Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_2425

putative CarD-like transcriptional regulator (NCBI)

CircVis
Functional Annotations (3)
Function System
Transcriptional regulators, similar to M. xanthus CarD 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 RSP_2425
(Mouseover regulator name to see its description)

RSP_2425 is regulated by 23 influences and regulates 24 modules.
Regulators for RSP_2425 (23)
Regulator Module Operator
RSP_0386 112 tf
RSP_0958 112 tf
RSP_1040 112 tf
RSP_1220 112 tf
RSP_1231 112 tf
RSP_1518 112 tf
RSP_1577 112 tf
RSP_1915 112 tf
RSP_2410 112 tf
RSP_2425 112 tf
RSP_2780 112 tf
RSP_2853 112 tf
RSP_3094 112 tf
RSP_3684 112 tf
RSP_0386 43 tf
RSP_1231 43 tf
RSP_1577 43 tf
RSP_1739 43 tf
RSP_2425 43 tf
RSP_2889 43 tf
RSP_3055 43 tf
RSP_3238 43 tf
RSP_3700 43 tf

Warning: RSP_2425 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
7806 2.90e-05 tgtccAaagGataaagatTct
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7807 1.00e-01 AtATcCGgC.c.tcctcaTTTtC
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7944 7.20e-10 AtTtTc
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7945 9.30e-03 CcTCaTgcGaAActTAT.cCA
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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 RSP_2425

RSP_2425 is enriched for 3 functions in 3 categories.
Module neighborhood information for RSP_2425

RSP_2425 has total of 47 gene neighbors in modules 43, 112
Gene neighbors (47)
Gene Common Name Description Module membership
RSP_0149 RSP_0149 CheY-like receiver protein (NCBI) 107, 112
RSP_0189 RSP_0189 NADPH-dependent glutamate synthase beta chain and related oxidoreductase (NCBI) 43, 208
RSP_0190 accB Biotin carboxyl carrier protein, AccB (NCBI) 43, 208
RSP_0191 accC Biotin carboxylase (NCBI) 43, 208
RSP_0192 aat possible leucyl/phenylalanyl-tRNA--protein transferase (NCBI) 43, 208
RSP_0352 RSP_0352 probable ferredoxin (NCBI) 108, 112
RSP_0381 RSP_0381 hypothetical protein (NCBI) 14, 43
RSP_0444 RSP_0444 hypothetical protein (NCBI) 43, 360
RSP_0842 RSP_0842 putative porin (NCBI) 43, 310
RSP_0887 MrcB Glycosyl transferase, family 51 (NCBI) 43, 112
RSP_0971 RSP_0971 Putative membrane protein (NCBI) 43, 118
RSP_0972 RSP_0972 hypothetical protein (NCBI) 43, 118
RSP_1039 atpI FoF1 ATP synthase, subunit I (NCBI) 43, 369
RSP_1064 RSP_1064 Putative preprotein translocase, YidC (NCBI) 43, 369
RSP_1109 cysK Cysteine synthase (NCBI) 112, 200
RSP_1140 ilvE Branched chain acid aminotransferase (NCBI) 64, 112
RSP_1157 PSrp1 Ribosomal subunit interface protein Y (NCBI) 43, 310
RSP_1169 secA preprotein translocase, SecA subunit, ATPase (NCBI) 43, 277
RSP_1201 RSP_1201 hypothetical protein (NCBI) 43, 327
RSP_1231 rho Transcription termination factor rho (NCBI) 43, 182
RSP_1377 RSP_1377 Carbonic anhydrase (NCBI) 112, 175
RSP_1519 prrC PrrC (NCBI) 43, 360
RSP_1577 putR Proline dehydrogenase transcriptional activator (NCBI) 68, 112
RSP_1614 RSP_1614 TRAP-T family transporter with fused DctQ/DctM subunits (NCBI) 25, 112
RSP_1615 RSP_1615 hypothetical protein (NCBI) 25, 112
RSP_1667 RSP_1667 hypothetical protein (NCBI) 43, 112
RSP_1668 FolK 2-amino-4-hydroxy-6- hydroxymethyldihydropteridine pyrophosphokinase (NCBI) 43, 112
RSP_1768 RSP_1768 Aminotransferase class IV , putative D-alanine aminotransferase (NCBI) 112, 171
RSP_1769 RSP_1769 Mandelate racemase / muconate lactonizing enzyme (NCBI) 112, 171
RSP_1770 RSP_1770 hypothetical protein (NCBI) 112, 171
RSP_1771 RSP_1771 beta subunit of citrate lyase (NCBI) 20, 112
RSP_1860 RSP_1860 hypothetical protein (NCBI) 43, 377
RSP_1889 RSP_1889 conserved hypothetical membrane protein (NCBI) 112, 366
RSP_2258 purC SAICAR synthetase (NCBI) 43, 109
RSP_2350 RSP_2350 hypothetical protein (NCBI) 112, 293
RSP_2425 RSP_2425 putative CarD-like transcriptional regulator (NCBI) 43, 112
RSP_2536 rhlE ATP-dependent helicase, DEAD-box (NCBI) 43, 195
RSP_2630 gyrA DNA gyrase/topoisomerase IV, subunit A (NCBI) 43, 182
RSP_2711 RSP_2711 putative outer membrane protein (NCBI) 43, 360
RSP_2764 RSP_2764 hypothetical protein (NCBI) 48, 112
RSP_2974 RSP_2974 Putative metalopeptidase (NCBI) 43, 118
RSP_3218 RSP_3218 Putative oxidoreductase NAD protein (NCBI) 112, 285
RSP_3313 RSP_3313 possible phage integrase family protein (NCBI) 67, 112
RSP_3454 RSP_3454 hypothetical protein (NCBI) 61, 112
RSP_3595 metK S-adenosylmethionine synthetase (NCBI) 43, 85
RSP_3810 RSP_3810 hypothetical protein (NCBI) 35, 112
RSP_4294 RSP_4294 16S ribosomal RNA (NCBI) 14, 43
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 RSP_2425
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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