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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 4708 to 4757 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
2354 rad54-like protein; rad54 homolog. [refseq;acc:nm_003579] Low confidence 200.683 197.018 1.0186
2355 26s proteasome non-atpase regulatory subunit 7 (26s proteasome regulatory subunit s12) (proteasome subunit p40) (mov34 protein homolog). [swissprot;acc:p51665] High confidence 217.232 218.162 1.00428
dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] Low confidence 201.038 197.369 1.01859
2356 40s ribosomal protein s28. [swissprot;acc:p25112] 201.372 197.696
importin 4. [refseq;acc:nm_024658] High confidence 220.921 221.863 1.00426
2357 endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] Low confidence 197.136 193.538 1.01859
ubiquitin-conjugating enzyme e2 g2 (ec 6.3.2.19) (ubiquitin-protein ligase g2) (ubiquitin carrier protein g2). [swissprot;acc:p56554] High confidence 198.181 197.346 1.00423
2358 38 kda fk-506 binding protein homolog (fkbpr38) (fk506-binding protein 8). [swissprot;acc:q14318]
superoxide dismutase [cu-zn] (ec 1.15.1.1). [swissprot;acc:p00441] Low confidence 200.81 197.146 1.01859
2359 phosphoglycerate kinase, testis specific (ec 2.7.2.3). [swissprot;acc:p07205] High confidence 207.196 208.056 1.00415
serine/threonine protein phosphatase 6 (ec 3.1.3.16) (pp6). [swissprot;acc:o00743] Low confidence 197.079 193.483 1.01859
2360 carbonic anhydrase-related protein 10 (carbonic anhydrase-related protein x) (carp x) (ca-rp x) (cerebral protein-15) (hucep-15). [swissprot;acc:q9ns85] 205.17 201.427 1.01858
gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [swissprot;acc:p09104] High confidence 207.186 208.046 1.00415
2361 beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [swissprot;acc:p13929]
ubiquinone biosynthesis monooxgenase coq6 (ec 1.14.13.-) (cgi-10). [swissprot;acc:q9y2z9] Low confidence 199.354 195.718 1.01858
2362 nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556] 205.597 201.849 1.01857
phosphoglycerate kinase 1 (ec 2.7.2.3) (primer recognition protein 2) (prp 2). [swissprot;acc:p00558] High confidence 207.178 208.037 1.00415
2363 alpha enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (non- neural enolase) (nne) (enolase 1) (phosphopyruvate hydratase). [swissprot;acc:p06733] 207.186 208.046
similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9] Low confidence 205.597 201.849 1.01857
2364 peroxisomal membrane protein 2 (22 kda peroxisomal membrane protein). [swissprot;acc:q9nr77] 201.843 198.163
transaldolase (ec 2.2.1.2). [swissprot;acc:p37837] High confidence 212.816 213.697 1.00414
2365 cyclin g2. [swissprot;acc:q16589] Low confidence 203.119 199.416 1.01857
glutamate carboxypeptidase-like protein 2 precursor. [swissprot;acc:q96kn2] High confidence 208.958 209.82 1.00413
2366 14.5 kda translational inhibitor protein (p14.5) (uk114 antigen homolog). [swissprot;acc:p52758] 203.353 202.529 1.00407
rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [swissprot;acc:q9y243] Low confidence 204.081 200.36 1.01857
2367 26s proteasome non-atpase regulatory subunit 11 (26s proteasome regulatory subunit s9) (26s proteasome regulatory subunit p44.5). [swissprot;acc:o00231] High confidence 217.589 218.475 1.00407
heat shock cognate 71 kda protein. [swissprot;acc:p11142] Low confidence 201.843 198.163 1.01857
2368 26s proteasome non-atpase regulatory subunit 1 (26s proteasome regulatory subunit s1) (26s proteasome subunit p112). [swissprot;acc:q99460] High confidence 218.555 219.434 1.00402
carbonic anhydrase-related protein 2 precursor (carp-2) (ca-rp ii) (ca-xi) (carbonic anhydrase-related protein 11) (carp xi) (ca-rp xi). [swissprot;acc:o75493] Low confidence 205.147 201.407 1.01857
2369 adhesion regulating molecule 1 precursor (110 kda cell membrane glycoprotein) (gp110). [swissprot;acc:q16186] High confidence 218.555 219.434 1.00402
dna polymerase delta subunit 2 (ec 2.7.7.7). [swissprot;acc:p49005] Low confidence 197.53 193.931 1.01856
2370 serine/threonine protein kinase 3 (ec 2.7.1.37) (ste20-like kinase mst2) (mst-2) (mammalian ste20-like protein kinase 2) (serine/threonine protein kinase krs-1). [swissprot;acc:q13188] 201.359 197.689
ubiquitin carboxyl-terminal hydrolase isozyme l5 (ec 3.4.19.12) (uch- l5) (ubiquitin thiolesterase l5) (ubiquitin c-terminal hydrolase uch37) (cgi-70) (ad-019). [swissprot;acc:q9y5k5] High confidence 218.555 219.434 1.00402
2371 nuclear protein ukp68. [refseq;acc:nm_024824] Low confidence 200.63 196.975 1.01856
rna polymerase ii subunit 5-mediating protein (rpb5-mediating protein). [swissprot;acc:o94763] High confidence 218.555 219.434 1.00402
2372 dna polymerase delta catalytic subunit (ec 2.7.7.7) (dna polymerase delta subunit p125). [swissprot;acc:p28340] Low confidence 197.53 193.931 1.01856
mothers against decapentaplegic homolog 2 (smad 2) (mothers against dpp homolog 2) (mad-related protein 2) (hmad-2) (jv18-1) (hsmad2). [swissprot;acc:q15796] High confidence 212.724 213.574 1.004
2373 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] Low confidence 200.997 197.335 1.01856
mothers against decapentaplegic homolog 1 (smad 1) (mothers against dpp homolog 1) (mad-related protein 1) (transforming growth factor- beta signaling protein-1) (bsp-1) (hsmad1) (jv4-1). [swissprot;acc:q15797] High confidence 212.724 213.574 1.004
2374 cop9 subunit 6 (mov34 homolog, 34 kd). [refseq;acc:nm_006833]
short-chain dehydrogenase/reductase 9; 17-beta hydroxysteroid dehydrogenase. [refseq;acc:nm_178135] Low confidence 197.541 193.944 1.01855
2375 mothers against decapentaplegic homolog 3 (smad 3) (mothers against dpp homolog 3) (mad3) (hmad-3) (mmad3) (jv15-2) (hsmad3). [swissprot;acc:q92940] High confidence 212.724 213.574 1.004
replication protein a 70 kda dna-binding subunit (rp-a) (rf-a) (replication factor-a protein 1) (single-stranded dna-binding protein). [swissprot;acc:p27694] Low confidence 201.46 197.791 1.01855
2376 acetyl-coenzyme a synthetase, cytoplasmic (ec 6.2.1.1) (acetate--coa ligase) (acyl-activating enzyme) (acetyl-coa synthetase) (acs) (acecs). [swissprot;acc:q9nr19] 199.85 196.211
histone deacetylase 11 (hd11). [swissprot;acc:q96db2] High confidence 212.724 213.574 1.004
2377 endothelial differentiation-related factor 1 isoform alpha; multiprotein bridging factor 1. [refseq;acc:nm_003792] Low confidence 202.259 198.575 1.01855
ethanolamine kinase-like protein eki2 (flj10761). [swissprot;acc:q9nvf9] High confidence 212.724 213.574 1.004
2378 cytochrome c oxidase polypeptide va, mitochondrial precursor (ec 1.9.3.1). [swissprot;acc:p20674] Low confidence 201.741 198.068 1.01854
ethanolamine kinase (ec 2.7.1.82) (eki). [swissprot;acc:q9hbu6] High confidence 212.724 213.574 1.004
2379 dynein intermediate chain 1, axonemal (axonemal dynein intermediate chain 1). [swissprot;acc:q9ui46] Low confidence 201.741 198.068 1.01854

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/