Organism : Clostridium acetobutylicum | Module List :
CAC1965 greA

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 CAC1965
(Mouseover regulator name to see its description)

CAC1965 is regulated by 20 influences and regulates 5 modules.
Regulators for CAC1965 greA (20)
Regulator Module Operator
CAC0023 63 tf
CAC0299 63 tf
CAC0445 63 tf
CAC0474 63 tf
CAC0865 63 tf
CAC1430 63 tf
CAC1469 63 tf
CAC1843 63 tf
CAC3603 63 tf
CAC3606 63 tf
CAC0113 109 tf
CAC0254 109 tf
CAC1696 109 tf
CAC1928 109 tf
CAC2060 109 tf
CAC2297 109 tf
CAC3152 109 tf
CAC3166 109 tf
CAC3247 109 tf
CAC3418 109 tf

Warning: CAC1965 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
6780 8.90e+02 AAgGgGGATga
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6781 1.40e+04 AaGaAAgtgGc
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6870 8.10e-02 CaCCTct
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6871 2.50e+03 GGaGTG
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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 CAC1965

CAC1965 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 CAC1965

CAC1965 has total of 46 gene neighbors in modules 63, 109
Gene neighbors (46)
Gene Common Name Description Module membership
CAC0034 CAC0034 Hypothetical protein (NCBI ptt file) 63, 298
CAC0089 serA D-3 phosphoglycerate dehydrogenase (NCBI ptt file) 109, 343
CAC0090 CAC0090 Xylanase/chitin deacetylase, NodB family (NCBI ptt file) 109, 312
CAC0115 CAC0115 Uncharacterized protein, Yje/RRF2 family (NCBI ptt file) 63, 232
CAC0207 CAC0207 Hypothetical protein, CF-6 family (NCBI ptt file) 63, 273
CAC0225 CAC0225 Sensory transduction histidine kinase (NCBI ptt file) 57, 109
CAC0277 CAC0277 HD-GYP hydrolase domain containing protein (NCBI ptt file) 109, 298
CAC0452 CAC0452 Permease (NCBI ptt file) 99, 109
CAC0641 CAC0641 Uncharacterized conserved protein (NCBI ptt file) 109, 348
CAC0910 CAC0910 Probably cellulosomal scaffolding protein precursor, secreted; cellulose-binding and cohesin domain (NCBI ptt file) 53, 63
CAC0945 ssb Single-stranded DNA-binding protein (NCBI ptt file) 63, 99
CAC1098 polA DNA polymerase I, polA (NCBI ptt file) 99, 109
CAC1297 CAC1297 N-terminal fragment of elongation factor Ts (NCBI ptt file) 49, 109
CAC1312 CAC1312 Hypothetical protein (NCBI ptt file) 109, 176
CAC1313 CAC1313 Hypothetical protein (NCBI ptt file) 63, 295
CAC1404 CAC1404 Transcriptional regulator of sugar metabolism (deoR family) (NCBI ptt file) 64, 109
CAC1488 CAC1488 Glycosyltransferase involved in cell wall biogenesis (NCBI ptt file) 63, 273
CAC1539 CAC1539 Gamma-glutamylcysteine synthetase (NCBI ptt file) 109, 222
CAC1559 CAC1559 Predicted transcriptional regulator (NCBI ptt file) 109, 151
CAC1635 CAC1635 Predicted nucleic acid binding protein, containing 2 S1 domains, YITL B.subtilis ortholog (NCBI ptt file) 109, 312
CAC1651 CAC1651 Predicted GTPase with uncharacterized domain, ortholog of T.maritima (4980952) (NCBI ptt file) 109, 283
CAC1652 aspA Aspartate ammonia-lyase (NCBI ptt file) 109, 329
CAC1661 CAC1661 Predicted secreted nucleic acid binding protein (NCBI ptt file) 25, 109
CAC1855 CAC1855 Hypothetical protein (NCBI ptt file) 63, 210
CAC1955 CAC1955 Hypothetical protein (NCBI ptt file) 57, 109
CAC1965 greA Transcription elongation factor GreA (NCBI ptt file) 63, 109
CAC2037 CAC2037 Hypothetical protein, CF-39 family (NCBI ptt file) 109, 312
CAC2072 CAC2072 Stage IV sporulation protein B, SpoIVB (NCBI ptt file) 63, 273
CAC2229 CAC2229 Pyruvate:ferredoxin oxidoreductase (NCBI ptt file) 59, 63
CAC2230 CAC2230 Uncharacterized protein of PR1 family, YkwD B.subtilis ortholog (NCBI ptt file) 63, 273
CAC2321 CAC2321 Predicted glycosyltransferase (NCBI ptt file) 63, 278
CAC2386 CAC2386 Predicted protein of beta-propeller fold (NCBI ptt file) 63, 321
CAC2437 CAC2437 Uncharacterized conserved protein (NCBI ptt file) 100, 109
CAC2787 CAC2787 Serine/threonine protein phosphatase (NCBI ptt file) 109, 128
CAC2858 mreV Shape-determining protein envB (HSP70 family charepones) (NCBI ptt file) 36, 63
CAC2873 CAC2873 Acetyl-CoA acetyltransferase (NCBI ptt file) 10, 109
CAC2893 CAC2893 Hypothetical protein (NCBI ptt file) 63, 137
CAC2942 CAC2942 Uncharacterized conserved protein fron YGAG family, predicted metal-dependent enzyme (NCBI ptt file) 47, 63
CAC3152 CAC3152 DNA-dependent RNA polymerase sigma subunit (NCBI ptt file) 5, 109
CAC3155 CAC3155 Uncharacterized conserved protein, THY1 family (NCBI ptt file) 19, 109
CAC3217 spoVC Stage V sporulation protein C, peptidyl-tRNA hydrolase (NCBI ptt file) 63, 105
CAC3219 CAC3219 Membrane associated histidine kinase with HAMP domain (NCBI ptt file) 19, 63
CAC3221 prs Phosphoribosylpyrophosphate synthetase (NCBI ptt file) 109, 251
CAC3251 CAC3251 Sensory transduction protein containing HD_GYP domain (NCBI ptt file) 63, 225
CAC3307 CAC3307 TPR-repeats containing protein (NCBI ptt file) 109, 190
CAC3602 CAC3602 HD superfamily hydrolase (NCBI ptt file) 86, 109
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 CAC1965
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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