Organism : Bacillus cereus ATCC14579 | Module List :
BC4374

Transcription elongation factor greA (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
Transcription elongation factor cog/ cog
DNA binding go/ molecular_function
transcription elongation regulator activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
greA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC4374
(Mouseover regulator name to see its description)

BC4374 is regulated by 26 influences and regulates 9 modules.
Regulators for BC4374 (26)
Regulator Module Operator
BC0213 238 tf
BC1032 238 tf
BC1080 238 tf
BC2362 238 tf
BC2526 238 tf
BC2551 238 tf
BC2670 238 tf
BC2738 238 tf
BC2801 238 tf
BC2811 238 tf
BC2936 238 tf
BC3449 238 tf
BC3493 238 tf
BC3589 238 tf
BC4316 238 tf
BC4374 238 tf
BC5205 238 tf
BC0230 241 tf
BC2358 241 tf
BC2434 241 tf
BC2551 241 tf
BC2680 241 tf
BC2811 241 tf
BC4181 241 tf
BC4336 241 tf
BC5250 241 tf

Warning: BC4374 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
4392 2.50e+03 agGgGgTgta
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4393 1.50e+03 gAAaaGGAGG
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4398 2.50e-03 aAgGgG
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4399 3.70e+00 aAaAgGAG
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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 BC4374

BC4374 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Transcription elongation factor cog/ cog
DNA binding go/ molecular_function
transcription elongation regulator activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
greA tigr/ tigrfam
Module neighborhood information for BC4374

BC4374 has total of 54 gene neighbors in modules 238, 241
Gene neighbors (54)
Gene Common Name Description Module membership
BC0260 BC0260 UV-endonuclease (UvsE/Uve1/UvdE Family) (NCBI ptt file) 76, 241
BC0318 BC0318 Transporter, Drug/Metabolite Exporter family (NCBI ptt file) 48, 241
BC0386 BC0386 hypothetical protein (NCBI ptt file) 241, 520
BC0427 BC0427 Hydroxymethylpyrimidine transport ATP-binding protein (NCBI ptt file) 104, 241
BC0480 BC0480 hypothetical protein (NCBI ptt file) 217, 241
BC0547 BC0547 Sensory box/GGDEF family protein (NCBI ptt file) 34, 238
BC0821 BC0821 CotJC protein (NCBI ptt file) 158, 241
BC0985 BC0985 hypothetical protein (NCBI ptt file) 85, 238
BC0989 BC0989 hypothetical protein (NCBI ptt file) 238, 241
BC1026 BC1026 Response regulator aspartate phosphatase (NCBI ptt file) 46, 238
BC1061 BC1061 hypothetical protein (NCBI ptt file) 59, 241
BC1261 BC1261 ATP/GTP-binding protein (NCBI ptt file) 238, 316
BC1262 BC1262 hypothetical protein (NCBI ptt file) 238, 316
BC1271 BC1271 hypothetical protein (NCBI ptt file) 238, 411
BC1356 BC1356 Transcriptional regulator, GntR family (NCBI ptt file) 75, 241
BC1450 BC1450 hypothetical protein (NCBI ptt file) 241, 504
BC1560 BC1560 Spore coat protein D (NCBI ptt file) 84, 241
BC1658 BC1658 Flagellin (NCBI ptt file) 52, 238
BC2111 BC2111 hypothetical protein (NCBI ptt file) 241, 393
BC2141 BC2141 Lipase (NCBI ptt file) 125, 238
BC2154 BC2154 Single-strand DNA binding protein (NCBI ptt file) 238, 255
BC2162 BC2162 Methyltransferase (NCBI ptt file) 25, 238
BC2314 BC2314 hypothetical protein (NCBI ptt file) 238, 316
BC2331 BC2331 Inosine-uridine preferring nucleoside hydrolase (NCBI ptt file) 154, 238
BC2349 BC2349 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 238, 525
BC2392 BC2392 FenI (NCBI ptt file) 241, 517
BC2404 BC2404 hypothetical Cytosolic Protein (NCBI ptt file) 217, 241
BC2415 BC2415 Collagen triple helix repeat protein (NCBI ptt file) 213, 241
BC2467 BC2467 D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) 189, 238
BC2515 BC2515 Macrolide-efflux protein (NCBI ptt file) 241, 491
BC2551 BC2551 Transcriptional activator tenA (NCBI ptt file) 25, 238
BC2553 BC2553 hypothetical protein (NCBI ptt file) 171, 238
BC2611 BC2611 Virginiamycin A acetyltransferase (NCBI ptt file) 56, 238
BC2643 BC2643 hydrolase (HAD superfamily) (NCBI ptt file) 123, 241
BC2725 BC2725 N-hydroxyarylamine O-acetyltransferase (NCBI ptt file) 241, 250
BC2747 BC2747 hypothetical Cytosolic Protein (NCBI ptt file) 238, 454
BC2858 BC2858 hypothetical protein (NCBI ptt file) 125, 238
BC2906 BC2906 hypothetical protein (NCBI ptt file) 25, 238
BC2927 BC2927 Prolyl endopeptidase (NCBI ptt file) 158, 238
BC3262 BC3262 hypothetical protein (NCBI ptt file) 34, 238
BC3296 BC3296 hypothetical protein (NCBI ptt file) 241, 245
BC3558 BC3558 Integral membrane protein (NCBI ptt file) 241, 370
BC4006 BC4006 hypothetical Cytosolic Protein (NCBI ptt file) 123, 238
BC4255 BC4255 Isochorismatase (NCBI ptt file) 72, 238
BC4374 BC4374 Transcription elongation factor greA (NCBI ptt file) 238, 241
BC4504 BC4504 Stress-responsive transcriptional regulator PspC (NCBI ptt file) 241, 398
BC4632 BC4632 hypothetical protein (NCBI ptt file) 220, 241
BC4651 BC4651 Transporter, Drug/Metabolite Exporter family (NCBI ptt file) 241, 415
BC4665 BC4665 Two-component response regulator (NCBI ptt file) 238, 316
BC4718 BC4718 Molybdopterin (MPT) converting factor, subunit 1 (NCBI ptt file) 241, 405
BC4858 BC4858 DnaK suppressor protein (NCBI ptt file) 217, 241
BC4905 BC4905 hypothetical protein (NCBI ptt file) 238, 308
BC4976 BC4976 hypothetical protein (NCBI ptt file) 241, 359
BC5391 BC5391 hypothetical protein (NCBI ptt file) 241, 351
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 BC4374
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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