Organism : Bacillus subtilis | Module List :
BSU16690 pnpA

polynucleotide phosphorylase/polyadenylase (RefSeq)

CircVis
Functional Annotations (10)
Function System
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) cog/ cog
3'-5'-exoribonuclease activity go/ molecular_function
RNA binding go/ molecular_function
polyribonucleotide nucleotidyltransferase activity go/ molecular_function
RNA processing go/ biological_process
mRNA catabolic process go/ biological_process
Purine metabolism kegg/ kegg pathway
Pyrimidine metabolism kegg/ kegg pathway
RNA degradation kegg/ kegg pathway
polynuc_phos tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU16690
(Mouseover regulator name to see its description)

BSU16690 is regulated by 14 influences and regulates 0 modules.
Regulators for BSU16690 pnpA (14)
Regulator Module Operator
BSU01070 289 tf
BSU05460 289 tf
BSU16600 289 tf
BSU23210 289 tf
BSU25250 289 tf
BSU27320 289 tf
BSU29740 289 tf
BSU37160 289 tf
BSU01070 253 tf
BSU01430 253 tf
BSU16600 253 tf
BSU23210 253 tf
BSU25250 253 tf
BSU37160 253 tf

Warning: BSU16690 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
5446 2.10e+00 AgGcgGgtgcTctgT
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5447 5.70e+03 ctgTTCtTTttttTC
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5516 1.30e+03 aGgAGgAa
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5517 1.10e+03 aCAgGCtGgtT
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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 BSU16690

BSU16690 is enriched for 10 functions in 3 categories.
Enrichment Table (10)
Function System
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) cog/ cog
3'-5'-exoribonuclease activity go/ molecular_function
RNA binding go/ molecular_function
polyribonucleotide nucleotidyltransferase activity go/ molecular_function
RNA processing go/ biological_process
mRNA catabolic process go/ biological_process
Purine metabolism kegg/ kegg pathway
Pyrimidine metabolism kegg/ kegg pathway
RNA degradation kegg/ kegg pathway
polynuc_phos tigr/ tigrfam
Module neighborhood information for BSU16690

BSU16690 has total of 35 gene neighbors in modules 253, 289
Gene neighbors (35)
Gene Common Name Description Module membership
BSU07955 BSU07955 None 211, 289
BSU08650 fabL enoyl-(acyl carrier protein) reductase (RefSeq) 116, 253
BSU14180 dapH tetrahydrodipicolinate N-acetyltransferase (RefSeq) 253, 313
BSU15410 ylmH factor involved in shape determination, RNA-binding fold (RefSeq) 194, 289
BSU15760 prpC phosphorylated protein phosphatase (RefSeq) 106, 289
BSU15770 prkC protein kinase (RefSeq) 106, 289
BSU15780 yloQ ribosome-associated GTPase (RefSeq) 106, 289
BSU15790 rpe ribulose-phosphate 3-epimerase (RefSeq) 106, 289
BSU15840 yloV putative dihydroxyacetone/glyceraldehyde kinase (RefSeq) 63, 289
BSU16010 ylqD hypothetical protein (RefSeq) 245, 253
BSU16020 rimM 16S rRNA-processing protein RimM (RefSeq) 125, 253
BSU16500 tsf elongation factor Ts (RefSeq) 104, 253
BSU16540 cdsA phosphatidate cytidylyltransferase (CDP-diglyceride synthase) (RefSeq) 253, 343
BSU16550 dxr 1-deoxy-D-xylulose 5-phosphate reductoisomerase (RefSeq) 253, 289
BSU16560 rseP inner membrane zinc metalloprotease required for the extracytoplasmic stress response mediated by sigma(E) (YaeL) (RefSeq) 253, 289
BSU16570 proS prolyl-tRNA synthetase (RefSeq) 253, 289
BSU16690 pnpA polynucleotide phosphorylase/polyadenylase (RefSeq) 253, 289
BSU16700 ylxY putative sugar deacetylase (RefSeq) 253, 289
BSU16710 mlpA specific processing protease (RefSeq) 253, 289
BSU16780 rnjB ribonuclease J2 (RefSeq) 155, 289
BSU19630 deoD purine nucleoside phosphorylase (RefSeq) 289, 313
BSU22740 hepT heptaprenyl diphosphate synthase component II (RefSeq) 15, 289
BSU22750 ubiE ubiquinone/menaquinone biosynthesis methyltransferase (RefSeq) 42, 289
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
BSU28010 mreD cell-shape determining protein (RefSeq) 104, 253
BSU28020 mreC rod shape-determining protein MreC (RefSeq) 104, 253
BSU28030 mreB rod shape-determining protein MreB (RefSeq) 104, 253
BSU28230 tig trigger factor (RefSeq) 104, 253
BSU29180 pyk pyruvate kinase (RefSeq) 253, 273
BSU29190 pfkA 6-phosphofructokinase (RefSeq) 194, 253
VIMSS36718 VIMSS36718 None 288, 289
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 BSU16690
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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