Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_4347

16S ribosomal RNA (NCBI)

CircVis
Functional Annotations (1)
Function System
Ribosome kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_4347
(Mouseover regulator name to see its description)

RSP_4347 is regulated by 28 influences and regulates 0 modules.
Regulators for RSP_4347 (28)
Regulator Module Operator
RSP_0018 131 tf
RSP_0443 131 tf
RSP_0611 131 tf
RSP_0698 131 tf
RSP_0755 131 tf
RSP_0958 131 tf
RSP_1032 131 tf
RSP_1606 131 tf
RSP_2346 131 tf
RSP_2591 131 tf
RSP_2888 131 tf
RSP_2889 131 tf
RSP_2950 131 tf
RSP_2963 131 tf
RSP_3341 131 tf
RSP_3514 131 tf
RSP_3684 131 tf
RSP_3731 131 tf
RSP_0386 257 tf
RSP_0443 257 tf
RSP_0601 257 tf
RSP_1032 257 tf
RSP_1055 257 tf
RSP_1191 257 tf
RSP_1220 257 tf
RSP_1518 257 tf
RSP_1660 257 tf
RSP_2888 257 tf

Warning: RSP_4347 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
7982 2.50e+01 gcCAtAAtgA
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7983 8.50e+02 AGgTccCGgagGaTT
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8232 6.90e+02 TTTgAt.ttT.cTGttaaC
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8233 8.70e+02 CGgCAttTTGaCGCa
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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_4347

RSP_4347 is enriched for 1 functions in 4 categories.
Enrichment Table (1)
Function System
Ribosome kegg/ kegg pathway
Module neighborhood information for RSP_4347

RSP_4347 has total of 25 gene neighbors in modules 131, 257
Gene neighbors (25)
Gene Common Name Description Module membership
RSP_0427 RSP_0427 hypothetical protein (NCBI) 250, 257
RSP_0682 hemF coproporphyrinogen III oxidase, aerobic (NCBI) 131, 274
RSP_0869 osp response regulator receive protein (NCBI) 257, 382
RSP_1418 RSP_1418 TRAP-T family transporter, large (12 TMs) inner membrane subunit (NCBI) 131, 228
RSP_1419 RSP_1419 TRAP-T family transporter, small (4 TMs) inner membrane subunit (NCBI) 131, 228
RSP_1420 RSP_1420 TRAP-T family transporter, periplasmic binding protein (NCBI) 131, 228
RSP_1826 coxII Cytochrome c oxidase polypeptide II precursor (Cytochrome AA3 subunit 2) (NCBI) 131, 186
RSP_1827 cox10 Heme O synthase (NCBI) 131, 186
RSP_1828 cox11 cytochrome C oxidase assembly protein (NCBI) 131, 186
RSP_1829 coxIII Cytochrome c oxidase, aa3-type, subunit III (NCBI) 131, 186
RSP_4293 RSP_4293 5S ribosomal RNA (NCBI) 165, 257
RSP_4326 RSP_4326 tRNA-Leu (NCBI) 34, 257
RSP_4344 RSP_4344 tRNA-Gly (NCBI) 50, 257
RSP_4347 RSP_4347 16S ribosomal RNA (NCBI) 131, 257
RSP_6014 RSP_6014 hypothetical protein (NCBI) 199, 257
RSP_6038 RSP_6038 methyltransferase MraW/YabC (NCBI) 50, 257
RSP_6075 RSP_6075 hypothetical protein (NCBI) 131, 295
RSP_6085 RSP_6085 hypothetical protein (NCBI) 50, 131
RSP_6088 RSP_6088 hypothetical protein (Sel1-like repeat) (NCBI) 50, 257
RSP_6127 RSP_6127 hypothetical protein (NCBI) 257, 276
RSP_6132 pqqA putative coenzyme PQQ synthesis protein A (NCBI) 50, 257
RSP_6151 RSP_6151 hypothetical protein (NCBI) 257, 275
RSP_6199 RSP_6199 hypothetical protein (NCBI) 205, 257
RSP_6232 RSP_6232 hypothetical protein (NCBI) 131, 295
RSP_6246 RSP_6246 bacteriophage head-tail adaptor (NCBI) 78, 131
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_4347
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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