Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Gene Rank Value Type description Filtered Interaction Map Network Comparison Type green red network_comparison
Results: HTML CSV LaTeX Showing element 3180 to 3229 of 33156 in total
Filtered  : 1
Network Comparison Type  : Divided
Rank
Value Type
description
Interaction Map
green
red
network_comparison
398 Ranked yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263] Low confidence 213.496 205.997 1.0364
Squared imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] High confidence 23222.8 18929.1 1.22683
serine/threonine protein phosphatase 6 (ec 3.1.3.16) (pp6). [swissprot;acc:o00743] Low confidence 47246.5 50510.9 1.06909
Rooted likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033] 75.7648 72.2945 1.048
serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537] High confidence 106.044 116.707 1.10055
399 Measured dimethylaniline monooxygenase [n-oxide forming] 4 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 4) (fmo 4) (dimethylaniline oxidase 4). [swissprot;acc:p31512] Low confidence 8085.57 7680.62 1.05272
neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] High confidence 4479.76 5201.41 1.16109
Ranked clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] 226.226 207.889 1.08821
transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664] Low confidence 186.506 193.291 1.03638
Squared atp synthase lipid-binding protein, mitochondrial precursor (ec 3.6.3.14) (atp synthase proteolipid p2) (atpase protein 9) (atpase subunit c). [swissprot;acc:q06055] 48907.2 52285.1 1.06907
microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] High confidence 23222.8 18929.1 1.22683
Rooted 3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [swissprot;acc:p46952] Low confidence 88.7007 84.6421 1.04795
cyclin g2. [swissprot;acc:q16589] High confidence 106.044 116.707 1.10055
400 Measured adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] 4479.76 5201.41 1.16109
mad protein (max dimerizer). [swissprot;acc:q05195] Low confidence 7337.73 6970.25 1.05272
Ranked phosducin-like protein (phlp). [swissprot;acc:q13371] High confidence 226.218 207.908 1.08807
solute carrier family 35, member e1. [refseq;acc:nm_024881] Low confidence 211.03 203.661 1.03618
Squared daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] 42750.3 45694.9 1.06888
glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] High confidence 48419 39478.8 1.22646
Rooted cyclin g1 (cyclin g). [swissprot;acc:p51959] 106.044 116.707 1.10055
tumor protein p73-like; tumor protein 63 kda with strong homology to p53; tumor protein p63. [refseq;acc:nm_003722] Low confidence 79.3726 75.7411 1.04795
401 Measured adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] High confidence 4479.76 5201.41 1.16109
gdp-mannose pyrophosphorylase a; mannose-1-phosphate guanylyltransferase (gdp). [refseq;acc:nm_013335] Low confidence 10260 10800.7 1.0527
Ranked replication protein a 70 kda dna-binding subunit (rp-a) (rf-a) (replication factor-a protein 1) (single-stranded dna-binding protein). [swissprot;acc:p27694] High confidence 226.218 207.908 1.08807
sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538] Low confidence 197.863 205.017 1.03616
Squared axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] High confidence 40524.8 33044.3 1.22638
prominin-like protein 1 precursor (antigen ac133) (cd133 antigen). [swissprot;acc:o43490] Low confidence 42750.3 45694.9 1.06888
Rooted serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172] High confidence 106.044 116.707 1.10055
tumor protein p73 (p53-like transcription factor) (p53-related protein). [swissprot;acc:o15350] Low confidence 79.3703 75.7395 1.04794
402 Measured leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] High confidence 4479.76 5201.41 1.16109
squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] Low confidence 8352.26 7934.21 1.05269
Ranked replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927] High confidence 226.218 207.908 1.08807
x-linked protein sts1769. [swissprot;acc:q99871] Low confidence 203.883 211.253 1.03615
Squared ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376] 45485.7 48608.6 1.06866
endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] High confidence 48393.1 39472 1.22601
Rooted cellular tumor antigen p53 (tumor suppressor p53) (phosphoprotein p53) (antigen ny-co-13). [swissprot;acc:p04637] Low confidence 79.3677 75.7377 1.04793
eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] High confidence 55.2294 50.1918 1.10037
403 Measured fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] 4479.76 5201.41 1.16109
seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [swissprot;acc:q9np81] Low confidence 9319.56 8853.13 1.05269
Ranked phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] High confidence 226.218 207.908 1.08807
three prime repair exonuclease 1 isoform c; deoxyribonuclease iii, dnaq/mutd (e. coli)-like; 3' repair exonuclease 1; atr interacting protein. [refseq;acc:nm_032166] Low confidence 203.883 211.253 1.03615
Squared glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] High confidence 48362.1 39463.9 1.22548
prolyl endopeptidase (ec 3.4.21.26) (post-proline cleaving enzyme) (pe). [swissprot;acc:p48147] Low confidence 45485.7 48608.6 1.06866
Rooted elongation factor 1-beta (ef-1-beta). [swissprot;acc:p24534] 73.6827 70.3162 1.04788
nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] High confidence 65.6741 59.6834 1.10037
404 Measured kinesin-like protein kif23 (mitotic kinesin-like protein-1) (kinesin- like protein 5). [swissprot;acc:q02241] Low confidence 9508.16 10008.8 1.05265
leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] High confidence 4479.76 5201.41 1.16109
Ranked dna repair protein rad52 homolog. [swissprot;acc:p43351] 226.218 207.908 1.08807
metabotropic glutamate receptor 2 precursor (mglur2). [swissprot;acc:q14416] Low confidence 196 203.081 1.03613
Squared adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520] High confidence 32855.4 26819.1 1.22507

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.
- http://analysis.yellowcouch.org/