Organism : Methanococcus maripaludis S2 | Module List :
MMP0108

ABC-type Iron(III)-binding periplasmic protein precursor

CircVis
Functional Annotations (4)
Function System
ABC-type Fe3+ transport system, periplasmic component cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
ABC transporters kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP0108
(Mouseover regulator name to see its description)

MMP0108 is regulated by 15 influences and regulates 0 modules.
Regulators for MMP0108 (15)
Regulator Module Operator
MMP0217
MMP1303
95 combiner
MMP1100
MMP1646
95 combiner
MMP1376
MMP1646
95 combiner
MMP0036
MMP0217
41 combiner
MMP0036
MMP1023
41 combiner
MMP0217
MMP1303
41 combiner
MMP0480 41 tf
MMP1100 41 tf
MMP1303
H2
41 combiner
MMP1376 41 tf
MMP0031
MMP0402
67 combiner
MMP0031
MMP1704
67 combiner
MMP0607
MMP1442
67 combiner
MMP1137 67 tf
MMP1210
MMP1704
67 combiner

Warning: MMP0108 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
743 1.60e+02 gctgCTGaAAc
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744 1.00e+02 TAttgtggA.aaaataGGG
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795 3.10e+03 GGGCGA
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796 1.70e+04 CTGcGGAG
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847 3.20e+01 GGCcaagGCc
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848 5.00e+01 CGaGGgAtaTg
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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 MMP0108

MMP0108 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
ABC-type Fe3+ transport system, periplasmic component cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
ABC transporters kegg/ kegg pathway
Module neighborhood information for MMP0108

MMP0108 has total of 78 gene neighbors in modules 41, 67, 95
Gene neighbors (78)
Gene Common Name Description Module membership
Antisense_6 None 52, 67
MMP0017 hypothetical protein MMP0017 67, 142
MMP0026 DP2 DNA polymerase II large subunit 25, 41, 92
MMP0035 hypothetical protein MMP0035 23, 67
MMP0104 polyferredoxin 95, 107
MMP0108 ABC-type Iron(III)-binding periplasmic protein precursor 41, 67, 95
MMP0124 membrane-bound metal-dependent hydrolase 14, 67
MMP0141 hypothetical protein MMP0141 41, 51
MMP0142 thiamine pyrophosphate dependent protein 17, 41, 51
MMP0144 hpcE 5-oxopent-3-ene-1,2,5-tricarboxylate decarboxylase 17, 41
MMP0146 hypothetical protein MMP0146 17, 41, 137
MMP0178 purQ phosphoribosylformylglycinamidine synthase I 95, 143
MMP0202 permease 52, 67
MMP0203 hypothetical protein MMP0203 52, 67
MMP0204 hypothetical protein MMP0204 67, 99
MMP0216 cation transport ATPase 4, 41, 95
MMP0227 nrdD anaerobic ribonucleoside-triphosphate reductase 15, 67
MMP0253 acd CoA-binding domain-containing protein 95, 124
MMP0262 hypothetical protein MMP0262 52, 67
MMP0271 putative ATP binding nickel incorporation protein 21, 95
MMP0274 hypE hydrogenase expression/formation protein HypE 67, 70
MMP0280 hisI phosphoribosyl-AMP cyclohydrolase 67, 90
MMP0322 rfcB replication factor C large subunit 23, 67
MMP0341 pycA pyruvate carboxylase subunit A 67, 86, 120
MMP0354 putative oligosaccharide transporter 80, 95
MMP0446 nitrogen fixation-like protein 52, 67
MMP0479 hypothetical protein MMP0479 4, 95
MMP0488 low molecular weight phosphotyrosine protein phosphatase 52, 67
MMP0489 hypothetical protein MMP0489 52, 67
MMP0493 cobN cobaltochelatase subunit CobN 41, 44
MMP0610 tgtA 7-cyano-7-deazaguanine tRNA-ribosyltransferase 25, 41
MMP0617 radB DNA repair and recombination protein RadB 52, 67
MMP0648 rtcA RNA 3'-terminal-phosphate cyclase 67, 146
MMP0670 hypothetical protein MMP0670 41, 51
MMP0682 hypothetical protein MMP0682 67, 92
MMP0760 hypothetical protein MMP0760 22, 67, 92
MMP0811 hypothetical protein MMP0811 52, 67
MMP0849 L-lysine/ homoserine-homoserine lactone exporter family protein 95, 117
MMP0861 kamA lysine 2,3-aminomutase 41, 95
MMP0862 yodP GCN5-like N-acetyltransferase 41, 95
MMP0866 proX glycine betaine ABC transporter substrate-binding protein 41, 89
MMP0867 binding-protein dependent transport system inner membrane protein 41, 89
MMP0868 proV ABC transporter ATPase 41, 66
MMP0873 hypothetical protein MMP0873 95, 107
MMP0993 XRE family transcriptional regulator 67, 144
MMP0994 hypothetical protein MMP0994 67, 144, 153
MMP0999 hypothetical protein MMP0999 95, 140
MMP1000 hypothetical protein MMP1000 4, 95
MMP1079 glycosyl transferase family protein 64, 67
MMP1099 phosphate transporter PhoU 66, 89, 95
MMP1120 ATPase-like ATP-binding protein 52, 67
MMP1123 radical SAM domain-containing protein 64, 67
MMP1150 mtaA uroporphyrinogen decarboxylase 4, 41, 95
MMP1199 phosphate transporter PhoU 95, 133
MMP1200 lysA diaminopimelate decarboxylase 21, 41
MMP1210 hypothetical protein MMP1210 89, 95
MMP1212 acetyl-CoA acetyltransferase 89, 95
MMP1219 putative dinG ATP-dependent helicase 95, 107
MMP1232 PP-loop domain-containing protein 95, 104
MMP1334 solute-binding protein/glutamate receptor 41, 129
MMP1337 hydrogenase maturation protease 95, 107
MMP1346 basic helix-loop-helix dimerization domain-containing protein 49, 67, 142
MMP1429 rpm DNA-directed RNA polymerase subunit M 95, 107
MMP1441 mobB putative molybdopterin-guanine dinucleotide biosynthesis protein MobB/FeS domain-containing protein 41, 89
MMP1466 ehaS putative CBS domain-containing signal transduction protein 95, 107, 133
MMP1585 arginase 41, 112
MMP1612 hypothetical protein MMP1612 41, 95
MMP1651 modA molybdenum ABC transporter periplasmic molybdate-binding protein 41, 95
MMP1652 molybdate ABC transporter periplasmic substrate-binding protein 89, 95
MMP1686 cbf5 H/ACA RNA-protein complex component Cbf5p 22, 67
MMP1700 SSS sodium solute transporter superfamily 39, 41
Unanno_12 None 89, 95
Unanno_14 None 52, 67
Unanno_24 None 95, 143
Unanno_28 None 41, 95
Unanno_49 None 95, 117
Unanno_5 None 95, 107
Unanno_60 None 95, 107
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 MMP0108
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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