Organism : Bacillus cereus ATCC14579 | Module List :
BC2988

Transcriptional regulator, Cro/CI family (NCBI ptt file)

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

Cytoscape Web
Regulation information for BC2988
(Mouseover regulator name to see its description)

BC2988 is regulated by 28 influences and regulates 20 modules.
Regulators for BC2988 (28)
Regulator Module Operator
BC0630 100 tf
BC0950 100 tf
BC1850 100 tf
BC1932 100 tf
BC1996 100 tf
BC2122 100 tf
BC2353 100 tf
BC3253 100 tf
BC4010 100 tf
BC4240 100 tf
BC4425 100 tf
BC4826 100 tf
BC4842 100 tf
BC5265 100 tf
BC5402 100 tf
BC0758 440 tf
BC0958 440 tf
BC0961 440 tf
BC1033 440 tf
BC1363 440 tf
BC1614 440 tf
BC1724 440 tf
BC2218 440 tf
BC2351 440 tf
BC2558 440 tf
BC2996 440 tf
BC4826 440 tf
BC5352 440 tf

Warning: BC2988 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
4116 1.40e-04 AgaaAaAgGgatgtt
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4117 2.00e+03 GGaGaTacgCC
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4790 1.40e+01 aggAGGag
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4791 2.40e+04 GCGTGcG
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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 BC2988

BC2988 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Predicted transcriptional regulator cog/ cog
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for BC2988

BC2988 has total of 56 gene neighbors in modules 100, 440
Gene neighbors (56)
Gene Common Name Description Module membership
BC0193 BC0193 hypothetical protein (NCBI ptt file) 343, 440
BC0405 BC0405 Arginine repressor, argR (NCBI ptt file) 100, 187
BC0645 BC0645 None 364, 440
BC0651 BC0651 Two component system histidine kinase (NCBI ptt file) 440, 478
BC0652 BC0652 Two-component response regulator (NCBI ptt file) 228, 440
BC1014 BC1014 Quinone oxidoreductase (NCBI ptt file) 364, 440
BC1074 BC1074 hypothetical protein (NCBI ptt file) 148, 440
BC1075 BC1075 Beta-lactamase repressor (NCBI ptt file) 219, 440
BC1077 BC1077 Transcriptional regulator, TetR family (NCBI ptt file) 304, 440
BC1130 BC1130 hypothetical protein (NCBI ptt file) 9, 440
BC1333 BC1333 CBS domain containing protein (NCBI ptt file) 100, 199
BC1336 BC1336 Sporulation kinase D (NCBI ptt file) 6, 440
BC1386 BC1386 hypothetical protein (NCBI ptt file) 100, 354
BC1850 BC1850 Transcriptional regulator (NCBI ptt file) 100, 294
BC1924 BC1924 L-lactate dehydrogenase (NCBI ptt file) 90, 100
BC1996 BC1996 Transcription state regulatory protein abrB (NCBI ptt file) 100, 517
BC2261 BC2261 Cobalt-zinc-cadmium resistance protein czcD (NCBI ptt file) 100, 214
BC2263 BC2263 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 100, 354
BC2356 BC2356 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 28, 100
BC2398 BC2398 putative integral membrane protein (NCBI ptt file) 100, 481
BC2527 BC2527 CAAX amino terminal protease family (NCBI ptt file) 100, 354
BC2558 BC2558 Transcriptional regulator (NCBI ptt file) 7, 440
BC2618 BC2618 hydrolase (HAD superfamily) (NCBI ptt file) 100, 401
BC2717 BC2717 hypothetical protein (NCBI ptt file) 100, 337
BC2718 BC2718 hypothetical protein (NCBI ptt file) 100, 337
BC2921 BC2921 hypothetical protein (NCBI ptt file) 100, 461
BC2988 BC2988 Transcriptional regulator, Cro/CI family (NCBI ptt file) 100, 440
BC2995 BC2995 hypothetical protein (NCBI ptt file) 7, 100
BC2996 BC2996 Transcriptional regulator, PadR family (NCBI ptt file) 7, 440
BC3226 BC3226 hypothetical protein (NCBI ptt file) 440, 449
BC3279 BC3279 hypothetical protein (NCBI ptt file) 7, 440
BC3318 BC3318 hypothetical protein (NCBI ptt file) 7, 100
BC3334 BC3334 2-haloalkanoic acid dehalogenase (NCBI ptt file) 15, 440
BC3636 BC3636 hypothetical Cytosolic Protein (NCBI ptt file) 308, 440
BC3665 BC3665 Bacitracin transport permease protein BCRB (NCBI ptt file) 100, 388
BC3996 BC3996 hypothetical Exported Protein (NCBI ptt file) 20, 440
BC4062 BC4062 IG hypothetical 17221 (NCBI ptt file) 100, 477
BC4337 BC4337 hypothetical Membrane Spanning Protein (NCBI ptt file) 440, 443
BC4370 BC4370 hypothetical protein (NCBI ptt file) 100, 477
BC4453 BC4453 Phage protein (NCBI ptt file) 62, 440
BC4532 BC4532 hypothetical protein (NCBI ptt file) 7, 440
BC4559 BC4559 Asparaginyl-tRNA synthetase (NCBI ptt file) 100, 412
BC4660 BC4660 Acetoin utilization protein acuA (NCBI ptt file) 440, 478
BC4664 BC4664 hypothetical protein (NCBI ptt file) 100, 228
BC4675 BC4675 Sex pheromone staph-cAM373 precursor (NCBI ptt file) 7, 100
BC4826 BC4826 hypothetical protein (NCBI ptt file) 100, 304
BC4842 BC4842 Transcriptional regulator, GntR family (NCBI ptt file) 100, 304
BC4929 BC4929 Macrolide-efflux protein (NCBI ptt file) 20, 100
BC4933 BC4933 Methyltransferase (NCBI ptt file) 303, 440
BC5011 BC5011 hypothetical protein (NCBI ptt file) 422, 440
BC5258 BC5258 Phosphoglycerate transporter protein (NCBI ptt file) 100, 290
BC5349 BC5349 PapR protein (NCBI ptt file) 100, 354
BC5352 BC5352 two-component response regulator YocG (NCBI) 41, 440
BC5353 BC5353 Two-component sensor kinase yocF (NCBI ptt file) 41, 440
BC5424 BC5424 Methyl-accepting chemotaxis protein (NCBI ptt file) 416, 440
BC5446 BC5446 None 416, 440
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 BC2988
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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