Organism : Bacillus cereus ATCC14579 | Module List :
BC0980

Transcriptional regulator, TetR family (NCBI ptt file)

CircVis
Functional Annotations (6)
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
DHAK_reg tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC0980
(Mouseover regulator name to see its description)

BC0980 is regulated by 32 influences and regulates 3 modules.
Regulators for BC0980 (32)
Regulator Module Operator
BC0123 308 tf
BC0950 308 tf
BC1033 308 tf
BC1037 308 tf
BC1337 308 tf
BC1732 308 tf
BC2444 308 tf
BC2526 308 tf
BC2670 308 tf
BC2742 308 tf
BC2904 308 tf
BC3175 308 tf
BC3497 308 tf
BC3961 308 tf
BC4650 308 tf
BC5141 308 tf
BC5340 308 tf
BC0158 364 tf
BC0953 364 tf
BC1032 364 tf
BC1253 364 tf
BC2362 364 tf
BC2367 364 tf
BC2470 364 tf
BC2558 364 tf
BC3175 364 tf
BC3244 364 tf
BC3522 364 tf
BC3961 364 tf
BC4212 364 tf
BC4336 364 tf
BC4661 364 tf

Warning: BC0980 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
4530 1.30e-02 AtAaaG.ggtg
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4531 2.80e+03 gTaAG.AGG..gAag
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4638 6.60e-04 gaAAgGaGga
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4639 7.10e+02 TTcttctcttTCctctc.ta.tTc
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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 BC0980

BC0980 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
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
DHAK_reg tigr/ tigrfam
Module neighborhood information for BC0980

BC0980 has total of 63 gene neighbors in modules 308, 364
Gene neighbors (63)
Gene Common Name Description Module membership
BC0035 BC0035 Arginine decarboxylase (NCBI ptt file) 263, 308
BC0299 BC0299 Two component system histidine kinase (NCBI ptt file) 163, 308
BC0369 BC0369 Zinc metalloprotease (NCBI ptt file) 8, 364
BC0460 BC0460 hypothetical protein (NCBI ptt file) 9, 364
BC0461 BC0461 General stress protein 26 (NCBI ptt file) 160, 364
BC0495 BC0495 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 246, 308
BC0575 BC0575 hypothetical protein (NCBI ptt file) 68, 308
BC0604 BC0604 hypothetical Exported Protein (NCBI ptt file) 62, 308
BC0645 BC0645 None 364, 440
BC0676 BC0676 hypothetical protein (NCBI ptt file) 257, 308
BC0780 BC0780 hypothetical protein (NCBI ptt file) 12, 364
BC0781 BC0781 hypothetical protein (NCBI ptt file) 20, 364
BC0885 BC0885 DNA-3-methyladenine glycosylase II (NCBI ptt file) 308, 364
BC0951 BC0951 hypothetical protein (NCBI ptt file) 341, 364
BC0953 BC0953 Transcriptional regulator, MerR family (NCBI ptt file) 364, 454
BC0980 BC0980 Transcriptional regulator, TetR family (NCBI ptt file) 308, 364
BC1014 BC1014 Quinone oxidoreductase (NCBI ptt file) 364, 440
BC1096 BC1096 hypothetical protein (NCBI ptt file) 25, 308
BC1129 BC1129 Trifolitoxin immunity protein (NCBI ptt file) 97, 364
BC1379 BC1379 Gentamicin resistance protein (NCBI ptt file) 364, 405
BC1544 BC1544 hypothetical protein (NCBI ptt file) 308, 417
BC1545 BC1545 hypothetical protein (NCBI ptt file) 308, 417
BC1711 BC1711 Short chain dehydrogenase (NCBI ptt file) 364, 475
BC1732 BC1732 Two-component response regulator (NCBI ptt file) 230, 308
BC1733 BC1733 Sensory Transduction Protein Kinase (NCBI ptt file) 230, 308
BC2097 BC2097 hypothetical protein (NCBI ptt file) 97, 364
BC2269 BC2269 hypothetical protein (NCBI ptt file) 364, 415
BC2367 BC2367 Transcriptional regulators, LysR family (NCBI ptt file) 97, 364
BC2444 BC2444 Transcription state regulatory protein abrB (NCBI ptt file) 10, 308
BC2445 BC2445 hypothetical protein (NCBI ptt file) 55, 308
BC2493 BC2493 hypothetical protein (NCBI ptt file) 265, 308
BC2537 BC2537 Acetamidase (NCBI ptt file) 68, 308
BC2582 BC2582 Terminase small subunit (NCBI ptt file) 138, 364
BC2607 BC2607 hypothetical protein (NCBI ptt file) 308, 489
BC2670 BC2670 Transcriptional regulator, DeoR family (NCBI ptt file) 154, 308
BC2716 BC2716 Glucose dehydrogenase [pyrroloquinoline-quinone] (NCBI ptt file) 55, 308
BC2876 BC2876 Acetyltransferase (NCBI ptt file) 30, 364
BC2950 BC2950 putative kinase (NCBI ptt file) 7, 364
BC3138 BC3138 hypothetical protein (NCBI ptt file) 85, 364
BC3148 BC3148 Streptothricin acetyltransferase (NCBI ptt file) 63, 364
BC3175 BC3175 Leucine-responsive regulatory protein (NCBI ptt file) 364, 428
BC3232 BC3232 hypothetical protein (NCBI ptt file) 85, 364
BC3237 BC3237 Chitin binding protein (NCBI ptt file) 308, 404
BC3238 BC3238 hypothetical protein (NCBI ptt file) 85, 364
BC3272 BC3272 hypothetical Cytosolic Protein (NCBI ptt file) 276, 308
BC3530 BC3530 Membrane protein, MgtC/SapB family (NCBI ptt file) 35, 364
BC3538 BC3538 DNA polymerase III, epsilon chain (NCBI ptt file) 62, 308
BC3545 BC3545 Chloramphenicol acetyltransferase (NCBI ptt file) 308, 370
BC3610 BC3610 hypothetical protein (NCBI ptt file) 212, 364
BC3636 BC3636 hypothetical Cytosolic Protein (NCBI ptt file) 308, 440
BC3675 BC3675 hypothetical protein (NCBI ptt file) 177, 308
BC3676 BC3676 hypothetical protein (NCBI ptt file) 163, 308
BC3714 BC3714 tRNA delta(2)-isopentenylpyrophosphate transferase (NCBI ptt file) 85, 308
BC3764 BC3764 NAD(FAD)-utilizing dehydrogenases (NCBI ptt file) 308, 460
BC3961 BC3961 putative transcriptional regulator (NCBI ptt file) 364, 489
BC3983 BC3983 CBS domain containing protein (NCBI ptt file) 308, 389
BC4404 BC4404 Cobalt-zinc-cadmium resistance protein czcD (NCBI ptt file) 72, 364
BC4439 BC4439 Ribonuclease G (NCBI ptt file) 256, 308
BC4666 BC4666 Two component system histidine kinase (NCBI ptt file) 63, 308
BC4698 BC4698 putative choline kinase involved in lipopolysaccharide biosynthesis (NCBI ptt file) 265, 308
BC4905 BC4905 hypothetical protein (NCBI ptt file) 238, 308
BC4920 BC4920 hypothetical Membrane Spanning Protein (NCBI ptt file) 26, 364
BC4966 BC4966 hypothetical Cytosolic Protein (NCBI ptt file) 265, 308
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 BC0980
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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