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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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 6564 to 6613 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1641 proteasome subunit beta type 4 precursor (ec 3.4.25.1) (proteasome beta chain) (macropain beta chain) (multicatalytic endopeptidase complex beta chain) (proteasome chain 3) (hsn3) (hsbpros26). [swissprot;acc:p28070] Ranked 218.167 215.034 1.01457
1642 40s ribosomal protein s7 (s8). [swissprot;acc:p23821] Measured 5782.92 6186.39 1.06977
doublecortin (lissencephalin-x) (lis-x) (doublin). [swissprot;acc:o43602] Squared 31032.5 34359.4 1.10721
fatty acid-binding protein, heart (h-fabp) (muscle fatty acid-binding protein) (m-fabp) (mammary-derived growth inhibitor) (mdgi). [swissprot;acc:p05413] Rooted 61.2707 63.3571 1.03405
m-phase inducer phosphatase 2 (ec 3.1.3.48) (dual specificity phosphatase cdc25b). [swissprot;acc:p30305] Ranked 260.269 256.531 1.01457
1643 26s proteasome-associated pad1 homolog. [refseq;acc:nm_005805] Measured 5782.92 6186.39 1.06977
myofibrillogenesis regulator 1; trans-activated by hepatitis c virus core protein 2; likely ortholog of mouse brain protein 17. [refseq;acc:nm_022572] Ranked 194.476 197.305 1.01455
peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9] Squared 24729.7 27380.6 1.10719
retinal pigment epithelium-specific protein 65kda; retinal pigment epithelium-specific protein (65kd); retinitis pigmentosa 20 (autosomal recessive). [refseq;acc:nm_000329] Rooted 61.2707 63.3571 1.03405
1644 26s protease regulatory subunit 4 (p26s4). [swissprot;acc:q03527] Squared 27191.5 30104.4 1.10713
apolipoprotein b-100 precursor (apo b-100) [contains: apolipoprotein b-48 (apo b-48)]. [swissprot;acc:p04114] Measured 5782.92 6186.39 1.06977
indolethylamine n-methyltransferase (ec 2.1.1.49) (aromatic alkylamine n-methyltransferase) (indolamine n-methyltransferase) (arylamine n- methyltransferase) (amine n-methyltransferase). [swissprot;acc:o95050] Rooted 61.2707 63.3571 1.03405
secreted modular calcium-binding protein 1. [refseq;acc:nm_022137] Ranked 217.256 214.149 1.01451
1645 prefoldin subunit 1. [swissprot;acc:o60925]
proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [swissprot;acc:p07332] Measured 6079.19 6503.12 1.06973
rad17 homolog isoform 1; rad17-like protein; cell cycle checkpoint protein (rad17); rf-c activator 1 homolog. [refseq;acc:nm_002873] Squared 26883.9 29760.1 1.10699
s-adenosylmethionine synthetase alpha and beta forms (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-i/iii). [swissprot;acc:q00266] Rooted 64.5909 66.7876 1.03401
1646 atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [swissprot;acc:p12956] Squared 26883.9 29760.1 1.10699
molybdenum cofactor synthesis protein 2 large subunit (molybdopterin synthase large subunit) (mpt synthase large subunit) (mocs2b) (moco1- b). [swissprot;acc:o96007] Measured 6079.19 6503.12 1.06973
protein-tyrosine phosphatase, non-receptor type 2 (ec 3.1.3.48) (t- cell protein-tyrosine phosphatase) (tcptp). [swissprot;acc:p17706] Rooted 65.3639 67.5862 1.034
secreted modular calcium-binding protein 2; smooth muscle associated protein 2. [refseq;acc:nm_022138] Ranked 217.256 214.149 1.01451
1647 anaphase-promoting complex subunit 10; anaphase-promoting complex 10. [refseq;acc:nm_014885] Measured 6079.19 6503.12 1.06973
atp-dependent dna helicase ii, 80 kda subunit (lupus ku autoantigen protein p86) (ku86) (ku80) (86 kda subunit of ku antigen) (thyroid- lupus autoantigen) (tlaa) (ctc box binding factor 85 kda subunit) (ctcbf) (ctc85) (nuclear factor iv) (dna-repair protein xrcc5). [swissprot;acc:p13010] Squared 26883.9 29760.1 1.10699
choline dehydrogenase. [refseq;acc:nm_018397] Ranked 217.256 214.149 1.01451
vam6/vps39-like protein (hvam6p). [swissprot;acc:q96jc1] Rooted 64.6737 62.547 1.034
1648 60s ribosomal protein l29 (cell surface heparin binding protein hip). [swissprot;acc:p47914] Measured 6079.19 6503.12 1.06973
breast cancer type 1 susceptibility protein. [swissprot;acc:p38398] Squared 23093.1 25562.8 1.10695
hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597] Ranked 219.745 222.928 1.01448
microtubule-associated protein 4 (map 4). [swissprot;acc:p27816] Rooted 64.6737 62.547 1.034
1649 neurotrypsin precursor (ec 3.4.21.-) (motopsin) (leydin). [swissprot;acc:p56730] Ranked 219.062 215.942 1.01445
proto-oncogene tyrosine-protein kinase fer (ec 2.7.1.112) (p94-fer) (c-fer). [swissprot;acc:p16591] Measured 6079.19 6503.12 1.06973
ubiquitin. [swissprot;acc:p02248] Rooted 63.4301 65.5846 1.03397
upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] Squared 15603.4 17270.2 1.10682
1650 bile acid coenzyme a: amino acid n-acyltransferase; glycine n-choloyltransferase. [refseq;acc:nm_001701] Rooted 62.0351 64.1375 1.03389
molybdenum cofactor synthesis protein 3 (molybdopterin synthase sulfurylase) (mpt synthase sulfurylase). [swissprot;acc:o95396] Measured 6079.19 6503.12 1.06973
neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [refseq;acc:nm_005863] Squared 16089.8 17808 1.10679
ring finger protein 44. [refseq;acc:nm_014901] Ranked 219.062 215.942 1.01445
1651 cbf1 interacting corepressor. [refseq;acc:nm_004882] Measured 5944.24 6358.1 1.06962
phosphatidylinositol 3-kinase regulatory alpha subunit (pi3-kinase p85-alpha subunit) (ptdins-3-kinase p85-alpha) (pi3k). [swissprot;acc:p27986] Ranked 219.062 215.942 1.01445
rho guanine nucleotide exchange factor 3; rhogef protein; 59.8 kda protein; exchange factor found in platelets and leukemic and neuronal tissues, xpln. [refseq;acc:nm_019555] Squared 16089.8 17808 1.10679
ubiquitin-like protein sumo-1 conjugating enzyme (ec 6.3.2.19) (sumo- 1-protein ligase) (ubiquitin carrier protein) (ubiquitin-conjugating enzyme ubce2a) (p18). [swissprot;acc:p50550] Rooted 62.1186 64.2224 1.03387
1652 down-regulated in metastasis. [refseq;acc:nm_014503] Squared 16089.8 17808 1.10679
evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025] Measured 5944.24 6358.1 1.06962
peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753] Rooted 62.0332 64.1338 1.03386
ring finger protein 38. [refseq;acc:nm_022781] Ranked 219.062 215.942 1.01445
1653 muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] Squared 14728.9 16301.3 1.10676
peroxisomal acyl-coa thioesterase 2b; likely ortholog of mouse peroxisomal acyl-coa thioesterase 2b. [refseq;acc:nm_152331] Rooted 62.0318 64.1312 1.03384
phosphatidylinositol 3-kinase regulatory gamma subunit (pi3-kinase p85-gamma subunit) (ptdins-3-kinase p85-gamma) (p55pik). [swissprot;acc:q92569] Ranked 219.062 215.942 1.01445
transcription factor mafg (v-maf musculoaponeurotic fibrosarcoma oncogene homolog g) (hmaf). [swissprot;acc:o15525] Measured 7433.73 7950.61 1.06953
1654 dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159] Squared 14714.3 16284.1 1.10669

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/