Organism : Bacillus subtilis | Module List :
BSU25000 pbpA

transpeptidase (penicillin-binding protein 2A) (RefSeq)

CircVis
Functional Annotations (4)
Function System
Cell division protein FtsI/penicillin-binding protein 2 cog/ cog
penicillin binding go/ molecular_function
peptidoglycan glycosyltransferase activity go/ molecular_function
peptidoglycan-based cell wall biogenesis go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU25000
(Mouseover regulator name to see its description)

BSU25000 is regulated by 19 influences and regulates 0 modules.
Regulators for BSU25000 pbpA (19)
Regulator Module Operator
BSU00700 13 tf
BSU01010 13 tf
BSU02680 13 tf
BSU03850 13 tf
BSU10860 13 tf
BSU13210 13 tf
BSU15970 13 tf
BSU23210 13 tf
BSU24220 13 tf
BSU36630 13 tf
BSU00700 188 tf
BSU00800 188 tf
BSU04680 188 tf
BSU05580 188 tf
BSU27080 188 tf
BSU27320 188 tf
BSU31530 188 tf
BSU40410 188 tf
BSU40990 188 tf

Warning: BSU25000 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
4988 6.70e+02 CggCTtTT
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4989 8.60e+02 ttTTtTtaCcA
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5322 7.70e+03 AGGAgGAA
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5323 1.50e+04 GGcGGCC
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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 BSU25000

BSU25000 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Cell division protein FtsI/penicillin-binding protein 2 cog/ cog
penicillin binding go/ molecular_function
peptidoglycan glycosyltransferase activity go/ molecular_function
peptidoglycan-based cell wall biogenesis go/ biological_process
Module neighborhood information for BSU25000

BSU25000 has total of 46 gene neighbors in modules 13, 188
Gene neighbors (46)
Gene Common Name Description Module membership
BSU00200 yaaK hypothetical protein (RefSeq) 188, 233
BSU00210 recR recombination protein RecR (RefSeq) 160, 188
BSU00220 yaaL hypothetical protein (RefSeq) 1, 188
BSU00700 coaX pantothenate kinase (RefSeq) 13, 314
BSU00720 yacD putative protein secretion PrsA homolog (RefSeq) 13, 166
BSU01140 ybaC putative proline iminopeptidase (RefSeq) 13, 37
BSU01830 ndhF NADH dehydrogenase subunit 5 (RefSeq) 13, 220
BSU03590 tcyC cystine ABC transporter (ATP-binding protein) (RefSeq) 13, 72
BSU03600 tcyB cystine ABC transporter (permease) (RefSeq) 13, 72
BSU03610 tcyA cystine ABC transporter (substrate-binding lipoprotein) (RefSeq) 13, 72
BSU03840 ycnB putative efflux transporter (RefSeq) 13, 240
BSU03850 ycnC putative transcriptional regulator (TetR/AcrR family) (RefSeq) 11, 13
BSU10120 hemE uroporphyrinogen decarboxylase (RefSeq) 188, 189
BSU10130 hemH ferrochelatase (RefSeq) 188, 189
BSU10140 hemY protoporphyrinogen oxidase (RefSeq) 188, 189
BSU14030 ykuC putative efflux transporter (RefSeq) 13, 265
BSU25000 pbpA transpeptidase (penicillin-binding protein 2A) (RefSeq) 13, 188
BSU26830 yrpE putative lipoprotein (RefSeq) 13, 327
BSU27370 yrrL hypothetical protein (RefSeq) 13, 255
BSU28120 hemL glutamate-1-semialdehyde aminotransferase (RefSeq) 188, 237
BSU28130 hemB delta-aminolevulinic acid dehydratase (RefSeq) 188, 237
BSU28140 hemD uroporphyrinogen III cosynthase (RefSeq) 188, 237
BSU28150 hemC porphobilinogen deaminase (RefSeq) 188, 237
BSU28160 hemX negative effector of the concentration of glutamyl-tRNA reductase HemA (RefSeq) 188, 237
BSU29060 coaE dephospho-CoA kinase (RefSeq) 188, 228
BSU29070 ytaF putative integral inner membrane protein (RefSeq) 188, 228
BSU29080 mutM formamidopyrimidine-DNA glycosylase (RefSeq) 160, 188
BSU29090 polA DNA polymerase I (RefSeq) 160, 188
BSU29220 ytsJ NADP-dependent malic enzyme (conversion of malate into pyruvate) (RefSeq) 188, 324
BSU29590 iscS cysteine desulfurase (RefSeq) 13, 265
BSU29600 braB branched-chain amino acid-Na+ symporter (RefSeq) 13, 319
BSU30990 thiT thiamin permease (RefSeq) 13, 319
BSU34730 yvcN putative acetyltransferase (RefSeq) 160, 188
BSU34740 crh phosphocarrier protein Chr (RefSeq) 160, 188
BSU34750 whiA putative morphogen (RefSeq) 160, 188
BSU34760 yvcK gluconeogenesis factor (RefSeq) 160, 188
BSU34770 yvcJ hypothetical protein (RefSeq) 160, 188
BSU34780 yvcI putative triphosphate pyrophosphate hydrolase (RefSeq) 160, 188
BSU35250 ftsX cell-division ABC transporter (RefSeq) 13, 128
BSU35260 ftsE cell-division ABC transporter (ATP-binding protein) (RefSeq) 13, 116
BSU36630 ywnA hypothetical protein (RefSeq) 13, 23
BSU39960 yxaI putative integral inner membrane protein (RefSeq) 11, 13
BSU40080 gntZ 6-phosphogluconate dehydrogenase (RefSeq) 13, 284
BSU40400 walK two-component sensor histidine kinase [YycF] (RefSeq) 188, 228
BSU40410 walR two-component response regulator [YycG] (RefSeq) 188, 228
BSU40500 rplI 50S ribosomal protein L9 (RefSeq) 188, 292
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 BSU25000
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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