Organism : Bacillus subtilis | Module List :
BSU27320 greA

transcription elongation factor GreA (RefSeq)

CircVis
Functional Annotations (5)
Function System
Transcription elongation factor cog/ cog
DNA binding go/ molecular_function
transcription elongation regulator activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
greA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU27320
(Mouseover regulator name to see its description)

BSU27320 is regulated by 21 influences and regulates 21 modules.
Regulators for BSU27320 greA (21)
Regulator Module Operator
BSU04680 63 tf
BSU04730 63 tf
BSU15690 63 tf
BSU16900 63 tf
BSU25250 63 tf
BSU27320 63 tf
BSU28820 63 tf
BSU29740 63 tf
BSU37650 63 tf
BSU40010 63 tf
BSU40970 63 tf
BSU04680 78 tf
BSU05330 78 tf
BSU15640 78 tf
BSU17450 78 tf
BSU19120 78 tf
BSU27320 78 tf
BSU28820 78 tf
BSU31530 78 tf
BSU33080 78 tf
BSU37650 78 tf

Warning: BSU27320 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
5082 1.30e+03 ACAtTtTATtTaga
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5083 6.60e+02 tTGCgggaAaAGc
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5110 1.60e-03 AAaAaAGG
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5111 1.30e+03 AaAAGGAgTgaAtag
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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 BSU27320

BSU27320 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Transcription elongation factor cog/ cog
DNA binding go/ molecular_function
transcription elongation regulator activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
greA tigr/ tigrfam
Module neighborhood information for BSU27320

BSU27320 has total of 51 gene neighbors in modules 63, 78
Gene neighbors (51)
Gene Common Name Description Module membership
BSU09790 yheB hypothetical protein (RefSeq) 63, 243
BSU09950 prsA molecular chaperone lipoprotein (RefSeq) 63, 324
BSU10030 hinT Hit-family hydrolase (RefSeq) 78, 398
BSU13200 rsbRB component of the piezosome (stressosome) (RefSeq) 78, 145
BSU14650 yktB hypothetical protein (RefSeq) 78, 398
BSU14670 suhB inositol monophosphatase (RefSeq) 78, 398
BSU14680 ykzC hypothetical protein (RefSeq) 78, 398
BSU15120 yllA putative nucleoid associated protein (RefSeq) 78, 113
BSU15280 ftsA cell-division protein essential fo Z-ring assembly (RefSeq) 63, 145
BSU15290 ftsZ cell division protein FtsZ (RefSeq) 63, 145
BSU15370 ylmD hypothetical protein (RefSeq) 63, 194
BSU15380 ylmE hypothetical protein (RefSeq) 63, 194
BSU15400 ylmG factor involved in shape determination (RefSeq) 63, 273
BSU15640 yloA putative persistent RNA/DNA binding protein (RefSeq) 78, 398
BSU15830 yloU hypothetical protein (RefSeq) 63, 155
BSU15840 yloV putative dihydroxyacetone/glyceraldehyde kinase (RefSeq) 63, 289
BSU16670 ribC bifunctional riboflavin kinase/FMN adenylyltransferase (RefSeq) 78, 324
BSU16910 ymfM hypothetical protein (RefSeq) 63, 194
BSU17280 ymaD putative peroxiredoxin-related protein (RefSeq) 78, 398
BSU18490 rtp replication terminator protein (RefSeq) 78, 381
BSU18500 fabG 3-ketoacyl-(acyl-carrier-protein) reductase (RefSeq) 78, 398
BSU19120 czrA transcriptional regulator (multiple metal-sensing ArsR-SmtB transcriptional repressors family) (RefSeq) 78, 291
BSU22880 rpsA 30S ribosomal protein S1 (RefSeq) 63, 193
BSU23490 pupG purine nucleoside phosphorylase (RefSeq) 63, 292
BSU23500 drm phosphopentomutase (RefSeq) 63, 273
BSU23850 zwf glucose-6-phosphate 1-dehydrogenase (RefSeq) 63, 78
BSU23860 yqjI 6-phosphogluconate dehydrogenase (RefSeq) 78, 194
BSU23990 yqiW hypothetical protein (RefSeq) 31, 78
BSU24790 yqgX putative metal-binding hydrolase (RefSeq) 78, 398
BSU24820 yqgU putative lipoprotein (RefSeq) 63, 247
BSU25020 sodA superoxide dismutase (RefSeq) 78, 398
BSU27320 greA transcription elongation factor GreA (RefSeq) 63, 78
BSU27630 yrvD hypothetical protein (RefSeq) 63, 187
BSU28200 lonA class III heat-shock ATP-dependent LonA protease (RefSeq) 63, 243
BSU28220 clpX ATP-dependent protease ATP-binding subunit ClpX (RefSeq) 78, 324
BSU29480 ytxK putative nucleic acid methyltransferase (RefSeq) 78, 398
BSU29490 tpx thiol peroxidase (RefSeq) 78, 398
BSU29610 ezrA septation ring formation regulator EzrA (RefSeq) 63, 194
BSU29740 ccpA transcriptional regulator (Lacl family) (RefSeq) 63, 155
BSU29860 ytoP glutamyl aminopeptidase (RefSeq) 78, 398
BSU31160 yubA putative integral inner membrane protein (RefSeq) 31, 63
BSU31170 yulF enzyme involved in biofilm formation (RefSeq) 63, 247
BSU31750 yueK nicotinate phosphoribosyltransferase (RefSeq) 63, 194
BSU32790 yusG hypothetical protein (RefSeq) 77, 78
BSU32800 yusH glycine cleavage system protein H (RefSeq) 78, 247
BSU33180 yvrC putative lipoprotein binding vitamin B12 (RefSeq) 48, 63
BSU34030 yvbY putative subunit of an iron-sulfur protein (RefSeq) 63, 256
BSU34040 yvfW putative iron-sulfur oxidoreductase (RefSeq) 63, 256
BSU37100 murAB UDP-N-acetylglucosamine 1-carboxyvinyltransferase (RefSeq) 63, 343
BSU38210 ywcD putative integral inner membrane protein (RefSeq) 63, 247
BSU38370 ywbC putative lyase (RefSeq) 77, 78
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 BSU27320
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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