Organism : Clostridium acetobutylicum | Module List :
CAC3095 thiK

Hydroxyethylthiazole kinase ThiM/ThiK (FS!) (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase cog/ cog
hydroxymethylpyrimidine kinase activity go/ molecular_function
phosphomethylpyrimidine kinase activity go/ molecular_function
thiamine biosynthetic process go/ biological_process
HMP-P_kinase tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC3095
(Mouseover regulator name to see its description)

CAC3095 is regulated by 22 influences and regulates 0 modules.
Regulators for CAC3095 thiK (22)
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
CAC0078 360 tf
CAC0571 360 tf
CAC0766 360 tf
CAC1320 360 tf
CAC1451 360 tf
CAC1799 360 tf
CAC2052 360 tf
CAC2113 360 tf
CAC3199 360 tf

Warning: CAC3095 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
7358 1.40e+01 TTGaAggGaaG
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7359 1.80e+02 gAGaAacGGC
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7370 8.90e-09 GGAGGtA
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7371 6.30e+03 GGCacGTG
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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 CAC3095

CAC3095 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase cog/ cog
hydroxymethylpyrimidine kinase activity go/ molecular_function
phosphomethylpyrimidine kinase activity go/ molecular_function
thiamine biosynthetic process go/ biological_process
HMP-P_kinase tigr/ tigrfam
Module neighborhood information for CAC3095

CAC3095 has total of 44 gene neighbors in modules 353, 360
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
CAC0306 CAC0306 SAM-dependent methyltransferase (NCBI ptt file) 217, 353
CAC0423 CAC0423 Fusion: PTS system, beta-glucosides specific IIABC component (NCBI ptt file) 284, 360
CAC0425 sacA Sucrase-6-phosphate hydrolase (gene sacA) (NCBI ptt file) 92, 360
CAC0436 CAC0436 Predicted xylanase/chitin deacetilase, similar to yxkH B.subtilis (NCBI ptt file) 320, 353
CAC0530 CAC0530 Hypothetical protein (NCBI ptt file) 102, 353
CAC0570 CAC0570 PTS enzyme II, ABC component (NCBI ptt file) 237, 360
CAC0571 CAC0571 Predicted transcriptional regulator (NCBI ptt file) 191, 353
CAC0572 CAC0572 Predicted membrane protein (NCBI ptt file) 191, 353
CAC0644 gerKA Spore germination protein gerKA (NCBI ptt file) 324, 360
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
CAC0766 CAC0766 Predicted transcriptional regulator (MerR family) (NCBI ptt file) 116, 360
CAC0802 CAC0802 Hypothetical protein (NCBI ptt file) 212, 353
CAC1396 purD Phosphoribosylamine-glycine ligase (NCBI ptt file) 249, 360
CAC1595 CAC1595 Integrase/recombinase, XerC/XerD family (NCBI ptt file) 249, 360
CAC1630 CAC1630 Zn-dependent peptidase from MPP family (NCBI ptt file) 22, 360
CAC1761 CAC1761 Predicted GTPase, YLQF B.subtilis ortholog (NCBI ptt file) 116, 360
CAC1789 smbA/pyrH Uridylate kinase (NCBI ptt file) 310, 360
CAC2358 CAC2358 RRNA methylase, YSGA B.subtilis ortholog (NCBI ptt file) 84, 353
CAC2617 CAC2617 Membrane associated methyl-chemotaxis protein, HAMP domain containing (NCBI ptt file) 66, 360
CAC2626 fabG Possible 3-ketoacyl-acyl carrier protein reductase (NCBI ptt file) 310, 360
CAC2627 CAC2627 Predicted S-adenosylmethionine-dependent methyltransferase, YtmQ B.subtilis ortholog (NCBI ptt file) 310, 360
CAC2628 CAC2628 Predicted metal-dependent peptidase (NCBI ptt file) 310, 360
CAC2650 pyrD Dihydroorotate dehydrogenase (NCBI ptt file) 116, 360
CAC2652 pyrF Orotidine-5'-phosphate decarboxylase (NCBI ptt file) 116, 360
CAC2653 pyrI Aspartate carbamoyltransferase regulatory subunit (NCBI ptt file) 116, 360
CAC2654 CAC2654 Aspartate carbamoyltransferase catalytic subunit (NCBI ptt file) 116, 360
CAC2697 CAC2697 Hypothetical protein (NCBI ptt file) 306, 353
CAC2918 pmi Mannose-6 phospate isomelase (NCBI ptt file) 270, 360
CAC2936 CAC2936 Alpha/beta superfamily hydrolase (NCBI ptt file) 236, 360
CAC3095 thiK Hydroxyethylthiazole kinase ThiM/ThiK (FS!) (NCBI ptt file) 353, 360
CAC3331 CAC3331 Alanine racemase (NCBI ptt file) 24, 353
CAC3332 CAC3332 Predicted amidohydrolase (dihydroorothase family) (NCBI ptt file) 150, 360
CAC3356 CAC3356 Lactoylglutathione lyase (LGUL) family protein, diverged (NCBI ptt file) 236, 360
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
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 CAC3095
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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