Organism : Bacillus subtilis | Module List :
BSU16600 nusA

transcription elongation factor NusA (RefSeq)

CircVis
Functional Annotations (6)
Function System
Transcription elongation factor cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
RNA binding go/ molecular_function
protein binding go/ molecular_function
regulation of transcription termination, DNA-dependent go/ biological_process
NusA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU16600
(Mouseover regulator name to see its description)

BSU16600 is regulated by 21 influences and regulates 43 modules.
Regulators for BSU16600 nusA (21)
Regulator Module Operator
BSU01080 122 tf
BSU02680 122 tf
BSU10860 122 tf
BSU15970 122 tf
BSU16600 122 tf
BSU23210 122 tf
BSU24250 122 tf
BSU24320 122 tf
BSU35050 122 tf
BSU00470 34 tf
BSU00700 34 tf
BSU01010 34 tf
BSU01070 34 tf
BSU01080 34 tf
BSU01810 34 tf
BSU02680 34 tf
BSU03850 34 tf
BSU08990 34 tf
BSU16600 34 tf
BSU24100 34 tf
BSU40990 34 tf

Warning: BSU16600 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
5028 2.90e+01 cGaca.GT.ct.CctTT.c
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5029 2.10e+02 CcTgcTTC
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5196 5.90e+00 AGggCgGG
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5197 2.90e+02 AccCTGCTTCA
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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 BSU16600

BSU16600 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Transcription elongation factor cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
RNA binding go/ molecular_function
protein binding go/ molecular_function
regulation of transcription termination, DNA-dependent go/ biological_process
NusA tigr/ tigrfam
Module neighborhood information for BSU16600

BSU16600 has total of 25 gene neighbors in modules 34, 122
Gene neighbors (25)
Gene Common Name Description Module membership
BSU00010 dnaA chromosomal replication initiation protein (RefSeq) 34, 97
BSU00020 dnaN DNA polymerase III subunit beta (RefSeq) 34, 204
BSU00030 yaaA putative RNA binding protein (RefSeq) 34, 221
BSU00040 recF recombination protein F (RefSeq) 34, 221
BSU00060 gyrB DNA gyrase subunit B (RefSeq) 34, 221
BSU00070 gyrA DNA gyrase subunit A (RefSeq) 34, 221
BSU01450 cbiO cobalt transporter ATP-binding subunit (RefSeq) 122, 176
BSU16590 ylxS hypothetical protein (RefSeq) 34, 374
BSU16600 nusA transcription elongation factor NusA (RefSeq) 34, 122
BSU16610 ylxR putative RNA binding protein; putative new fold (RefSeq) 34, 122
BSU16620 ylxQ hypothetical protein (RefSeq) 34, 122
BSU16630 infB translation initiation factor IF-2 (RefSeq) 34, 122
BSU16650 rbfA ribosome-binding factor A (RefSeq) 122, 292
BSU24280 ispA geranyltranstransferase (RefSeq) 122, 234
BSU24290 xseB exodeoxyribonuclease VII small subunit (RefSeq) 122, 234
BSU25430 rimO ribosomal protein S12 methylthiotransferase (RefSeq) 34, 122
BSU25440 yqeU 16S ribosomal RNA methyltransferase RsmE (RefSeq) 34, 122
BSU25450 prmA ribosomal protein L11 methyltransferase (RefSeq) 34, 122
BSU25460 dnaJ chaperone protein DnaJ (RefSeq) 34, 122
BSU25500 hemN coproporphyrinogen III oxidase (RefSeq) 34, 204
BSU27340 yrrO putative hydrolase (RefSeq) 122, 234
BSU27350 yrrN putative hydrolase (RefSeq) 122, 234
BSU27360 yrrM putative acyl-CoA O-methyltransferase (RefSeq) 122, 234
VIMSS37174 VIMSS37174 None 122, 204
VIMSS37717 VIMSS37717 None 34, 164
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 BSU16600
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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