Organism : Bacillus subtilis | Module List :
BSU01640 ybbB

putative transcriptional regulator (AraC/XylS family) (RefSeq)

CircVis
Functional Annotations (8)
Function System
ABC-type Fe3+-hydroxamate transport system, periplasmic component cog/ cog
DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
iron ion transmembrane transporter activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
high-affinity iron ion transport go/ biological_process
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU01640
(Mouseover regulator name to see its description)

BSU01640 is regulated by 18 influences and regulates 8 modules.
Regulators for BSU01640 ybbB (18)
Regulator Module Operator
BSU00700 25 tf
BSU01640 25 tf
BSU02220 25 tf
BSU10560 25 tf
BSU10860 25 tf
BSU24250 25 tf
BSU24610 25 tf
BSU29630 25 tf
BSU30150 25 tf
BSU35050 25 tf
BSU37620 25 tf
BSU01640 65 tf
BSU03960 65 tf
BSU10420 65 tf
BSU12560 65 tf
BSU19090 65 tf
BSU21020 65 tf
BSU40410 65 tf

Warning: BSU01640 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
5012 5.00e-04 aaAGGaGG
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5013 8.60e+03 TTttttCAtaA
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5086 1.50e-20 AaTGAtAaTCATTaTCAaTTA
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5087 2.90e+03 gaTG.ctTTTt
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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 BSU01640

BSU01640 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
ABC-type Fe3+-hydroxamate transport system, periplasmic component cog/ cog
DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
iron ion transmembrane transporter activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
high-affinity iron ion transport go/ biological_process
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for BSU01640

BSU01640 has total of 48 gene neighbors in modules 25, 65
Gene neighbors (48)
Gene Common Name Description Module membership
BSU00490 spoVG regulatory protein SpoVG (RefSeq) 25, 353
BSU01600 ybbA putative iron-chelator esterase (RefSeq) 25, 65
BSU01610 feuC iron-uptake protein (RefSeq) 25, 65
BSU01620 feuB iron-uptake protein (RefSeq) 65, 93
BSU01630 feuA iron hydroxamate-binding lipoprotein (RefSeq) 65, 93
BSU01640 ybbB putative transcriptional regulator (AraC/XylS family) (RefSeq) 25, 65
BSU02040 ybdN hypothetical protein (RefSeq) 25, 141
BSU03270 ycgT putative thioredoxin reductase (RefSeq) 65, 93
BSU04530 ydbN hypothetical protein (RefSeq) 65, 218
BSU07150 yetG putative monooxygenase (RefSeq) 65, 218
BSU08440 yfiY putative iron(III) dicitrate transporter binding lipoprotein (RefSeq) 65, 93
BSU08480 yfhC putative oxidoreductase (nitroreductase family) (RefSeq) 65, 93
BSU10730 yisI Spo0A-P phosphatase (RefSeq) 25, 215
BSU11990 yjdB hypothetical protein (RefSeq) 25, 91
BSU12450 yjpA putative enzyme (RefSeq) 25, 404
BSU14120 ykzF hypothetical protein (RefSeq) 25, 350
BSU14150 ykuN flavodoxin (RefSeq) 65, 218
BSU14160 ykuO hypothetical protein (RefSeq) 65, 218
BSU14170 ykuP short-chain flavodoxin (RefSeq) 65, 218
BSU14940 ylbA hypothetical protein (RefSeq) 25, 404
BSU17100 pksC malonyl-CoA-acyltransferase involved in polyketide synthesis (RefSeq) 25, 91
BSU18630 exlX extracellular endoglucanase precursor (expansin) (RefSeq) 25, 90
BSU18780 yoaW biofilm forming exported protein (RefSeq) 25, 114
BSU21670 BSU21670 None 25, 159
BSU22280 yppD hypothetical protein (RefSeq) 25, 33
BSU24600 sinI antagonist of SinR (RefSeq) 25, 302
BSU24800 yqgW hypothetical protein (RefSeq) 25, 404
BSU25840 phrE regulator of the activity of phosphatase RapE (RefSeq) 25, 114
BSU26230 yqaP conserved hypothetical protein; skin element (RefSeq) 25, 64
BSU26820 yrpD putative lipoprotein (RefSeq) 25, 359
BSU31960 dhbF siderophore 2,3-dihydroxybenzoate-glycine-threonine trimeric ester bacillibactin synthetase (RefSeq) 65, 218
BSU31970 dhbB isochorismatase (RefSeq) 65, 218
BSU31980 dhbE 2,3-dihydroxybenzoate-AMP ligase (RefSeq) 65, 218
BSU31990 dhbC isochorismate synthase DhbC (RefSeq) 65, 218
BSU32000 dhbA 2,3-dihydroxybenzoate-2,3-dehydrogenase (RefSeq) 65, 218
BSU32010 besA bacillibactin trilactone hydrolase (RefSeq) 65, 218
BSU32930 yusU hypothetical protein (RefSeq) 65, 93
BSU32940 yusV iron(III)-siderophore transporter (ATP binding component) (RefSeq) 65, 93
BSU33320 fhuD ferrichrome ABC transporter (ferrichrome-binding lipoprotein) (RefSeq) 65, 218
BSU35050 yvnA putative transcriptional regulator (RefSeq) 25, 91
BSU37030 racA polar chromosome segregation protein (RefSeq) 25, 114
BSU37800 yweA member of the processed secretome (RefSeq) 25, 91
BSU38260 efeN iron-dependent peroxidase convert ferric iron into ferrous iron (RefSeq) 65, 93
BSU38270 efeM lipoprotein binding ferrous or ferric iron for transport (RefSeq) 65, 93
BSU38280 efeU ferrous ion permease (RefSeq) 65, 93
BSU39610 yxeB ABC transporter (ferrioxamine binding lipoprotein) (RefSeq) 65, 302
BSU39870 yxbD putative acetyltransferase (RefSeq) 25, 359
VIMSS39966 VIMSS39966 None 25, 240
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 BSU01640
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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