Organism : Bacillus cereus ATCC14579 | Module List :
BC0690

Transcriptional regulator, PBSX family (NCBI ptt file)

CircVis
Functional Annotations (2)
Function System
Predicted transcriptional regulators cog/ cog
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC0690
(Mouseover regulator name to see its description)

BC0690 is regulated by 23 influences and regulates 4 modules.
Regulators for BC0690 (23)
Regulator Module Operator
BC0213 141 tf
BC0690 141 tf
BC1731 141 tf
BC2526 141 tf
BC3175 141 tf
BC3593 141 tf
BC4181 141 tf
BC4314 141 tf
BC4703 141 tf
BC5175 141 tf
BC5222 141 tf
BC0051 485 tf
BC0518 485 tf
BC0690 485 tf
BC1363 485 tf
BC1731 485 tf
BC2410 485 tf
BC2914 485 tf
BC3356 485 tf
BC4076 485 tf
BC4206 485 tf
BC4211 485 tf
BC5256 485 tf

Warning: BC0690 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
4198 5.30e-09 aa.aAagGaG.ta
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4199 2.40e+04 ATgTTTGG.AGgGG
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4880 3.60e+01 AGGaGg
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4881 1.00e+04 cGAGAGGGaG
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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 BC0690

BC0690 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Predicted transcriptional regulators cog/ cog
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for BC0690

BC0690 has total of 62 gene neighbors in modules 141, 485
Gene neighbors (62)
Gene Common Name Description Module membership
BC0172 BC0172 hypothetical protein (NCBI ptt file) 141, 158
BC0690 BC0690 Transcriptional regulator, PBSX family (NCBI ptt file) 141, 485
BC0826 BC0826 hypothetical DNA-binding protein (NCBI ptt file) 141, 257
BC0827 BC0827 hypothetical protein (NCBI ptt file) 141, 218
BC0828 BC0828 Alkaline phosphatase like protein (NCBI ptt file) 141, 245
BC0831 BC0831 hypothetical protein (NCBI ptt file) 141, 487
BC0832 BC0832 None 165, 485
BC0933 BC0933 hypothetical protein (NCBI ptt file) 141, 175
BC0997 BC0997 hypothetical protein (NCBI ptt file) 141, 358
BC1132 BC1132 hypothetical protein (NCBI ptt file) 141, 263
BC1281 BC1281 Cell envelope-bound metalloprotease (camelysin) (NCBI ptt file) 141, 293
BC1558 BC1558 hypothetical protein (NCBI ptt file) 346, 485
BC1672 BC1672 Metal-dependent hydrolase related to alanyl-tRNA synthetase (NCBI ptt file) 141, 329
BC1677 BC1677 Dienelactone hydrolase family (NCBI ptt file) 141, 428
BC1691 BC1691 Phosphoglycerate mutase (NCBI ptt file) 25, 141
BC1727 BC1727 hypothetical protein (NCBI ptt file) 177, 485
BC1729 BC1729 Multi-TM2 domain protein (NCBI ptt file) 161, 485
BC1730 BC1730 hypothetical protein (NCBI ptt file) 161, 485
BC1731 BC1731 RNA polymerase ECF-type sigma factor (NCBI ptt file) 25, 485
BC1840 BC1840 Transporter, Drug/Metabolite Exporter family (NCBI ptt file) 63, 141
BC1893 BC1893 Scaffold protein (NCBI ptt file) 141, 468
BC2165 BC2165 hypothetical Membrane Spanning Protein (NCBI ptt file) 369, 485
BC2296 BC2296 Exonuclease SbcC (NCBI ptt file) 141, 193
BC2495 BC2495 hypothetical protein (NCBI ptt file) 85, 141
BC2593 BC2593 Phage protein (NCBI ptt file) 25, 141
BC2620 BC2620 Penicillin-binding protein transpeptidase (NCBI ptt file) 9, 141
BC2625 BC2625 DNA integration/recombination/invertion protein (NCBI ptt file) 150, 485
BC2626 BC2626 DNA integration/recombination/invertion protein (NCBI ptt file) 150, 485
BC2692 BC2692 Phosphohydrolase (MutT/nudix family protein) (NCBI ptt file) 141, 405
BC2821 BC2821 Transposase (NCBI ptt file) 141, 245
BC2883 BC2883 hypothetical Cytosolic Protein (NCBI ptt file) 369, 485
BC2913 BC2913 hypothetical protein (NCBI ptt file) 60, 485
BC2914 BC2914 Transcriptional regulator, TetR family (NCBI ptt file) 60, 485
BC2922 BC2922 hypothetical protein (NCBI ptt file) 141, 361
BC3089 BC3089 Integral membrane protein (NCBI ptt file) 141, 396
BC3105 BC3105 Transcriptional regulator, AraC family (NCBI ptt file) 9, 141
BC3277 BC3277 hypothetical Cytosolic Protein (NCBI ptt file) 60, 141
BC3421 BC3421 Transcriptional regulator, MarR family (NCBI ptt file) 20, 485
BC3551 BC3551 D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) 97, 485
BC3594 BC3594 PhnB protein (NCBI ptt file) 141, 218
BC3690 BC3690 LexA repressor (NCBI ptt file) 141, 158
BC3703 BC3703 Phage protein (NCBI ptt file) 9, 141
BC3763 BC3763 None 225, 485
BC3964 BC3964 hypothetical protein (NCBI ptt file) 417, 485
BC3966 BC3966 hypothetical protein (NCBI ptt file) 417, 485
BC4027 BC4027 hypothetical protein (NCBI ptt file) 60, 485
BC4120 BC4120 hypothetical protein (NCBI ptt file) 141, 184
BC4206 BC4206 Transcriptional regulator, PadR family (NCBI ptt file) 369, 485
BC4207 BC4207 hypothetical protein (NCBI ptt file) 369, 485
BC4233 BC4233 Prolyl 4-hydroxylase alpha subunit (NCBI ptt file) 246, 485
BC4428 BC4428 ABC transporter permease protein (NCBI ptt file) 108, 141
BC4451 BC4451 hypothetical protein (NCBI ptt file) 141, 464
BC4612 BC4612 hypothetical protein (NCBI ptt file) 76, 141
BC4617 BC4617 hypothetical Membrane Spanning Protein (NCBI ptt file) 9, 141
BC4740 BC4740 TrkA C-terminal domain protein (NCBI ptt file) 219, 485
BC4759 BC4759 hypothetical Membrane Spanning Protein (NCBI ptt file) 141, 281
BC4780 BC4780 ABC transporter permease protein (NCBI ptt file) 141, 199
BC4825 BC4825 ABC transporter ATP-binding protein (NCBI ptt file) 141, 385
BC5254 BC5254 ABC transporter ATP-binding protein (NCBI ptt file) 141, 327
BC5303 BC5303 Integral membrane protein (NCBI ptt file) 141, 327
BC5346 BC5346 Cardiolipin synthetase (NCBI ptt file) 141, 456
BC5348 BC5348 None 141, 410
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 BC0690
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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