Organism : Synechococcus elongatus PCC 7942 | Module List :
Synpcc7942_2119

"RNA methyltransferase TrmH, group 3 (EC:2.1.1.-)"

CircVis
Functional Annotations (6)
Function System
rRNA methylases cog/ cog
RNA binding go/ molecular_function
RNA processing go/ biological_process
RNA methyltransferase activity go/ molecular_function
RNA modification go/ biological_process
rRNA_methyl_3 tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Synpcc7942_2119
(Mouseover regulator name to see its description)

Warning: No Regulators were found for Synpcc7942_2119!

Warning: Synpcc7942_2119 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 6 motifs predicted.

Motif Table (6)
Motif Id e-value Consensus Motif Logo
1997 5.70e-01 AATcctcgacttTGcTgaTgg
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1998 1.20e+00 AAactgCcAATaatggtcAGa
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1999 1.70e+03 CAGGaCtCAcC
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2141 6.70e+02 aGaAaaCAcccTGa
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2142 9.00e+03 aTTttAGAtcC
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2143 4.20e+04 tGtCT.AA
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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 Synpcc7942_2119

Synpcc7942_2119 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
rRNA methylases cog/ cog
RNA binding go/ molecular_function
RNA processing go/ biological_process
RNA methyltransferase activity go/ molecular_function
RNA modification go/ biological_process
rRNA_methyl_3 tigr/ tigrfam
Module neighborhood information for Synpcc7942_2119

Synpcc7942_2119 has total of 39 gene neighbors in modules 160, 208
Gene neighbors (39)
Gene Common Name Description Module membership
Synpcc7942_0075 aminopeptidase P (EC:3.4.11.9). Metallo peptidase. MEROPS family M24B (IMGterm) 160, 163
Synpcc7942_0158 Rhodanese-like 160, 194
Synpcc7942_0270 TPR repeat 160, 165
Synpcc7942_0631 rplL LSU ribosomal protein L12P (IMGterm) 195, 208
Synpcc7942_0632 rplJ LSU ribosomal protein L10P (IMGterm) 195, 208
Synpcc7942_0697 photosystem II core light harvesting protein 145, 208
Synpcc7942_1122 rpmG LSU ribosomal protein L33P (IMGterm) 42, 208
Synpcc7942_1123 rpsR SSU ribosomal protein S18P (IMGterm) 42, 208
Synpcc7942_1267 hypothetical protein 118, 160
Synpcc7942_1277 rplT LSU ribosomal protein L20P (IMGterm) 195, 208
Synpcc7942_1310 ndhF3 operon transcriptional regulator 72, 160
Synpcc7942_1443 fructose-bisphosphate aldolase (EC 4.1.2.13) (IMGterm) 5, 160
Synpcc7942_1485 hypothetical protein 80, 160
Synpcc7942_1486 Protein of unknown function DUF37 132, 160
Synpcc7942_1617 inner membrane protein-like 48, 160
Synpcc7942_1862 hypothetical protein 73, 160
Synpcc7942_1888 hypothetical protein 44, 160
Synpcc7942_1892 Rhodanese-like 118, 160
Synpcc7942_1900 dcd Deoxycytidine triphosphate deaminase (EC:3.5.4.13) 118, 160
Synpcc7942_1908 hypothetical protein 160, 163
Synpcc7942_1943 cell division protein Ftn2-like 160, 165
Synpcc7942_1965 exopolyphosphatase (EC:3.6.1.11) 160, 165
Synpcc7942_2119 "RNA methyltransferase TrmH, group 3 (EC:2.1.1.-)" 160, 208
Synpcc7942_2120 Ribonuclease III 160, 208
Synpcc7942_2204 rpmE LSU ribosomal protein L31P (IMGterm) 195, 208
Synpcc7942_2205 rpsI SSU ribosomal protein S9P (IMGterm) 195, 208
Synpcc7942_2206 rplM LSU ribosomal protein L13P (IMGterm) 195, 208
Synpcc7942_2207 truA tRNA pseudouridine synthase A (EC:5.4.99.12) 195, 208
Synpcc7942_2208 rplQ LSU ribosomal protein L17P (IMGterm) 195, 208
Synpcc7942_2209 DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) (IMGterm) 195, 208
Synpcc7942_2210 SSU ribosomal protein S11P (IMGterm) 195, 208
Synpcc7942_2211 rpsM SSU ribosomal protein S13P (IMGterm) 195, 208
Synpcc7942_2216 rpsE SSU ribosomal protein S5P (IMGterm) 195, 208
Synpcc7942_2259 rimM 16S rRNA processing protein RimM (IMGterm) 41, 160
Synpcc7942_2262 hypothetical protein 72, 160
Synpcc7942_2320 hypothetical protein 122, 160
Synpcc7942_2469 hypothetical protein 160, 161
Synpcc7942_2588 3-octaprenyl-4hydroxybenzoate decarboxylase (EC 4.1.1.-) (IMGterm) 72, 160
Synpcc7942_2589 2-phosphosulfolactate phosphatase (EC 3.1.3.71) (IMGterm) 160, 186
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 Synpcc7942_2119
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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