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 2927 to 2976 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1464 mbd2 (methyl-cpg-binding protein)-interacting zinc finger protein. [refseq;acc:nm_015517] Subtracted 4757.46 5198.91 441.45
zasp protein (fragment). [sptrembl;acc:q9y4z3] Divided 5671.93 6103.49 1.07609
1465 glycerol-3-phosphate dehydrogenase [nad+], cytoplasmic (ec 1.1.1.8) (gpd-c) (gpdh-c). [swissprot;acc:p21695] 5686.74 6119.36 1.07608
skeletal muscle tropomodulin (sk-tmod) (tropomodulin 4). [swissprot;acc:q9nzq9] Subtracted 4757.46 5198.91 441.45
1466 proteasome subunit beta type 5 precursor (ec 3.4.25.1) (proteasome epsilon chain) (macropain epsilon chain) (multicatalytic endopeptidase complex epsilon chain) (proteasome subunit x) (proteasome chain 6) (proteasome subunit mb1). [swissprot;acc:p28074] Divided 6523.17 7019.44 1.07608
ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9] Subtracted 4757.46 5198.91 441.45
1467 p47 protein isoform a. [refseq;acc:nm_016143] Divided 6444.4 6932.39 1.07572
tropomodulin 1 (erythrocyte tropomodulin) (e-tmod). [swissprot;acc:p28289] Subtracted 4757.46 5198.91 441.45
1468 sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1]
sphingosine-1-phosphate lyase 1; sphingosine-1-phosphate lyase. [refseq;acc:nm_003901] Divided 5473.09 5887.45 1.07571
1469 4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404]
neuronal tropomodulin (n-tmod) (tropomodulin 2). [swissprot;acc:q9nzr1] Subtracted 4757.46 5198.91 441.45
1470 homeobox protein dlx-2. [swissprot;acc:q07687]
ornithine aminotransferase, mitochondrial precursor (ec 2.6.1.13) (ornithine--oxo-acid aminotransferase). [swissprot;acc:p04181] Divided 5473.09 5887.45 1.07571
1471 40s ribosomal protein s8. [swissprot;acc:p09058] 5659.45 6087.55 1.07564
homeobox protein dlx-5. [swissprot;acc:p56178] Subtracted 4757.46 5198.91 441.45
1472 26s proteasome non-atpase regulatory subunit 6 (26s proteasome regulatory subunit s10) (p42a) (proteasome regulatory particle subunit p44s10). [swissprot;acc:q15008] Divided 5984.47 6435.42 1.07535
fetal brain protein 239 (239fb). [swissprot;acc:q15777] Subtracted 4757.46 5198.91 441.45
1473 calmegin precursor. [swissprot;acc:o14967] Divided 5910.06 6355.08 1.0753
homeobox protein dlx-3. [swissprot;acc:o60479] Subtracted 4757.46 5198.91 441.45
1474 activated p21cdc42hs kinase. [refseq;acc:nm_005781]
calnexin precursor (major histocompatibility complex class i antigen-binding protein p88) (p90) (ip90). [swissprot;acc:p27824] Divided 5910.06 6355.08 1.0753
1475 mitogen-activated protein kinase kinase kinase 7 interacting protein 2 isoform 1; tak1-binding protein 2. [refseq;acc:nm_015093] Subtracted 4757.46 5198.91 441.45
soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825] Divided 5910.06 6355.08 1.0753
1476 rna (guanine-7-) methyltransferase. [refseq;acc:nm_003799]
vacuolar protein sorting 16 (hvps16). [swissprot;acc:q9h269] Subtracted 6078.43 6519.6 441.17
1477 malonyl-coa decarboxylase, mitochondrial precursor (ec 4.1.1.9) (mcd). [swissprot;acc:o95822] 6176.82 6617.91 441.09
palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] Divided 3687.37 3429.37 1.07523
1478 cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [swissprot;acc:p17544] 5659.22 6084.68 1.07518
itchy homolog e3 ubiquitin protein ligase; atrophin-1 interacting protein 4; itchy (mouse homolog) e3 ubiquitin protein ligase; nfe2-associated polypeptide 1; ubiquitin protein ligase itch. [refseq;acc:nm_031483] Subtracted 6176.82 6617.91 441.09
1479 hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [swissprot;acc:p55317] Divided 5787.03 6221.72 1.07511
parafibromin. [refseq;acc:nm_024529] Subtracted 4331.17 4771.22 440.05
1480 cyclic-amp-dependent transcription factor atf-2 (activating transcription factor 2) (camp response element binding protein cre- bp1) (hb16). [swissprot;acc:p15336] Divided 5660.17 6085.22 1.07509
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] Subtracted 5770.74 6210.65 439.91
1481 dna topoisomerase iii alpha (ec 5.99.1.2). [swissprot;acc:q13472] 5692.34 6131.71 439.37
egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] Divided 3688.8 3431.33 1.07504
1482 leng5 protein. [refseq;acc:nm_024075] 5372.25 5775.21 1.07501
ubiquitin. [swissprot;acc:p02248] Subtracted 6158.22 6597.55 439.33
1483 tryptophanyl-trna synthetase (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) (ifp53) (hwrs). [swissprot;acc:p23381] Divided 5372.25 5775.21 1.07501
vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267] Subtracted 6048.57 6487.65 439.08
1484 ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916] Divided 5372.25 5775.21 1.07501
vacuolar protein sorting 11 (hvps11) (pp3476). [swissprot;acc:q9h270] Subtracted 6048.57 6487.65 439.08
1485 tryptophanyl-trna synthetase, mitochondrial precursor (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) ((mt)trprs). [swissprot;acc:q9ugm6] Divided 5372.25 5775.21 1.07501
vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1] Subtracted 6048.57 6487.65 439.08
1486 p300/cbp-associated factor (ec 2.3.1.-) (p/caf) (histone acetylase pcaf). [swissprot;acc:q92831] 7210.87 7649.23 438.36
thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445] Divided 5372.25 5775.21 1.07501
1487 glucose-6-phosphate 1-dehydrogenase (ec 1.1.1.49) (g6pd). [swissprot;acc:p11413] Subtracted 6025.86 6464.16 438.3
nicotinamide nucleotide adenylyltransferase 3; pyridine nucleotide adenylyltransferase 3. [refseq;acc:nm_178177] Divided 5573.64 5991.58 1.07499
1488 delta 1-pyrroline-5-carboxylate synthetase (p5cs) [includes: glutamate 5-kinase (ec 2.7.2.11) (gamma-glutamyl kinase) (gk); gamma-glutamyl phosphate reductase (gpr) (ec 1.2.1.41) (glutamate-5-semialdehyde dehydrogenase) (glutamyl-gamma-semialdehyde dehydrogenase)]. [swissprot;acc:p54886]
dna-repair protein xrcc3 (x-ray repair cross-complementing protein 3). [swissprot;acc:o43542] Subtracted 6025.86 6464.16 438.3

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/