Organism : Clostridium acetobutylicum | Module List :
CAC3198 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 CAC3198
(Mouseover regulator name to see its description)

CAC3198 is regulated by 11 influences and regulates 7 modules.
Regulators for CAC3198 greA (11)
Regulator Module Operator
CAC0197 224 tf
CAC0265 224 tf
CAC0461 224 tf
CAC0723 224 tf
CAC0763 224 tf
CAC1333 224 tf
CAC1850 224 tf
CAC2859 224 tf
CAC3487 224 tf
CAC3553 224 tf
CAC3729 224 tf

Warning: CAC3198 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
6984 4.50e+02 GAGGgg.G
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6985 2.60e+03 GGGGaaTCG
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7100 1.00e-06 GgaGG.aa.aa
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7101 2.60e+03 GGGGGAAtTcG
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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 CAC3198

CAC3198 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 CAC3198

CAC3198 has total of 36 gene neighbors in modules 166, 224
Gene neighbors (36)
Gene Common Name Description Module membership
CAC0051 CAC0051 Hypothetical protein, CF-3 family (NCBI ptt file) 224, 246
CAC0052 CAC0052 Hypothetical protein, CF-18 family (NCBI ptt file) 224, 252
CAC0212 CAC0212 Biotin-(acetyl-CoA carboxylase) ligase (NCBI ptt file) 132, 224
CAC0329 spoVD Sporulation specific penicillin-binding protein (NCBI ptt file) 34, 224
CAC0372 CAC0372 Sensory transduction histidine kinase (HisKA and HATPase damains) (NCBI ptt file) 216, 224
CAC0461 CAC0461 Mercuric resistance operon regulatory protein, MerR family (NCBI ptt file) 79, 224
CAC0462 CAC0462 Protein of short-chain alcohol dehydrogenase family (NCBI ptt file) 48, 224
CAC0510 murB UDP-N-acetylenolpyruvoylglucosamine reductase (murB) (NCBI ptt file) 215, 224
CAC0772 CAC0772 Cobalt permease (NCBI ptt file) 132, 224
CAC0890 CAC0890 Uncharacterized conserved membrane protein (NCBI ptt file) 224, 252
CAC1022 CAC1022 Thioesterase II of alpha/beta hydrolase superfamily (NCBI ptt file) 166, 322
CAC1057 CAC1057 Uncharcterized protein, shares conserved domain among different RHS family proteins and WAPA of B.subtilis (NCBI ptt file) 224, 240
CAC1464 CAC1464 UVRA-like protein, probably involved in MDR transport (NCBI ptt file) 4, 166
CAC1763 CAC1763 Predicted endonuclease (NCBI ptt file) 166, 270
CAC1990 CAC1990 ABC-type iron (III) transport system, permease component (NCBI ptt file) 166, 294
CAC1992 moaC Molybdenum cofactor biosynthesis enzyme, MoaC (NCBI ptt file) 68, 166
CAC1995 CAC1995 Hypothetical protein (NCBI ptt file) 69, 166
CAC2001 iorA Indolepyruvate ferredoxin oxidoreductase, subunit alpha (NCBI ptt file) 97, 166
CAC2003 CAC2003 Predicted permease (NCBI ptt file) 97, 166
CAC2005 CAC2005 Siderophore/Surfactin synthetase related protein (NCBI ptt file) 97, 166
CAC2009 mmgB 3-Hydroxyacyl-CoA dehydrogenase (NCBI ptt file) 97, 166
CAC2010 CAC2010 Predicted Fe-S oxidoreductase (NCBI ptt file) 97, 166
CAC2014 CAC2014 Predicted esterase (NCBI ptt file) 97, 166
CAC2019 CAC2019 Malonyl CoA-acyl carrier protein transacylase (NCBI ptt file) 166, 238
CAC2288 CAC2288 Acyl-protein synthetase, luxE (NCBI ptt file) 166, 314
CAC2374 oppC Oligopeptide ABC-type transporter, permease component OPPC (NCBI ptt file) 224, 297
CAC2375 oppB Oligopeptide ABC-type transporter, permease (NCBI ptt file) 224, 297
CAC2439 CAC2439 Predicted membrane protein (NCBI ptt file) 224, 306
CAC3197 lysS Lysyl-tRNA synthetase (NCBI ptt file) 224, 306
CAC3198 greA Transcription elongation factor, greA (NCBI ptt file) 166, 224
CAC3262 CAC3262 ATPase with chaperone activity, ATP-binding domain, diverged (NCBI ptt file) 224, 297
CAC3445 CAC3445 Predicted acetyltransferase (NCBI ptt file) 9, 224
CAC3448 CAC3448 Probable tesA-like protease (NCBI ptt file) 132, 224
CAC3449 CAC3449 TPR-repeat-containing protein (NCBI ptt file) 34, 224
CAC3553 CAC3553 Transcriptional regulator (LacI family) (NCBI ptt file) 224, 322
CAC3729 spoOJ Stage 0 sporulation J, ParB family of DNA-binding proteins (NCBI ptt file) 49, 224
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 CAC3198
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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