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 6008 to 6057 of 7460 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
2502 presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7] Subtracted 4751.74 4900.37 148.63
2503 succinyl-coa ligase [gdp-forming] alpha-chain, mitochondrial precursor (ec 6.2.1.4) (succinyl-coa synthetase, alpha chain) (scs-alpha). [swissprot;acc:p53597] Divided 5996.06 6155.81 1.02664
suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169] Subtracted 3690.79 3543.33 147.46
2504 succinyl-coa ligase [adp-forming] beta-chain, mitochondrial precursor (ec 6.2.1.5) (succinyl-coa synthetase, betaa chain) (scs-betaa) (atp- specific succinyl-coa synthetase beta subunit). [swissprot;acc:q9p2r7] Divided 5996.06 6155.81 1.02664
trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606] Subtracted 3650.02 3502.81 147.21
2505 adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819] 3716.43 3569.68 146.75
succinate dehydrogenase [ubiquinone] iron-sulfur protein, mitochondrial precursor (ec 1.3.5.1) (ip) (iron-sulfur subunit of complex ii). [swissprot;acc:p21912] Divided 6237.83 6400.74 1.02612
2506 2-oxoglutarate dehydrogenase e1 component, mitochondrial precursor (ec 1.2.4.2) (alpha-ketoglutarate dehydrogenase). [swissprot;acc:q02218] 6200.39 6362.25 1.0261
dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602] Subtracted 3667.94 3521.41 146.53
2507 60s ribosomal protein l30. [swissprot;acc:p04645] 3674.02 3529.35 144.67
mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426] Divided 4243.44 4352.56 1.02571
2508 lipoic acid synthetase, mitochondrial (lip-syn) (lipoate synthase) (hussy-01) (fragment). [swissprot;acc:o43766] 6469.44 6634.31 1.02548
sorting nexin 1. [swissprot;acc:q13596] Subtracted 5932.05 6071.35 139.3
2509 peroxiredoxin 5, mitochondrial precursor (prx-v) (peroxisomal antioxidant enzyme) (plp) (thioredoxin peroxidase pmp20) (antioxidant enzyme b166) (aoeb166) (tpx type vi) (liver tissue 2d-page spot 71b) (alu co-repressor 1) (sbbi10). [swissprot;acc:p30044] 6239.69 6378.35 138.66
reticulon protein 3 (neuroendocrine-specific protein-like 2) (nsp-like protein ii) (nsplii). [swissprot;acc:o95197] Divided 6202.78 6360.79 1.02547
2510 kruppel-related zinc finger protein hckrox. [refseq;acc:nm_015872] Subtracted 7056.13 7194.65 138.52
succinate dehydrogenase cytochrome b560 subunit, mitochondrial precursor (integral membrane protein cii-3) (qps1) (qps-1) (succinate dehydrogenase complex subunit c) (succinate-ubiquinone oxidoreductase cytochrome b large subunit) (cybl). [swissprot;acc:q99643] Divided 6256.49 6415.21 1.02537
2511 integral membrane protein cii-3b. [sptrembl;acc:o75609] 6256.42 6415.04 1.02535
zinc finger protein 288 (dendritic-derived btb/poz zinc finger protein). [swissprot;acc:q9hc78] Subtracted 7056.42 7194.87 138.45
2512 peroxisomal targeting signal 2 receptor (pts2 receptor) (peroxin-7). [swissprot;acc:o00628] 7056.58 7194.99 138.41
reticulon protein 2 (neuroendocrine-specific protein-like 1) (nsp-like protein 1) (nspli). [swissprot;acc:o75298] Divided 6203.05 6360.18 1.02533
2513 dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [swissprot;acc:o15514] Subtracted 4031.94 4166.99 135.05
reticulon 1 (neuroendocrine-specific protein). [swissprot;acc:q16799] Divided 6204.25 6360.69 1.02521
2514 eh-domain containing protein 1 (testilin) (hpast1). [swissprot;acc:q9h4m9] 6203.92 6360.25 1.0252
ubiquitin-conjugating enzyme e2-17 kda 2 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 2). [swissprot;acc:p51669] Subtracted 8104.84 7970.2 134.64
2515 60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7] 3598.55 3467.65 130.9
eh-domain containing protein 3. [swissprot;acc:q9nzn3] Divided 6203.94 6360.25 1.0252
2516 chromobox protein homolog 5 (heterochromatin protein 1 homolog alpha) (hp1 alpha) (antigen p25). [swissprot;acc:p45973] Subtracted 7551.88 7422.68 129.2
eh-domain containing protein 4 (eh domain-containing protein fksg7) (hepatocellular carcinoma-associated protein 10/11). [swissprot;acc:q9h223] Divided 6203.95 6360.24 1.02519
2517 activator of camp-responsive element modulator (crem) in testis; lim protein act. [refseq;acc:nm_020482] Subtracted 3669.33 3797.78 128.45
eh-domain containing protein 2. [swissprot;acc:q9nzn4] Divided 6203.96 6360.24 1.02519
2518 chromobox protein homolog 3 (heterochromatin protein 1 homolog gamma) (hp1 gamma) (modifier 2 protein) (hech). [swissprot;acc:q13185] Subtracted 7550.12 7422.01 128.11
sin3 associated polypeptide p18 (2hor0202). [swissprot;acc:o00422] Divided 6204.15 6360.27 1.02516
2519 adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741] 5964.17 6113.96 1.02511
putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] Subtracted 3754.39 3629.51 124.88
2520 40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] 3708.67 3584.47 124.2
estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [swissprot;acc:p14061] Divided 5964.17 6113.96 1.02511
2521 17 beta-hydroxysteroid dehydrogenase. [sptrembl;acc:q13034]
40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232] Subtracted 3708.67 3584.47 124.2
2522 apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] 7181.3 7057.99 123.31
retinol dehydrogenase 8 (all-trans); photoreceptor outer segment all-trans retinol dehydrogenase. [refseq;acc:nm_015725] Divided 5964.17 6113.96 1.02511
2523 dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160] 3803.04 3710.01 1.02508
skeletal muscle lim-protein 2 (slim 2) (four and a half lim domains protein 3) (fhl-3). [swissprot;acc:q13643] Subtracted 3634.59 3756.67 122.08
2524 myo-inositol 1-phosphate synthase a1. [refseq;acc:nm_016368] Divided 8695.15 8912.98 1.02505
skeletal muscle lim-protein 3 (slim 3) (lim-domain protein dral) (four and a half lim domains protein 2) (fhl-2). [swissprot;acc:q14192] Subtracted 3633.14 3754.96 121.82
2525 arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [swissprot;acc:o43681] Divided 8695.15 8912.98 1.02505
translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [swissprot;acc:p13693] Subtracted 7169.01 7047.98 121.03
2526 chromobox protein homolog 1 (heterochromatin protein 1 homolog beta) (hp1 beta) (modifier 1 protein) (m31) (heterochromatin protein p25). [swissprot;acc:p23197] 7538.48 7417.58 120.9
ubiquitin-like protein gdx (ubiquitin-like protein 4). [swissprot;acc:p11441] Divided 8695.15 8912.98 1.02505
2527 60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] Subtracted 3730.53 3611.05 119.48

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/