Organism : Bacillus subtilis | Module List :
BSU40960 parB

site-specific DNA-binding protein (RefSeq)

CircVis
Functional Annotations (5)
Function System
Predicted transcriptional regulators cog/ cog
DNA binding go/ molecular_function
plasmid partitioning go/ biological_process
sequence-specific DNA binding go/ molecular_function
parB_part tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU40960
(Mouseover regulator name to see its description)

BSU40960 is regulated by 17 influences and regulates 5 modules.
Regulators for BSU40960 parB (17)
Regulator Module Operator
BSU00330 173 tf
BSU08520 173 tf
BSU14240 173 tf
BSU29000 173 tf
BSU40410 173 tf
BSU40960 173 tf
BSU40970 173 tf
BSU09990 169 tf
BSU10510 169 tf
BSU10560 169 tf
BSU14140 169 tf
BSU16900 169 tf
BSU23520 169 tf
BSU26430 169 tf
BSU28820 169 tf
BSU40010 169 tf
BSU40970 169 tf

Warning: BSU40960 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
5286 5.60e-01 aaagGGGA
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5287 1.00e+02 AaAATGaAag
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5294 1.50e+05 taTaatATa.gAAtgagAaa
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5295 1.90e+04 AGGgGG
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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 BSU40960

BSU40960 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Predicted transcriptional regulators cog/ cog
DNA binding go/ molecular_function
plasmid partitioning go/ biological_process
sequence-specific DNA binding go/ molecular_function
parB_part tigr/ tigrfam
Module neighborhood information for BSU40960

BSU40960 has total of 44 gene neighbors in modules 169, 173
Gene neighbors (44)
Gene Common Name Description Module membership
BSU00300 yaaR hypothetical protein (RefSeq) 54, 173
BSU00310 holB DNA polymerase III subunit delta' (RefSeq) 54, 173
BSU00330 yabA DNA replication intiation control protein YabA (RefSeq) 54, 173
BSU03130 nadE NAD synthetase (RefSeq) 29, 169
BSU03900 gabT 4-aminobutyrate aminotransferase (RefSeq) 173, 231
BSU04390 ydbA hypothetical protein (RefSeq) 169, 334
BSU06840 yeeI hypothetical protein (RefSeq) 173, 327
BSU09420 lytE cell wall hydrolase; phosphatase-associated protein (major autolysin) (RefSeq) 169, 256
BSU10230 yhfH hypothetical protein (RefSeq) 169, 405
BSU13970 ykwD hypothetical protein (RefSeq) 121, 173
BSU14240 rok repressor of comK (RefSeq) 35, 173
BSU14440 ykpB 2-dehydropantoate 2-reductase (RefSeq) 170, 173
BSU14490 kinC two-component sensor histidine kinase (RefSeq) 173, 219
BSU16090 sucC succinyl-CoA synthetase subunit beta (RefSeq) 169, 256
BSU16100 sucD succinyl-CoA synthetase subunit alpha (RefSeq) 169, 256
BSU16890 ymfK hypothetical protein (RefSeq) 169, 194
BSU16900 ymfK ymfL (VIMSS) 169, 194
BSU19360 odhB dihydrolipoamide succinyltransferase (RefSeq) 169, 256
BSU19370 sucA 2-oxoglutarate dehydrogenase E1 component (RefSeq) 169, 256
BSU22960 gudB cryptic glutamate dehydrogenase (RefSeq) 169, 256
BSU23160 rluB pseudouridine synthase (RefSeq) 173, 284
BSU24550 gcvPB glycine dehydrogenase subunit 2 (RefSeq) 169, 334
BSU24570 gcvT glycine cleavage system aminomethyltransferase T (RefSeq) 169, 334
BSU25340 phoH phosphate starvation-induced protein (RefSeq) 173, 220
BSU26350 yqaE putative transcriptional regulator (Xre family); skin element (RefSeq) 35, 173
BSU27220 yrhE putative oxido-reductase (RefSeq) 169, 340
BSU27230 yrhD hypothetical protein (RefSeq) 169, 340
BSU28170 hemA glutamyl-tRNA reductase (RefSeq) 173, 237
BSU28440 sdhA succinate dehydrogenase flavoprotein subunit (RefSeq) 169, 256
BSU28450 sdhC succinate dehydrogenase (cytochrome b558 subunit) (RefSeq) 169, 256
BSU28460 yslB hypothetical protein (RefSeq) 173, 315
BSU29120 mdh malate dehydrogenase (RefSeq) 169, 256
BSU29130 icd isocitrate dehydrogenase (RefSeq) 169, 256
BSU29140 citZ citrate synthase (RefSeq) 169, 256
BSU29805 BSU29805 None 98, 169
BSU29880 malS malate dehydrogenase (RefSeq) 149, 169
BSU29890 ytnP putative metal-dependent hydrolase (RefSeq) 169, 340
BSU29950 ytlQ putative hydrolase (RefSeq) 169, 256
BSU29960 ytlP 2'-5' RNA-ligase family protein (RefSeq) 169, 256
BSU34050 yvfV putative iron-sulfur heterodisulfide reductase (RefSeq) 169, 256
BSU34680 yvcT putative 2-hydroxyacid dehydrogenase (RefSeq) 29, 169
BSU40340 rocD ornithine--oxo-acid transaminase (RefSeq) 169, 229
BSU40960 parB site-specific DNA-binding protein (RefSeq) 169, 173
BSU40970 parA chromosome partitioning protein; transcriptional regulator (RefSeq) 169, 173
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 BSU40960
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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