Organism : Bacillus cereus ATCC14579 | Module List :
BC2631

Transcriptional regulator, ArsR family (NCBI ptt file)

CircVis
Functional Annotations (3)
Function System
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC2631
(Mouseover regulator name to see its description)

BC2631 is regulated by 31 influences and regulates 15 modules.
Regulators for BC2631 (31)
Regulator Module Operator
BC0057 189 tf
BC1080 189 tf
BC1115 189 tf
BC2178 189 tf
BC2469 189 tf
BC2517 189 tf
BC2631 189 tf
BC2672 189 tf
BC2811 189 tf
BC3588 189 tf
BC4104 189 tf
BC4316 189 tf
BC4393 189 tf
BC4930 189 tf
BC0114 358 tf
BC0477 358 tf
BC0566 358 tf
BC0607 358 tf
BC0801 358 tf
BC1037 358 tf
BC1077 358 tf
BC1337 358 tf
BC1732 358 tf
BC2068 358 tf
BC2250 358 tf
BC2631 358 tf
BC2988 358 tf
BC3095 358 tf
BC3434 358 tf
BC4057 358 tf
BC4525 358 tf

Warning: BC2631 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
4294 7.90e+03 GACcGGC
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4295 2.90e+00 aaaggGGatGagt
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4626 4.20e-10 gGGGGA
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4627 8.30e+03 G.aAgaGGgtTTtCa
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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 BC2631

BC2631 is enriched for 3 functions in 2 categories.
Enrichment Table (3)
Function System
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for BC2631

BC2631 has total of 41 gene neighbors in modules 189, 358
Gene neighbors (41)
Gene Common Name Description Module membership
BC0170 BC0170 KINB signaling pathway activation protein (NCBI ptt file) 23, 358
BC0407 BC0407 Ornithine carbamoyltransferase (NCBI ptt file) 189, 464
BC0511 BC0511 Glutamate synthase [NADPH] large chain (NCBI ptt file) 358, 520
BC0552 BC0552 Internalin protein (NCBI ptt file) 358, 496
BC0557 BC0557 hypothetical protein (NCBI ptt file) 340, 358
BC0558 BC0558 Flottilin (NCBI ptt file) 340, 358
BC0561 BC0561 Two-component response regulator (NCBI ptt file) 189, 472
BC0633 BC0633 Spore germination protein KC (NCBI ptt file) 189, 446
BC0997 BC0997 hypothetical protein (NCBI ptt file) 141, 358
BC1182 BC1182 Oligopeptide transport ATP-binding protein oppD (NCBI ptt file) 137, 358
BC1332 BC1332 None 340, 358
BC1745 BC1745 hypothetical protein (NCBI ptt file) 46, 358
BC2068 BC2068 Transcriptional regulator, GntR family (NCBI ptt file) 294, 358
BC2251 BC2251 Lysine 2,3-aminomutase (NCBI ptt file) 340, 358
BC2252 BC2252 hypothetical Cytosolic Protein (NCBI ptt file) 340, 358
BC2347 BC2347 Acetyltransferase (NCBI ptt file) 189, 522
BC2467 BC2467 D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) 189, 238
BC2631 BC2631 Transcriptional regulator, ArsR family (NCBI ptt file) 189, 358
BC2694 BC2694 hypothetical protein (NCBI ptt file) 128, 189
BC2728 BC2728 hypothetical Cytosolic Protein (NCBI ptt file) 189, 358
BC2784 BC2784 Phosphohydrolase (MutT/nudix family protein) (NCBI ptt file) 150, 358
BC2786 BC2786 hypothetical protein (NCBI ptt file) 358, 496
BC2850 BC2850 Mandelate racemase/muconate lactonizing enzyme family protein (NCBI ptt file) 358, 446
BC2945 BC2945 hypothetical protein (NCBI ptt file) 189, 224
BC2998 BC2998 hypothetical Secreted Protein (NCBI ptt file) 13, 358
BC3012 BC3012 Adenine deaminase (NCBI ptt file) 112, 358
BC3066 BC3066 Lactam utilization protein LAMB (NCBI ptt file) 303, 358
BC3076 BC3076 Acetyltransferase (NCBI ptt file) 189, 340
BC3119 BC3119 D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) 155, 189
BC3363 BC3363 hypothetical protein (NCBI ptt file) 23, 189
BC3450 BC3450 hypothetical Membrane Spanning Protein (NCBI ptt file) 358, 496
BC3502 BC3502 IG hypothetical 17676 (NCBI ptt file) 189, 520
BC3646 BC3646 Ferredoxin-dependent glutamate synthase (NCBI ptt file) 358, 407
BC3952 BC3952 GTPase (NCBI ptt file) 358, 473
BC4040 BC4040 hypothetical Membrane Spanning Protein (NCBI ptt file) 338, 358
BC4047 BC4047 hypothetical protein (NCBI ptt file) 128, 358
BC4288 BC4288 Membrane-attached cytochrome c550 (NCBI ptt file) 358, 405
BC4526 BC4526 acyl-CoA synthase (RefSeq) 358, 387
BC4695 BC4695 Metal-dependent hydrolase (NCBI ptt file) 23, 189
BC5345 BC5345 Iron-sulphur-binding reductase (NCBI ptt file) 358, 473
BC5416 BC5416 Carbon starvation protein A (NCBI ptt file) 23, 358
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 BC2631
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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