Organism : Bacillus subtilis | Module List :
BSU00370 abrB

transcriptional regulator for transition state genes (RefSeq)

CircVis
Functional Annotations (2)
Function System
Regulators of stationary/sporulation gene expression cog/ cog
lp_hng_hel_AbrB tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU00370
(Mouseover regulator name to see its description)

BSU00370 is regulated by 17 influences and regulates 5 modules.
Regulators for BSU00370 abrB (17)
Regulator Module Operator
BSU01430 273 tf
BSU01810 273 tf
BSU05850 273 tf
BSU15880 273 tf
BSU16170 273 tf
BSU16900 273 tf
BSU23210 273 tf
BSU25250 273 tf
BSU29740 273 tf
BSU05850 317 tf
BSU23210 317 tf
BSU25250 317 tf
BSU25810 317 tf
BSU33010 317 tf
BSU34630 317 tf
BSU38420 317 tf
BSU38450 317 tf

Warning: BSU00370 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
5484 1.50e+03 GAcAGAAa
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5485 1.80e+02 aaGGgaGGaga
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5572 1.90e+02 TgctGAtgaAtGA
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5573 1.40e+04 gCc.gTTTTtcCgcc
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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 BSU00370

BSU00370 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Regulators of stationary/sporulation gene expression cog/ cog
lp_hng_hel_AbrB tigr/ tigrfam
Module neighborhood information for BSU00370

BSU00370 has total of 42 gene neighbors in modules 273, 317
Gene neighbors (42)
Gene Common Name Description Module membership
BSU00050 yaaB hypothetical protein (RefSeq) 138, 317
BSU00290 yaaQ hypothetical protein (RefSeq) 54, 317
BSU00370 abrB transcriptional regulator for transition state genes (RefSeq) 273, 317
BSU00680 hprT hypoxanthine-guanine phosphoribosyltransferase (RefSeq) 138, 317
BSU02580 ycbO putative Na+-driven exporter or maturation protein (RefSeq) 138, 317
BSU04150 ycsN putative oxidoreductase (RefSeq) 138, 317
BSU04300 ydaM putative glycosyltransferase associated to biofilm formation (RefSeq) 50, 317
BSU06570 yerB putative lipoprotein (RefSeq) 138, 317
BSU08960 yhbF hypothetical protein (RefSeq) 54, 317
BSU14000 patA aminotransferase A (RefSeq) 138, 317
BSU15050 ylbL putative degradative enzyme (RefSeq) 138, 317
BSU15260 ylxX hypothetical protein (RefSeq) 7, 273
BSU15270 sbp putative integral inner membrane protein (RefSeq) 7, 273
BSU15400 ylmG factor involved in shape determination (RefSeq) 63, 273
BSU15900 fabD malonyl CoA:acyl carrier protein transacylase (RefSeq) 273, 343
BSU15910 fabG beta-ketoacyl-acyl carrier protein reductase (RefSeq) 273, 309
BSU15920 acpP acyl carrier protein (RefSeq) 273, 343
BSU16150 clpQ ATP-dependent protease peptidase subunit (RefSeq) 272, 273
BSU16160 hslU ATP-dependent protease ATP-binding subunit HslU (RefSeq) 272, 273
BSU16660 truB tRNA pseudouridine synthase B (RefSeq) 106, 273
BSU17890 tkt transketolase (RefSeq) 128, 273
BSU23210 spcB chromosome condensation and segregation factor (RefSeq) 138, 317
BSU23500 drm phosphopentomutase (RefSeq) 63, 273
BSU23900 yqjF hypothetical protein (RefSeq) 254, 317
BSU23910 yqjE putative deacylase (RefSeq) 194, 273
BSU24330 yqhY hypothetical protein (RefSeq) 273, 289
BSU24340 accC acetyl-CoA carboxylase biotin carboxylase subunit (RefSeq) 273, 289
BSU24350 accB acetyl-CoA carboxylase biotin carboxyl carrier protein subunit (RefSeq) 273, 289
BSU25240 yqfL hypothetical protein (RefSeq) 253, 273
BSU25250 ccpN negative regulator of gluconeogenesis (RefSeq) 253, 273
BSU27650 secDF bifunctional preprotein translocase subunit SecD/SecF (RefSeq) 155, 273
BSU27660 comN post-transcriptional regulator (RefSeq) 138, 317
BSU29180 pyk pyruvate kinase (RefSeq) 253, 273
BSU30800 menB naphthoate synthase (RefSeq) 272, 273
BSU31710 comQ isoprenyl transferase (pre-ComX modification) (RefSeq) 145, 317
BSU32150 paiA polyamine N-acetyltransferase (RefSeq) 241, 317
BSU32730 metN methionine ABC transporter, substrate binding lipoprotein (RefSeq) 138, 317
BSU33380 yvgL putative molybdate-binding lipoprotein (RefSeq) 138, 317
BSU34800 cwlO secreted cell wall DL-endopeptidase (RefSeq) 155, 273
BSU36850 atpF F0F1 ATP synthase subunit B (RefSeq) 138, 317
BSU37090 glpX fructose 1,6-bisphosphatase II (RefSeq) 273, 343
BSU38540 dltE putative oxidoreductase (RefSeq) 197, 273
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 BSU00370
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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