Organism : Bacillus cereus ATCC14579 | Module List :
BC5340

Transcriptional regulator, TetR family (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
specific transcriptional repressor activity go/ molecular_function
negative regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC5340
(Mouseover regulator name to see its description)

BC5340 is regulated by 35 influences and regulates 21 modules.
Regulators for BC5340 (35)
Regulator Module Operator
BC0114 449 tf
BC0758 449 tf
BC0851 449 tf
BC0882 449 tf
BC0993 449 tf
BC1732 449 tf
BC1889 449 tf
BC2386 449 tf
BC3072 449 tf
BC3438 449 tf
BC3756 449 tf
BC4073 449 tf
BC4212 449 tf
BC4505 449 tf
BC5097 449 tf
BC5340 449 tf
BC0057 243 tf
BC0059 243 tf
BC0114 243 tf
BC1337 243 tf
BC1490 243 tf
BC1531 243 tf
BC2680 243 tf
BC2794 243 tf
BC3062 243 tf
BC3160 243 tf
BC3320 243 tf
BC3332 243 tf
BC3593 243 tf
BC3653 243 tf
BC3982 243 tf
BC4316 243 tf
BC4525 243 tf
BC4714 243 tf
BC5340 243 tf

Warning: BC5340 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
4402 3.90e-03 gA.aG.gAAgG
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4403 4.20e+03 GgGGGC
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4808 2.80e-02 aaAgggAG
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4809 2.20e+04 cTgaTgctgCgc.a.tA.gtgttA
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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 BC5340

BC5340 is enriched for 5 functions in 3 categories.
Module neighborhood information for BC5340

BC5340 has total of 68 gene neighbors in modules 243, 449
Gene neighbors (68)
Gene Common Name Description Module membership
BC0056 BC0056 Peptidyl-tRNA hydrolase (NCBI ptt file) 117, 243
BC0057 BC0057 hypothetical protein (NCBI ptt file) 243, 394
BC0105 BC0105 hypothetical Membrane Associated Protein (NCBI ptt file) 22, 243
BC0234 BC0234 Sec-independent secretion TatD (NCBI ptt file) 98, 449
BC0254 BC0254 Homogentisate 1,2-dioxygenase (NCBI ptt file) 243, 263
BC0388 BC0388 hypothetical protein (NCBI ptt file) 261, 449
BC0392 BC0392 hypothetical protein (NCBI ptt file) 351, 449
BC0425 BC0425 Hydroxymethylpyrimidine transport system permease protein (NCBI ptt file) 449, 467
BC0426 BC0426 Hydroxymethylpyrimidine-binding protein (NCBI ptt file) 449, 467
BC0513 BC0513 Daunorubicin resistance ATP-binding protein drrA (NCBI ptt file) 243, 467
BC0515 BC0515 ABC transporter permease protein (NCBI ptt file) 243, 467
BC0516 BC0516 LCTB protein (NCBI ptt file) 243, 467
BC0517 BC0517 Thioredoxin-dependent thiol peroxidase (NCBI ptt file) 243, 443
BC0694 BC0694 Na+/H+ antiporter NapA (NCBI ptt file) 243, 252
BC0752 BC0752 hypothetical protein (NCBI ptt file) 265, 449
BC0788 BC0788 hypothetical protein (NCBI ptt file) 104, 449
BC0790 BC0790 hypothetical protein (NCBI ptt file) 98, 449
BC0839 BC0839 hypothetical protein (NCBI ptt file) 261, 449
BC0851 BC0851 Mercuric resistance operon regulatory protein (NCBI ptt file) 389, 449
BC0879 BC0879 hypothetical Membrane Associated Protein (NCBI ptt file) 257, 449
BC1095 BC1095 hypothetical protein (NCBI ptt file) 449, 511
BC1184 BC1184 Na+ driven multidrug efflux pump (NCBI ptt file) 243, 527
BC1294 BC1294 hypothetical Membrane Spanning Protein (NCBI ptt file) 385, 449
BC1319 BC1319 Oxidoreductase (NCBI ptt file) 257, 449
BC1578 BC1578 hypothetical protein (NCBI ptt file) 243, 256
BC1743 BC1743 Two-component response regulator (NCBI ptt file) 243, 252
BC1807 BC1807 Amino acid permease (NCBI ptt file) 134, 449
BC1931 BC1931 Branched-chain amino acid transport system permease protein livM (NCBI ptt file) 48, 449
BC2042 BC2042 putative NAD-dependent dehydrogenase (NCBI ptt file) 218, 243
BC2262 BC2262 Thioredoxin (NCBI ptt file) 306, 449
BC2351 BC2351 Transcriptional regulator, MerR family (NCBI ptt file) 263, 449
BC2386 BC2386 RNA polymerase ECF-type sigma factor (NCBI ptt file) 438, 449
BC2388 BC2388 Caffeoyl-CoA O-methyltransferase (NCBI ptt file) 98, 449
BC2476 BC2476 phosphoesterase (NCBI ptt file) 263, 449
BC2520 BC2520 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily (NCBI ptt file) 98, 449
BC2538 BC2538 Two-component response regulator yxdJ (NCBI ptt file) 265, 449
BC2578 BC2578 Phage protein (NCBI ptt file) 449, 480
BC2691 BC2691 Acetyltransferase (NCBI ptt file) 25, 449
BC2955 BC2955 hypothetical protein (NCBI ptt file) 449, 511
BC3072 BC3072 Transcriptional regulator, ArsR family (NCBI ptt file) 47, 449
BC3118 BC3118 Cytochrome p450 (NCBI ptt file) 449, 465
BC3160 BC3160 Transcriptional regulator, TetR family (NCBI ptt file) 243, 260
BC3200 BC3200 Two-component response regulator (NCBI ptt file) 6, 449
BC3226 BC3226 hypothetical protein (NCBI ptt file) 440, 449
BC3252 BC3252 hypothetical protein (NCBI ptt file) 299, 449
BC3471 BC3471 hypothetical protein (NCBI ptt file) 243, 306
BC3490 BC3490 Penicillin-binding protein (NCBI ptt file) 299, 449
BC3595 BC3595 Oxidoreductase (NCBI ptt file) 243, 306
BC3756 BC3756 Transcriptional regulator, GntR family (NCBI ptt file) 193, 449
BC3772 BC3772 tRNA 2-methylthioadenosine synthase (NCBI ptt file) 243, 399
BC3930 BC3930 Methyltransferase (NCBI ptt file) 243, 260
BC3948 BC3948 Cell division protein ftsW (NCBI ptt file) 243, 260
BC3985 BC3985 hypothetical Cytosolic Protein (NCBI ptt file) 55, 449
BC4246 BC4246 hypothetical protein (NCBI ptt file) 55, 449
BC4315 BC4315 Coproporphyrinogen oxidase, anaerobic (NCBI ptt file) 243, 252
BC4334 BC4334 hypothetical protein (NCBI ptt file) 261, 449
BC4373 BC4373 hypothetical protein (NCBI ptt file) 130, 449
BC4416 BC4416 Ferrichrome-binding protein (NCBI ptt file) 263, 449
BC4495 BC4495 Germination protein germ (NCBI ptt file) 449, 455
BC4673 BC4673 hypothetical protein (NCBI ptt file) 243, 252
BC4809 BC4809 Two component system histidine kinase (NCBI ptt file) 263, 449
BC4848 BC4848 Sensor protein vanS (NCBI ptt file) 222, 449
BC4975 BC4975 hypothetical Membrane Associated Protein (NCBI ptt file) 288, 449
BC5094 BC5094 Transposase (NCBI ptt file) 375, 449
BC5096 BC5096 hypothetical protein (NCBI ptt file) 26, 449
BC5245 BC5245 SWF/SNF family helicase (NCBI ptt file) 193, 243
BC5287 BC5287 Stage II sporulation protein D (NCBI ptt file) 193, 449
BC5340 BC5340 Transcriptional regulator, TetR family (NCBI ptt file) 243, 449
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 BC5340
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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