Organism : Clostridium acetobutylicum | Module List :
CAC0949

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 CAC0949
(Mouseover regulator name to see its description)

CAC0949 is regulated by 24 influences and regulates 9 modules.
Regulators for CAC0949 (24)
Regulator Module Operator
CAC0289 29 tf
CAC0949 29 tf
CAC1264 29 tf
CAC1467 29 tf
CAC1670 29 tf
CAC1799 29 tf
CAC1945 29 tf
CAC2242 29 tf
CAC2306 29 tf
CAC2307 29 tf
CAC3507 29 tf
CAC3649 29 tf
CAC0081 352 tf
CAC0949 352 tf
CAC0977 352 tf
CAC1355 352 tf
CAC1670 352 tf
CAC1799 352 tf
CAC1900 352 tf
CAC2084 352 tf
CAC2236 352 tf
CAC2568 352 tf
CAC3200 352 tf
CAC3475 352 tf

Warning: CAC0949 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
6712 1.40e-12 AGggGgg
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6713 5.70e+03 GCGGGac
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7356 2.40e+04 GTGTGC
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7357 2.50e+02 CTGCcCA
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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 CAC0949

CAC0949 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Predicted transcriptional regulators cog/ cog
Module neighborhood information for CAC0949

CAC0949 has total of 41 gene neighbors in modules 29, 352
Gene neighbors (41)
Gene Common Name Description Module membership
CAC0007 gyrA DNA gyrase (topoisomerase II) A subunit (NCBI ptt file) 29, 278
CAC0302 CAC0302 Predicted metal-binding protein of ferredoxin fold (NCBI ptt file) 29, 47
CAC0437 CAC0437 Sensory transduction histidine kinase (NCBI ptt file) 53, 352
CAC0489 CAC0489 Holo-acyl-carrier protein synthase (NCBI ptt file) 29, 42
CAC0490 CAC0490 Predicted sugar kinase, N-terminal region - uncharacterized conserved protein (NCBI ptt file) 29, 56
CAC0651 CAC0651 Hypothetical protein (NCBI ptt file) 292, 352
CAC0882 CAC0882 Predicted membrane protein, hemolysin III homolog (NCBI ptt file) 29, 334
CAC0888 CAC0888 Phosphoglycerol transferase MdoB related protein, alkaline phosphatase superfamily (NCBI ptt file) 194, 352
CAC0949 CAC0949 Predicted transcriptional regulator (NCBI ptt file) 29, 352
CAC0993 dacF D-alanyl-D-alanine carboxypeptidase (penicilin binding protein) (NCBI ptt file) 201, 352
CAC1053 CAC1053 LPS glycosyltransferase (NCBI ptt file) 29, 317
CAC1285 CAC1285 Uncharacterized conserved protein, ortholog of YQEU B.subtilis (NCBI ptt file) 201, 352
CAC1286 CAC1286 Fe-S oxidoreductases (NCBI ptt file) 29, 352
CAC1489 CAC1489 Protein of phosphatidic acid phosphatase family, YNBD E.coli ortholog (NCBI ptt file) 286, 352
CAC1586 CAC1586 Integral membrane protein possibly involved in chromosome condensation (NCBI ptt file) 29, 99
CAC1625 CAC1625 Phosphoserine phosphatase family protein (NCBI ptt file) 29, 51
CAC1674 gltB Small subunit of NADPH-dependent glutamate synthase (NCBI ptt file) 29, 269
CAC1692 ftsA Cell division protein, ftsA (NCBI ptt file) 29, 201
CAC1710 CAC1710 Fe-S oxidoreductase, related to NifB/MoaA family with PDZ N-terminal domain (NCBI ptt file) 350, 352
CAC1750 CAC1750 SpoVS-related protein (NCBI ptt file) 29, 278
CAC1752 ftsY Signal recognition particle GTPase, FtsY (NCBI ptt file) 29, 269
CAC1792 cdsA CDP-diglyceride synthetase (NCBI ptt file) 282, 352
CAC1807 rpsO Ribosomal Protein S15 (NCBI ptt file) 201, 352
CAC1812 CAC1812 Sporulation protein SpoIIIE, DNA segregation ATPase (NCBI ptt file) 29, 269
CAC1831 CAC1831 Protein containing Zn-finger domain (NCBI ptt file) 29, 73
CAC2115 lspA Lipoprotein signal peptidase (NCBI ptt file) 51, 352
CAC2130 spoVD Stage V sporulation protein D, spoVD, FtsI/pbp family (NCBI ptt file) 11, 29
CAC2270 CAC2270 Hypothetical protein (NCBI ptt file) 38, 352
CAC2285 ruvA Holliday junction specific DNA helicase, subunit ruvA (NCBI ptt file) 25, 352
CAC2286 CAC2286 Uncharacterized protein, similar to protein from Clostridium histolyticum (GI:3892648) (NCBI ptt file) 292, 352
CAC2308 spoIIAA Anti-anti-sigma factor (antagonist of SpoIIAB) (NCBI ptt file) 29, 164
CAC2507 CAC2507 Predicted membrane protein (NCBI ptt file) 29, 269
CAC2508 CAC2508 Nitroreductase family protein (NCBI ptt file) 29, 267
CAC2584 CAC2584 Protein containing ChW-repeats (NCBI ptt file) 29, 142
CAC2642 CAC2642 Predicted endonuclease (NCBI ptt file) 159, 352
CAC2660 pykA Pyruvate carboxylase, PYKA (NCBI ptt file) 29, 345
CAC2672 CAC2672 Predicted membrane protein (NCBI ptt file) 5, 352
CAC3176 ilvN Acetolactate synthase, small subunit (NCBI ptt file) 29, 367
CAC3319 CAC3319 Signal transduction histidine kinase (NCBI ptt file) 29, 219
CAC3630 oppC Oligopeptide ABC transporter, permease component (NCBI ptt file) 29, 87
CAC3631 oppB Oligopeptide ABC transporter, permease component (NCBI ptt file) 29, 87
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 CAC0949
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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