Organism : Clostridium acetobutylicum | Module List :
CAC3216 mfd

Transcription-repair coupling factor, MFD (superfamily II helicase ) (NCBI ptt file)

CircVis
Functional Annotations (8)
Function System
Transcription-repair coupling factor (superfamily II helicase) cog/ cog
damaged DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
ATP binding go/ molecular_function
DNA repair go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
ATP-dependent helicase activity go/ molecular_function
mfd tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC3216
(Mouseover regulator name to see its description)

CAC3216 is regulated by 26 influences and regulates 12 modules.
Regulators for CAC3216 mfd (26)
Regulator Module Operator
CAC0155 58 tf
CAC0569 58 tf
CAC0768 58 tf
CAC0849 58 tf
CAC0977 58 tf
CAC1463 58 tf
CAC1941 58 tf
CAC2084 58 tf
CAC2546 58 tf
CAC2690 58 tf
CAC3037 58 tf
CAC3063 58 tf
CAC3216 58 tf
CAC3236 58 tf
CAC3731 58 tf
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

Warning: CAC3216 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
6770 5.30e-02 AgGaGGtatT
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6771 2.00e+03 GcGGAGC
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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 CAC3216

CAC3216 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Transcription-repair coupling factor (superfamily II helicase) cog/ cog
damaged DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
ATP binding go/ molecular_function
DNA repair go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
ATP-dependent helicase activity go/ molecular_function
mfd tigr/ tigrfam
Module neighborhood information for CAC3216

CAC3216 has total of 49 gene neighbors in modules 58, 283
Gene neighbors (49)
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
CAC0282 CAC0282 Cytosine/guanine deaminase related protein (NCBI ptt file) 283, 366
CAC0458 CAC0458 Permease (NCBI ptt file) 283, 286
CAC0483 CAC0483 Conserved membrane protein, possible homolog of CAAX-like membrane endopeptidase (NCBI ptt file) 58, 306
CAC0504 CAC0504 FHA-domain containing secreted protein (NCBI ptt file) 58, 268
CAC0505 CAC0505 Cell division membrane protein (NCBI ptt file) 52, 58
CAC0617 CAC0617 Hypothetical protein, CF-25 family (NCBI ptt file) 58, 296
CAC0627 CAC0627 Transcriptional regulator, MarR/EmrR family (NCBI ptt file) 278, 283
CAC0679 CAC0679 Unsharacterized protein, BmrU family (NCBI ptt file) 25, 58
CAC0688 CAC0688 1-acyl-sn-glycerol-3-phosphate acyltransferase (NCBI ptt file) 58, 286
CAC0689 ntH Predicted endonuclease, gene nth (NCBI ptt file) 58, 201
CAC0701 CAC0701 Uncharacterised protein, DegV family (NCBI ptt file) 20, 58
CAC0702 CAC0702 Predicted lipoprotein, Med/BMP family (NCBI ptt file) 58, 278
CAC0728 CAC0728 SAM-dependent methyltransferase (NCBI ptt file) 72, 283
CAC0768 CAC0768 Transcriptional regulator, LysR family (NCBI ptt file) 58, 296
CAC0963 bacA Bacitracin resistance protein (NCBI ptt file) 58, 260
CAC0965 CAC0965 1-acyl-sn-glycerol-3-phosphate acyltransferase (NCBI ptt file) 58, 281
CAC1235 thrB Homoserine kinase (thrB) (NCBI ptt file) 58, 296
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
CAC1542 CAC1542 Predicted membrane protein (NCBI ptt file) 278, 283
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
CAC1833 CAC1833 Cystathionine beta-lyase family protein, YNBB B.subtilis ortholog (NCBI ptt file) 58, 277
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
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
CAC2566 CAC2566 Possible rRNA methylase (SAM-dependent methyltransferase superfamily), YTQB B.subtilis (NCBI ptt file) 58, 351
CAC2633 CAC2633 Uncharaterized conserved protein, YOME B.subtilis ortholog (NCBI ptt file) 20, 58
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
CAC3209 CAC3209 Uncharacterized protein, YABP B.subtilis (NCBI ptt file) 58, 211
CAC3216 mfd Transcription-repair coupling factor, MFD (superfamily II helicase ) (NCBI ptt file) 58, 283
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
CAC3541 CAC3541 2'-5' RNA ligase family protein, diverged (NCBI ptt file) 58, 87
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 CAC3216
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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