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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Interaction Map Value Type Gene Rank description Filtered red green Network Comparison Type network_comparison
Results: HTML CSV LaTeX Showing element 951 to 1000 of 29840 in total
Interaction Map  : High confidence
Value Type  : Measured
Rank
description
Filtered
red
green
Network Comparison Type
network_comparison
238 signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556] 0 494.417 359.631 Subtracted 134.786
star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502] 1 9649.61 11053.5 1403.89
239 carboxypeptidase b precursor. [refseq;acc:nm_020361] 7711.38 6265.8 Divided 1.23071
guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] 0 382.142 434.366 1.13666
leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735] 11170.7 11305 Subtracted 134.3
neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822] 1 9649.61 11053.5 1403.89
240 mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] 7711.36 6265.79 Divided 1.23071
mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] 9649.61 11053.5 Subtracted 1403.89
putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] 0 1475.83 1676.18 Divided 1.13575
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 903.967 771.309 Subtracted 132.658
241 hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712] 3614.24 3481.87 132.37
keratin associated protein 9.2. [refseq;acc:nm_031961] 1225.47 1079.01 Divided 1.13574
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] 1 9649.61 11053.5 Subtracted 1403.89
plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] 7711.31 6265.76 Divided 1.23071
242 likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] 0 1293.73 1161.64 Subtracted 132.09
max protein. [swissprot;acc:p25912] 1 4640.26 5704.87 Divided 1.22943
neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] 9649.61 11053.5 Subtracted 1403.89
splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] 0 729.216 642.343 Divided 1.13524
243 dead-box protein. [refseq;acc:nm_018665] 313.667 183 Subtracted 130.667
homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] 1 4246.95 5208.98 Divided 1.22652
keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4] 0 1225.09 1079.36 1.13502
neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] 1 9649.61 11053.5 Subtracted 1403.89
244 keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184] 0 1225.09 1079.36 Divided 1.13502
sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0] 1 9649.61 11053.5 Subtracted 1403.89
sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] 0 1334.19 1205.1 129.09
ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] 1 4250.14 5211.25 Divided 1.22614
245 basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811] 0 292 421 Subtracted 129
homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] 1 4251.65 5212.33 Divided 1.22595
keratin associated protein 1.5. [refseq;acc:nm_031957] 0 1225.09 1079.36 1.13502
methyltransferase like 2. [refseq;acc:nm_018396] 1 13241.4 11864 Subtracted 1377.4
246 cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763]
f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] 0 150.673 279.24 128.567
homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] 1 4252.66 5213.05 Divided 1.22583
keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371] 0 1225.09 1079.36 1.13502
247 fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] 1 13241.4 11864 Subtracted 1377.4
keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966] 0 1225.09 1079.36 Divided 1.13502
tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] 271.484 142.981 Subtracted 128.503
wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] 1 6416.68 7865.15 Divided 1.22574
248 adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741] 0 2323.8 2452.23 Subtracted 128.43
keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060] 1225.09 1079.37 Divided 1.135
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] 1 13241.4 11864 Subtracted 1377.4
proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] 6417.18 7859.6 Divided 1.22477
249 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] 0 2323.8 2452.23 Subtracted 128.43
keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059] 1225.08 1079.37 Divided 1.135
small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] 1 4405.4 5782.08 Subtracted 1376.68
tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] 6417.18 7859.59 Divided 1.22477
250 keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8] 0 1225.08 1079.37 1.135
proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] 1 6417.18 7859.6 1.22477
ptd016 protein. [refseq;acc:nm_016125] 0 30 158 Subtracted 128
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] 1 4578.09 5939.91 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/