Organism : Methanococcus maripaludis S2 | Module List :
RNA_7 tRNA-Lys2

Lys tRNA

CircVis
Functional Annotations (1)
Function System
Aminoacyl-tRNA biosynthesis kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RNA_7
(Mouseover regulator name to see its description)

Warning: No Regulators were found for RNA_7!

Warning: RNA_7 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 8 motifs predicted.

Motif Table (8)
Motif Id e-value Consensus Motif Logo
835 0.00e+00 gcagaGgtaGct.AGcCTG
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836 5.80e-05 Cgg.Gtcc.A.T.C.tgcCcgc.C
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857 0.00e+00 CaGgCTa..CtACctc
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858 1.00e-06 caGGGTTCaaAtCCC.gagaccgc
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859 0.00e+00 CaGgCTggaC.Acc
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860 1.30e+02 aaCacttTTcaAAGGcc.ac
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977 0.00e+00 gGgT.Gtc.AGcCTG
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978 1.60e-03 ccccCtatgCtaCC
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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 RNA_7

RNA_7 is enriched for 1 functions in 4 categories.
Enrichment Table (1)
Function System
Aminoacyl-tRNA biosynthesis kegg/ kegg pathway
Module neighborhood information for RNA_7

RNA_7 has total of 55 gene neighbors in modules 88, 100, 101, 165
Gene neighbors (55)
Gene Common Name Description Module membership
MMP0139 fdhB formate dehydrogenase subunit beta 9, 101
MMP0254 carbohydrate kinase 65, 101
MMP0459 hypothetical protein MMP0459 85, 101
MMP0509 fmdA formylmethanofuran dehydrogenase subunit A 100, 101
MMP0512 fmdB molybdenum containing formylmethanofuran dehydrogenase subunit B 85, 101
MMP1330 hydrogenase assembly chaperone hypC/hupF 100, 117
MMP1525 modulator of DNA gyrase 100, 151
MMP1586 hypothetical protein MMP1586 19, 100
MMP1684 metallophosphoesterase 65, 101
Mma-sR04 None 100, 146
RNA_1 tRNA-Gln1 Gln tRNA 93, 101, 165
RNA_11 tRNA-Glu1 Glu tRNA 34, 93, 100
RNA_13 tRNA-Ser1 Ser tRNA 88, 100, 101, 165
RNA_14 tRNA-Arg2 Arg tRNA 100, 101
RNA_16 tRNA-Ser2 Ser tRNA 88, 100, 101, 165
RNA_17 tRNA-Pro2 Pro tRNA 4, 100
RNA_18 tRNA-Ile1 Ile tRNA 34, 93, 100
RNA_19 tRNA-Met1 Met tRNA 101, 165
RNA_2 tRNA-Thr1 Thr tRNA 88, 100, 101, 165
RNA_20 tRNA-Phe1 Phe tRNA 88, 100, 101, 165
RNA_21 tRNA-Asn1 Asn tRNA 88, 93
RNA_22 tRNA-Met2 Met tRNA 88, 100, 101, 165
RNA_23 tRNA-Glu2 Glu tRNA 88, 100, 101, 151, 165
RNA_24 tRNA-Leu2 Leu tRNA 88, 100, 101, 165
RNA_26 tRNA-Leu3 Leu tRNA 88, 100, 101, 165
RNA_27 tRNA-Val2 Val tRNA 88, 101, 165
RNA_28 tRNA-Cys1 Cys tRNA 93, 100
RNA_3 tRNA-Pro1 Pro tRNA 88, 100, 101, 165
RNA_30 tRNA-Gly2 Gly tRNA 34, 93, 100
RNA_31 tRNA-Ala1 Ala tRNA 101, 165
RNA_33 tRNA-Met3 Met tRNA 45, 100
RNA_34 tRNA-Met4 Met tRNA 42, 100
RNA_37 rrnD5S 5S ribosomal RNA 100, 132
RNA_43 tRNA-Trp Trp tRNA 101, 165
RNA_45 RNaseP None 100, 101
RNA_46 rrnA5S 5S ribosomal RNA 100, 101
RNA_47 rrnB5S 5S ribosomal RNA 100, 101, 151
RNA_48 rnnC5S 5S ribosomal RNA 100, 101
RNA_49 srp None 100, 101
RNA_5 tRNA-Lys1 Lys tRNA 88, 100, 101, 165
RNA_50 tRNA-SeC1 Sec tRNA 88, 165
RNA_6 tRNA-Asp1 Asp tRNA 100, 101, 165
RNA_7 tRNA-Lys2 Lys tRNA 88, 100, 101, 165
RNA_8 tRNA-Asp2 Asp tRNA 88, 100, 101, 165
RNA_9 tRNA-Leu1 Leu tRNA 88, 100, 165
Unanno_11 None 100, 101
Unanno_16 None 42, 100
Unanno_21 None 89, 100
Unanno_23 None 4, 101
Unanno_26 None 42, 100
Unanno_27 None 4, 101
Unanno_34 None 65, 101
Unanno_35 None 100, 101
Unanno_48 None 44, 101
Unanno_54 None 100, 101
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 RNA_7
Please add your comments for this gene by using the form below. Your comments will be publicly available.

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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