, 193
BSU29820 ytpR putative protein with RNA binding domain (RefSeq) 193, 398
BSU29830 ytpQ hypothetical protein (RefSeq) 193, 398
BSU29840 ytpP putative thiol-disulfide oxidoreductase with thiredoxin domain (RefSeq) 193, 398
BSU31600 mrpA monovalent cation/H+ antiporter subunit A (RefSeq) 72, 193
BSU31610 mrpB putative monovalent cation/H+ antiporter subunit B (RefSeq) 72, 193
BSU31620 mrpC putative monovalent cation/H+ antiporter subunit C (RefSeq) 72, 193
BSU31630 mrpD putative monovalent cation/H+ antiporter subunit D (RefSeq) 72, 193
BSU31640 mrpE putative monovalent cation/H+ antiporter subunit E (RefSeq) 72, 193
BSU31650 mrpF putative monovalent cation/H+ antiporter subunit F (RefSeq) 72, 193
BSU31660 mrpG putative monovalent cation/H+ antiporter subunit G (RefSeq) 72, 193
BSU33600 smpB SsrA-binding protein (RefSeq) 53, 193
BSU37500 speE spermidine synthase (RefSeq) 62, 193
BSU41030 jag SpoIIIJ-associated RNA/ssDNA-binding protein (RefSeq) 313, 385
BSU41040 spoIIIJ OxaA-like protein precursor (RefSeq) 313, 385
Gene Page Help

Network Tab

If the gene is associated with a module(s), its connection to given modules along with other members of that module are shown as network by using CytoscapeWeb. In this view, each green colored circular nodes represent module member genes, purple colored diamonds represent module motifs and red triangles represent regulators. Each node is connected to module (Bicluster) via edges. This representation provides quick overview of all genes, regulators and motifs for modules. It also allows one to see shared genes/motifs/regulators among diferent modules.

Network representation is interactive. You can zoom in/out and move nodes/edges around. Clicking on a node will open up a window to give more details. For genes, Locus tag, organism, genomic coordinates, NCBI gene ID, whether it is transcription factor or not and any associated functional information will be shown. For regulators, number of modules are shown in addition to gene details. For motifs, e-value, consensus sequence and sequence logo will be shown. For modules, expression profile plot, motif information, functional associations and motif locations for each member of the module will be shown.
You can pin information boxes by using button in the box title and open up additional ones on the same screen for comparative analysis.

Regulation Tab

Regulation tab for each gene includes regulatory influences such as environmental factors or transcription factors or their combinations identified by regulatory network inference algorithms.

If the gene is a member of a module, regulators influencing that module are also considered to regulate the gene. Regulators table list total number of regulatory influences, regulators, modules and type of the influence.

You can see description of the regulator inside the tooltip when you mouseover. In certain cases the regulatory influence is predicted to be the result of the combination of two influences. These are indicated as combiner in the column labeled "Operator".

For transcription factors, an additional table next to regulator table will be show. This table show modules that are influenced by the transcription factor.

Motifs Tab

Network inference algorithm uses de novo motif prediction for assigning genes to modules. If there are any motifs identified in the upstream region of a gene, the motif will be shown here. For each motif sequence logo, consensus and e-value will be shown.

Functions Tab

Identification of functional enrichment for the module members is important in associating predicted motifs and regulatory influences with pathways. As described above, the network inference pipeline includes a functional enrichment module by which hypergeometric p-values are used to identify over representation of functional ontology terms among module members.

Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.

Module Members Tab

Identity of gene members in a module may help to identify potential interactions between different functional modules. Therefore, neighbor genes that share the same module(s) with gene under consideration are shown here. For each memebr, gene name, description and modules that contain it are listed.

Help Tab

This help page. More general help can be accessed by clicking help menu in the main navigation bar.

Social Tab

Network Portal is designed to promote collaboration through social interactions. Therefore interested researchers can share information, questions and updates for a particular gene.

Users can use their Disqus, Facebook, Twitter or Google accounts to connect to this page (We recommend Google). Each module and gene page includes comments tab that lists history of the interactions for that gene. You can browse the history, make updates, raise questions and share these activities with social web.

In the next releases of the network portal, we are planning to create personal space for each user where you can share you space that contains all the analysis steps you did along with relevant information.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend
Comments for BSU19620
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Gene Help

Overview

Gene landing pages present genomic, functional, and regulatory information for individual genes. A circular visualization displays connections between the selected gene and genes in the same modules, with as edges drawn between the respective coordinates of the whole genome.

The gene page also lists functional ontology assignments, module membership, and motifs associated with these modules. Genes in the network inherit regulatory influences from the modules to which they belong. Therefore, the regulatory information for each gene is a collection of all regulatory influences on these modules. These are listed as a table that includes influence name, type, and target module. If the gene is a transcription factor, its target modules are also displayed in a table that provides residual values and number of genes.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend