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 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
2354 transaldolase (ec 2.2.1.2). [swissprot;acc:p37837] Subtracted 212.816 213.697 0.881
2355 26s proteasome non-atpase regulatory subunit 1 (26s proteasome regulatory subunit s1) (26s proteasome subunit p112). [swissprot;acc:q99460] 218.555 219.434 0.879
26s proteasome non-atpase regulatory subunit 7 (26s proteasome regulatory subunit s12) (proteasome subunit p40) (mov34 protein homolog). [swissprot;acc:p51665] Divided 217.232 218.162 1.00428
2356 adhesion regulating molecule 1 precursor (110 kda cell membrane glycoprotein) (gp110). [swissprot;acc:q16186] Subtracted 218.555 219.434 0.879
importin 4. [refseq;acc:nm_024658] Divided 220.921 221.863 1.00426
2357 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] Subtracted 218.555 219.434 0.879
ubiquitin-conjugating enzyme e2 g2 (ec 6.3.2.19) (ubiquitin-protein ligase g2) (ubiquitin carrier protein g2). [swissprot;acc:p56554] Divided 198.181 197.346 1.00423
2358 38 kda fk-506 binding protein homolog (fkbpr38) (fk506-binding protein 8). [swissprot;acc:q14318]
rna polymerase ii subunit 5-mediating protein (rpb5-mediating protein). [swissprot;acc:o94763] Subtracted 218.555 219.434 0.879
2359 phosphoglycerate kinase, testis specific (ec 2.7.2.3). [swissprot;acc:p07205] Divided 207.196 208.056 1.00415
ring finger protein 20. [refseq;acc:nm_019592] Subtracted 224.414 225.289 0.875
2360 gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [swissprot;acc:p09104] Divided 207.186 208.046 1.00415
ring finger protein 40; 95 kda retinoblastoma protein binding protein; likely ortholog of rat staring. [refseq;acc:nm_014771] Subtracted 224.414 225.289 0.875
2361 beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [swissprot;acc:p13929] Divided 207.186 208.046 1.00415
glutamate carboxypeptidase-like protein 2 precursor. [swissprot;acc:q96kn2] Subtracted 208.958 209.82 0.862
2362 phosphoglycerate kinase 1 (ec 2.7.2.3) (primer recognition protein 2) (prp 2). [swissprot;acc:p00558] Divided 207.178 208.037 1.00415
phosphoglycerate kinase, testis specific (ec 2.7.2.3). [swissprot;acc:p07205] Subtracted 207.196 208.056 0.86
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] Divided 207.186 208.046 1.00415
gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [swissprot;acc:p09104] Subtracted 0.86
2364 beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [swissprot;acc:p13929]
transaldolase (ec 2.2.1.2). [swissprot;acc:p37837] Divided 212.816 213.697 1.00414
2365 alpha enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (non- neural enolase) (nne) (enolase 1) (phosphopyruvate hydratase). [swissprot;acc:p06733] Subtracted 207.186 208.046 0.86
glutamate carboxypeptidase-like protein 2 precursor. [swissprot;acc:q96kn2] Divided 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
phosphoglycerate kinase 1 (ec 2.7.2.3) (primer recognition protein 2) (prp 2). [swissprot;acc:p00558] Subtracted 207.178 208.037 0.859
2367 26s proteasome non-atpase regulatory subunit 11 (26s proteasome regulatory subunit s9) (26s proteasome regulatory subunit p44.5). [swissprot;acc:o00231] Divided 217.589 218.475 1.00407
protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] Subtracted 162.331 163.187 0.856
2368 26s proteasome non-atpase regulatory subunit 1 (26s proteasome regulatory subunit s1) (26s proteasome subunit p112). [swissprot;acc:q99460] Divided 218.555 219.434 1.00402
tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625] Subtracted 162.86 163.712 0.852
2369 adhesion regulating molecule 1 precursor (110 kda cell membrane glycoprotein) (gp110). [swissprot;acc:q16186] Divided 218.555 219.434 1.00402
mothers against decapentaplegic homolog 2 (smad 2) (mothers against dpp homolog 2) (mad-related protein 2) (hmad-2) (jv18-1) (hsmad2). [swissprot;acc:q15796] Subtracted 212.724 213.574 0.85
2370 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]
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] Divided 218.555 219.434 1.00402
2371 cop9 subunit 6 (mov34 homolog, 34 kd). [refseq;acc:nm_006833] Subtracted 212.724 213.574 0.85
rna polymerase ii subunit 5-mediating protein (rpb5-mediating protein). [swissprot;acc:o94763] Divided 218.555 219.434 1.00402
2372 mothers against decapentaplegic homolog 2 (smad 2) (mothers against dpp homolog 2) (mad-related protein 2) (hmad-2) (jv18-1) (hsmad2). [swissprot;acc:q15796] 212.724 213.574 1.004
mothers against decapentaplegic homolog 3 (smad 3) (mothers against dpp homolog 3) (mad3) (hmad-3) (mmad3) (jv15-2) (hsmad3). [swissprot;acc:q92940] Subtracted 0.85
2373 histone deacetylase 11 (hd11). [swissprot;acc:q96db2]
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] Divided 1.004
2374 cop9 subunit 6 (mov34 homolog, 34 kd). [refseq;acc:nm_006833]
ethanolamine kinase-like protein eki2 (flj10761). [swissprot;acc:q9nvf9] Subtracted 0.85
2375 ethanolamine kinase (ec 2.7.1.82) (eki). [swissprot;acc:q9hbu6]
mothers against decapentaplegic homolog 3 (smad 3) (mothers against dpp homolog 3) (mad3) (hmad-3) (mmad3) (jv15-2) (hsmad3). [swissprot;acc:q92940] Divided 1.004
2376 hepatocellular carcinoma susceptibility protein; x 003 protein; hdcmc29p; hspc260; likely ortholog of mouse cd40 ligand-activated specific transcript 3 (clast3). [refseq;acc:nm_020232] Subtracted 0.85
histone deacetylase 11 (hd11). [swissprot;acc:q96db2] Divided 1.004
2377 cop9 constitutive photomorphogenic homolog subunit 5; jun activation domain-binding protein. [refseq;acc:nm_006837] Subtracted 0.85
ethanolamine kinase-like protein eki2 (flj10761). [swissprot;acc:q9nvf9] Divided 1.004
2378 ethanolamine kinase (ec 2.7.1.82) (eki). [swissprot;acc:q9hbu6]
mothers against decapentaplegic homolog 9 (smad 9) (mothers against dpp homolog 9) (smad9) (madh6). [swissprot;acc:o15198] Subtracted 0.85
2379 hepatocellular carcinoma susceptibility protein; x 003 protein; hdcmc29p; hspc260; likely ortholog of mouse cd40 ligand-activated specific transcript 3 (clast3). [refseq;acc:nm_020232] Divided 1.004

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/