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 Network Comparison Type Gene Value Type description Interaction Map green red Filtered network_comparison
Results: HTML CSV LaTeX Showing element 951 to 1000 of 16578 in total
Value Type  : Measured
Filtered  : 1
Rank
Network Comparison Type
description
Interaction Map
green
red
network_comparison
238 Subtracted hcdi protein. [refseq;acc:nm_020195] Low confidence 9590.3 9070.12 520.18
star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502] High confidence 11053.5 9649.61 1403.89
239 Divided carboxypeptidase b precursor. [refseq;acc:nm_020361] 6265.8 7711.38 1.23071
dna fragmentation factor 40 kda subunit (ec 3.-.-.-) (dff-40) (caspase-activated deoxyribonuclease) (caspase-activated dnase) (cad) (caspase-activated nuclease) (cpan). [swissprot;acc:o76075] Low confidence 6872.38 6456.05 1.06449
Subtracted neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822] High confidence 11053.5 9649.61 1403.89
oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] Low confidence 8153.06 7633.16 519.9
240 Divided mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] High confidence 6265.79 7711.36 1.23071
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Low confidence 8163.95 7671.08 1.06425
Subtracted mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] High confidence 11053.5 9649.61 1403.89
serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] Low confidence 9670.96 9152.21 518.75
241 Divided glucosamine-6-phosphate isomerase. [refseq;acc:nm_138335] 4311.52 4585.58 1.06356
plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] High confidence 6265.76 7711.31 1.23071
Subtracted mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [swissprot;acc:q16539] 11053.5 9649.61 1403.89
u1 small nuclear ribonucleoprotein a (u1 snrnp a protein). [swissprot;acc:p09012] Low confidence 8171.53 7653.44 518.09
242 Divided glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] 4311.52 4585.58 1.06356
max protein. [swissprot;acc:p25912] High confidence 5704.87 4640.26 1.22943
Subtracted natural resistance-associated macrophage protein 2 (nramp 2) (divalent metal transporter 1) (dmt1). [swissprot;acc:p49281] Low confidence 7503.62 6985.66 517.96
neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] High confidence 11053.5 9649.61 1403.89
243 Divided dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804] Low confidence 8133.69 7648.9 1.06338
homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] High confidence 5208.98 4246.95 1.22652
Subtracted mitochondrial gtp binding protein isoform v. [refseq;acc:nm_032620] Low confidence 9720.58 9204.48 516.1
neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] High confidence 11053.5 9649.61 1403.89
244 Divided protein phosphatase 1, regulatory (inhibitor) subunit 12b isoform a; myosin phosphatase regulatory subunit; myosin phosphatase, target subunit 2. [refseq;acc:nm_002481] Low confidence 9314.48 8759.92 1.06331
ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] High confidence 5211.25 4250.14 1.22614
Subtracted 60s ribosomal protein l37a. [swissprot;acc:p12751] Low confidence 6277.91 5762.4 515.51
sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0] High confidence 11053.5 9649.61 1403.89
245 Divided homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] 5212.33 4251.65 1.22595
tumor protein p73-like; tumor protein 63 kda with strong homology to p53; tumor protein p63. [refseq;acc:nm_003722] Low confidence 9047.26 8509.99 1.06313
Subtracted methyltransferase like 2. [refseq;acc:nm_018396] High confidence 11864 13241.4 1377.4
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] Low confidence 9745 9229.69 515.31
246 Divided homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] High confidence 5213.05 4252.66 1.22583
tumor protein p73 (p53-like transcription factor) (p53-related protein). [swissprot;acc:o15350] Low confidence 9046.87 8509.76 1.06312
Subtracted cgi-121 protein; prpk (p53-related protein kinase)-binding protein. [refseq;acc:nm_016058] 9654.91 9142.34 512.57
cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] High confidence 11864 13241.4 1377.4
247 Divided cellular tumor antigen p53 (tumor suppressor p53) (phosphoprotein p53) (antigen ny-co-13). [swissprot;acc:p04637] Low confidence 9046.45 8509.51 1.0631
wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] High confidence 7865.15 6416.68 1.22574
Subtracted fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] 11864 13241.4 1377.4
Low confidence 9218.39 8708.47 509.92
248 Divided proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] High confidence 7859.6 6417.18 1.22477
rabaptin, rab gtpase binding effector protein 1; rabaptin-5; neurocrescin. [refseq;acc:nm_004703] Low confidence 8095.68 7615.71 1.06302
Subtracted fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] 8732.25 8223.39 508.86
proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824] High confidence 11864 13241.4 1377.4
249 Divided apg3p; pc3-96 protein. [refseq;acc:nm_022488] Low confidence 9924.56 10547.4 1.06276
tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] High confidence 7859.59 6417.18 1.22477
Subtracted microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] Low confidence 8298.46 7789.89 508.57
small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] High confidence 5782.08 4405.4 1376.68
250 Divided large neutral amino acids transporter small subunit 2 (l-type amino acid transporter 2) (hlat2). [swissprot;acc:q9uhi5] Low confidence 7412.76 6975.98 1.06261
proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] High confidence 7859.6 6417.18 1.22477
Subtracted dj842g6.2 (novel protein imilar to sel1l (sel-1 (suppressor of lin-12, c.elegans)-like)) (fragment). [sptrembl;acc:q9ugd3] Low confidence 8727.87 8219.97 507.9
sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489] High confidence 5939.91 4578.09 1361.82

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/