Organism : Clostridium acetobutylicum | Module List :
CAC0571

Predicted transcriptional regulator (NCBI ptt file)

CircVis
Functional Annotations (1)
Function System
Predicted transcriptional regulators cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC0571
(Mouseover regulator name to see its description)

CAC0571 is regulated by 27 influences and regulates 12 modules.
Regulators for CAC0571 (27)
Regulator Module Operator
CAC0289 353 tf
CAC0571 353 tf
CAC0681 353 tf
CAC0723 353 tf
CAC0766 353 tf
CAC0841 353 tf
CAC1465 353 tf
CAC1467 353 tf
CAC2254 353 tf
CAC3199 353 tf
CAC3399 353 tf
CAC3438 353 tf
CAC3502 353 tf
CAC0032 191 tf
CAC0078 191 tf
CAC0093 191 tf
CAC0240 191 tf
CAC0289 191 tf
CAC0571 191 tf
CAC0860 191 tf
CAC1467 191 tf
CAC2242 191 tf
CAC3361 191 tf
CAC3409 191 tf
CAC3487 191 tf
CAC3518 191 tf
CAC3673 191 tf

Warning: CAC0571 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
7034 9.50e-03 G.ggggaGgcA
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7035 7.30e+03 CGccCT
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7358 1.40e+01 TTGaAggGaaG
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7359 1.80e+02 gAGaAacGGC
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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 CAC0571

CAC0571 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Predicted transcriptional regulators cog/ cog
Module neighborhood information for CAC0571

CAC0571 has total of 44 gene neighbors in modules 191, 353
Gene neighbors (44)
Gene Common Name Description Module membership
CAC0035 CAC0035 Serine/threonine phosphatase (inactivated protein) (NCBI ptt file) 236, 353
CAC0037 CAC0037 MinD family ATPase from ParA/SOJ subfamily (NCBI ptt file) 264, 353
CAC0066 CAC0066 ABC transporter, ATP-binding protein (NCBI ptt file) 28, 353
CAC0095 hemA Glutamil-tRNA reductase (NCBI ptt file) 92, 191
CAC0096 hemW Precorrin-2 dehydrogenase (NCBI ptt file) 92, 191
CAC0097 hemC Hydroxymrthylbilane syntase (porphobilinogen deaminase) (NCBI ptt file) 92, 191
CAC0098 hemD Uroporphyrinogen III syntase (NCBI ptt file) 92, 191
CAC0099 hemL Glutamate-1-semialdehyde aminotransferase (NCBI ptt file) 92, 191
CAC0100 hemB Delta-aminolevulinic acid dehydratase (porphobilinogen synthase) (NCBI ptt file) 92, 191
CAC0167 CAC0167 Possible sigma factor, diverged member of sigF/sigE/sigG family (NCBI ptt file) 191, 223
CAC0293 CAC0293 MccF-like protein (NCBI ptt file) 49, 191
CAC0306 CAC0306 SAM-dependent methyltransferase (NCBI ptt file) 217, 353
CAC0307 CAC0307 Predicted methyltransferase (NCBI ptt file) 191, 217
CAC0332 manB Beta-mannanase (NCBI ptt file) 191, 301
CAC0436 CAC0436 Predicted xylanase/chitin deacetilase, similar to yxkH B.subtilis (NCBI ptt file) 320, 353
CAC0517 pfk 6-phosphofructokinase (NCBI ptt file) 10, 191
CAC0518 pykA Pyruvate kinase (pykA) (NCBI ptt file) 191, 242
CAC0530 CAC0530 Hypothetical protein (NCBI ptt file) 102, 353
CAC0571 CAC0571 Predicted transcriptional regulator (NCBI ptt file) 191, 353
CAC0572 CAC0572 Predicted membrane protein (NCBI ptt file) 191, 353
CAC0628 CAC0628 Putative Mn transporter, NRAMR family (NCBI ptt file) 191, 207
CAC0652 CAC0652 Uncharacterized conserved membrane protein, similar to MDR (VANZ) ORF of Enterococcus (NCBI ptt file) 246, 353
CAC0752 CAC0752 Homolog of eukaryotic DNA ligase III (NCBI ptt file) 327, 353
CAC0753 CAC0753 PolyA polymerase related protein (HD hydrolase) and P-loop ATP-ase domain (NCBI ptt file) 137, 353
CAC0754 CAC0754 Hypothetical protein (NCBI ptt file) 165, 353
CAC0802 CAC0802 Hypothetical protein (NCBI ptt file) 212, 353
CAC1485 CAC1485 Glycosyltransferase, involved in cell wall biogenesis (NCBI ptt file) 191, 298
CAC1972 CAC1972 Predicted membrane protein (NCBI ptt file) 191, 351
CAC2358 CAC2358 RRNA methylase, YSGA B.subtilis ortholog (NCBI ptt file) 84, 353
CAC2523 CAC2523 Glycosyltransferase (NCBI ptt file) 191, 359
CAC2524 CAC2524 Uncharacterized conserved membrane protein (NCBI ptt file) 107, 191
CAC2526 CAC2526 6-pyruvoyl-tetrahydropterin synthase related protein (NCBI ptt file) 9, 191
CAC2697 CAC2697 Hypothetical protein (NCBI ptt file) 306, 353
CAC3095 thiK Hydroxyethylthiazole kinase ThiM/ThiK (FS!) (NCBI ptt file) 353, 360
CAC3177 cysS Cysteinyl-tRNA synthetase (NCBI ptt file) 191, 217
CAC3178 proS Prolyl-tRNA synthetase (NCBI ptt file) 191, 217
CAC3331 CAC3331 Alanine racemase (NCBI ptt file) 24, 353
CAC3430 CAC3430 Membrane associated, signal transduction histidine kinase-like ATPase (NCBI ptt file) 4, 353
CAC3440 CAC3440 Hypothetical protein (NCBI ptt file) 353, 360
CAC3441 CAC3441 DNA/RNA helicase, SNF2 (NCBI ptt file) 28, 353
CAC3442 polC DNA polymerase III (alpha subunit) (NCBI ptt file) 28, 353
CAC3476 CAC3476 Methyl-accepting chemotaxis protein (NCBI ptt file) 208, 353
CAC3544 CAC3544 Membrane associated GGDEF domain containing protein (NCBI ptt file) 191, 217
CAC3545 CAC3545 Methyl-accepting chemotaxis protein (NCBI ptt file) 191, 217
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 CAC0571
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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