Organism : Clostridium acetobutylicum | Module List :
CAC3466

Transcriptional regulator, LysR family (NCBI ptt file)

CircVis
Functional Annotations (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC3466
(Mouseover regulator name to see its description)

CAC3466 is regulated by 22 influences and regulates 20 modules.
Regulators for CAC3466 (22)
Regulator Module Operator
CAC0201 283 tf
CAC0627 283 tf
CAC0768 283 tf
CAC0951 283 tf
CAC1915 283 tf
CAC2084 283 tf
CAC2486 283 tf
CAC2962 283 tf
CAC3216 283 tf
CAC3466 283 tf
CAC3673 283 tf
CAC0461 115 tf
CAC1070 115 tf
CAC2054 115 tf
CAC2055 115 tf
CAC2307 115 tf
CAC3283 115 tf
CAC3349 115 tf
CAC3466 115 tf
CAC3494 115 tf
CAC3646 115 tf
CAC3649 115 tf

Warning: CAC3466 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
6882 1.70e-02 cTTcCCCTcttTaTAaatata
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6883 2.30e+00 TTATaaAgcaggtTTTtgTat
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7218 2.50e+01 AAgtGGGgaaGaAgg
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7219 4.10e+01 aggaAttAtacgagG.gcGAT
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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 CAC3466

CAC3466 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for CAC3466

CAC3466 has total of 54 gene neighbors in modules 115, 283
Gene neighbors (54)
Gene Common Name Description Module membership
CAC0002 dnaN DNA polymerase III beta subunit (NCBI ptt file) 3, 283
CAC0010 CAC0010 Uncharacterized conserved protein, possible metal-binding (NCBI ptt file) 283, 312
CAC0174 CAC0174 Response regulator, CheY-like receiver domain and HTH DNA-binding domain (NCBI ptt file) 140, 283
CAC0185 CAC0185 Uncharacterized membrane protein, YBBC B.subtilis ortholog (NCBI ptt file) 115, 314
CAC0204 srta Sortase (surface protein transpeptidase), YHCS B.subtilis ortholog (NCBI ptt file) 115, 207
CAC0282 CAC0282 Cytosine/guanine deaminase related protein (NCBI ptt file) 283, 366
CAC0352 CAC0352 Uncharacterized conserved membrane protein, SANA family (NCBI ptt file) 115, 345
CAC0458 CAC0458 Permease (NCBI ptt file) 283, 286
CAC0576 CAC0576 Hypothetical protein (NCBI ptt file) 115, 183
CAC0597 gerKB Spore germination protein, gerKB (NCBI ptt file) 115, 185
CAC0627 CAC0627 Transcriptional regulator, MarR/EmrR family (NCBI ptt file) 278, 283
CAC0728 CAC0728 SAM-dependent methyltransferase (NCBI ptt file) 72, 283
CAC0830 CAC0830 Response regulator (NCBI ptt file) 67, 115
CAC0833 CAC0833 ABC-type multidrug transport system (daunorubicin resistance), ATPase component (NCBI ptt file) 115, 207
CAC0834 CAC0834 Predicted integral membrane protein (NCBI ptt file) 75, 115
CAC0835 CAC0835 Predicted integral membrane protein (NCBI ptt file) 115, 207
CAC0852 CAC0852 Amino acid permease (NCBI ptt file) 115, 317
CAC1292 CAC1292 Membrane protein containing HD superfamily hydrolase domain, YQFF ortholog (NCBI ptt file) 51, 283
CAC1419 CAC1419 Uncharacterized proteins, homologs of microcin C7 resistance protein MccF (NCBI ptt file) 283, 346
CAC1439 CAC1439 Uncharacterized conserved protein (NCBI ptt file) 115, 158
CAC1440 CAC1440 Hypothetical protein (NCBI ptt file) 115, 158
CAC1542 CAC1542 Predicted membrane protein (NCBI ptt file) 278, 283
CAC1591 CAC1591 Uncharacterized membrane protein, YCGQ B. subtilis homolog (NCBI ptt file) 113, 115
CAC1643 CAC1643 Hypothetical protein, CF-38 family (NCBI ptt file) 115, 140
CAC1651 CAC1651 Predicted GTPase with uncharacterized domain, ortholog of T.maritima (4980952) (NCBI ptt file) 109, 283
CAC1749 CAC1749 BioB/LipA-like protein (NCBI ptt file) 5, 283
CAC2116 CAC2116 General stress protein, DnaK suppressor DskA, YTEA B.subtilis ortholog (NCBI ptt file) 239, 283
CAC2129 murE UDP-N-acetylmuramyl tripeptide synthase, MurE (NCBI ptt file) 2, 283
CAC2169 CAC2169 UDP-galactopyranose mutase (NCBI ptt file) 283, 286
CAC2170 CAC2170 Predicted membrane protein (NCBI ptt file) 282, 283
CAC2231 murG Undecaprenyl-PP-MurNAc-pentapeptide-UDPGlcNAc GlcNAc transferase, MurG (NCBI ptt file) 283, 286
CAC2403 CAC2403 Predicted membrane protein (NCBI ptt file) 68, 115
CAC2410 recX Uncharacterized protein recX (NCBI ptt file) 282, 283
CAC2413 CAC2413 Predicted membrane protein (NCBI ptt file) 105, 283
CAC2414 CAC2414 Uncharacterized conserved protein, related to alpha-amylase/alpha-mannosidase (NCBI ptt file) 283, 345
CAC2662 CAC2662 Hypothetical protein (NCBI ptt file) 60, 115
CAC2812 CAC2812 Hypothetical protein (NCBI ptt file) 24, 115
CAC3011 CAC3011 Predicted membrane protein (NCBI ptt file) 65, 115
CAC3089 CAC3089 Hypothetical protein (NCBI ptt file) 3, 283
CAC3185 CAC3185 Membrane-associated protein containing a homolog of PilT-like ATPase N-terminal domain, YACL B.subtilis ortholog (NCBI ptt file) 283, 295
CAC3203 hprT Hypoxanthine-guanine phosphoribosyltransferase (NCBI ptt file) 58, 283
CAC3207 CAC3207 Hypothetical protein (NCBI ptt file) 25, 283
CAC3216 mfd Transcription-repair coupling factor, MFD (superfamily II helicase ) (NCBI ptt file) 58, 283
CAC3351 CAC3351 Uncharacterized membrane protein, YCBP B.subtilis ortholog (NCBI ptt file) 1, 115
CAC3400 CAC3400 Predicted dehydrogenase (NCBI ptt file) 72, 283
CAC3465 CAC3465 Amidase from nicotinamidase family (NCBI ptt file) 115, 283
CAC3466 CAC3466 Transcriptional regulator, LysR family (NCBI ptt file) 115, 283
CAC3467 CAC3467 Uncharacterized conserved protein, phnB family (NCBI ptt file) 115, 283
CAC3613 CAC3613 Hypothetical protein (NCBI ptt file) 115, 293
CAC3614 CAC3614 Uncharacterized conserved membrane protein, possible permease (NCBI ptt file) 115, 158
CAC3615 CAC3615 Uncharacterized conserved membrane protein, possible permease (NCBI ptt file) 115, 158
CAC3616 CAC3616 ABC transport system, ATPase component (NCBI ptt file) 115, 158
CAC3657 CAC3657 NADP-dependent glyceraldehyde-3-phosphate dehydrogenase (NCBI ptt file) 239, 283
CAC3673 xylR XylR transcriptional regulator (NCBI ptt file) 72, 283
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 CAC3466
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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