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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Gene red Network Comparison Type Value Type Rank green Interaction Map description Filtered network_comparison
Results: HTML CSV LaTeX Showing element 2100 to 2149 of 3228 in total
Network Comparison Type  : Divided
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
red
Rank
green
description
network_comparison
5916.05 1536 6350.53 26s proteasome non-atpase regulatory subunit 8 (26s proteasome regulatory subunit s14) (p31). [swissprot;acc:p48556] 1.07344
5916.13 1710 6321.77 camp-dependent protein kinase type ii-alpha regulatory chain. [swissprot;acc:p13861] 1.06857
5917.22 1711 6322.72 protein kinase pkx1 (ec 2.7.1.-). [swissprot;acc:p51817] 1.06853
5917.23 1712 6322.73 camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612]
1713 camp-dependent protein kinase, beta-catalytic subunit (ec 2.7.1.37) (pka c-beta). [swissprot;acc:p22694]
1714 camp-dependent protein kinase, alpha-catalytic subunit (ec 2.7.1.37) (pka c-alpha). [swissprot;acc:p17612]
5918.48 1715 6323.83 camp-dependent protein kinase type ii-beta regulatory chain. [swissprot;acc:p31323] 1.06849
5920.55 1628 6337.28 glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434] 1.07039
5923.66 1576 6349.04 mitochondrial ribosomal protein l30 isoform a. [refseq;acc:nm_145212] 1.07181
1577 26s protease regulatory subunit s10b (proteasome subunit p42) (p44) (conserved atpase domain protein 44) (cadp44). [swissprot;acc:q92524]
5925.65 1736 6326.43 twinkle; likely ortholog of mouse t7 gp4-like protein with intramitochondrial nucleoid localization. [refseq;acc:nm_021830] 1.06763
1737 rabaptin, rab gtpase binding effector protein 1; rabaptin-5; neurocrescin. [refseq;acc:nm_004703]
5926.76 1527 6362.33 26s protease regulatory subunit 6a (tat-binding protein 1) (tbp-1) (proteasome subunit p50). [swissprot;acc:p17980] 1.07349
5929.48 897 6531.48 histone deacetylase 2 (hd2). [swissprot;acc:q92769] 1.10153
5929.55 898 6531.52 multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279] 1.10152
899 dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8]
5929.61 901 6531.55 histone deacetylase 1 (hd1). [swissprot;acc:q13547] 1.10151
5932.05 2536 6071.35 sorting nexin 1. [swissprot;acc:q13596] 1.02348
5933.25 1584 6358.78 glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [swissprot;acc:p23378] 1.07172
5934.08 2014 6281.2 kinesin-like protein kif3b (microtubule plus end-directed kinesin motor 3b) (hh0048). [swissprot;acc:o15066] 1.0585
5934.68 2021 6281.49 kinesin-like protein kif3c. [swissprot;acc:o14782] 1.05844
5935.71 2642 5876.22 vam6/vps39-like protein (hvam6p). [swissprot;acc:q96jc1] 1.01012
2643 microtubule-associated protein 4 (map 4). [swissprot;acc:p27816]
5938.56 1521 6376.76 26s protease regulatory subunit 4 (p26s4). [swissprot;acc:q03527] 1.07379
5939.71 1639 6354.79 putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [swissprot;acc:o95544] 1.06988
5939.85 1976 6294.91 splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [swissprot;acc:q05519] 1.05978
5941.24 1962 6297.78 c-jun-amino-terminal kinase interacting protein 3 (jnk-interacting protein 3) (jip-3) (jnk map kinase scaffold protein 3) (mitogen- activated protein kinase 8-interacting protein 3). [swissprot;acc:q9upt6] 1.06001
5941.29 1752 6339.93 copper-transporting atpase 1 (ec 3.6.3.4) (copper pump 1) (menkes disease-associated protein). [swissprot;acc:q04656] 1.0671
5941.83 1754 6340.32 copper-transporting atpase 2 (ec 3.6.3.4) (copper pump 2) (wilson disease-associated protein). [swissprot;acc:p35670] 1.06707
5942.49 426 6853.15 pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392] 1.15325
5944.24 1651 6358.1 cbf1 interacting corepressor. [refseq;acc:nm_004882] 1.06962
1652 evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025]
5945.56 1496 6389.63 apoptosis-inducing factor (aif)-homologous mitochondrion-associated inducer of death; p53-responsive gene 3. [refseq;acc:nm_032797] 1.07469
5945.96 1545 6380.28 aminomethyltransferase, mitochondrial precursor (ec 2.1.2.10) (glycine cleavage system t protein) (gcvt). [swissprot;acc:p48728] 1.07304
5946.33 1204 6459.79 suppressor of cytokine signaling 1 (socs-1) (jak-binding protein) (jab) (stat induced stat inhibitor 1) (ssi-1) (tec-interacting protein 3) (tip-3). [swissprot;acc:o15524] 1.08635
1205 glia maturation factor gamma (gmf-gamma). [swissprot;acc:o60234]
1206 asc-1 complex subunit p100. [refseq;acc:nm_032204]
1207 fk506-binding protein 1a (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (12 kda fkbp) (fkbp-12) (immunophilin fkbp12). [swissprot;acc:p20071]
5947.53 1110 6481.56 nadph:adrenodoxin oxidoreductase, mitochondrial precursor (ec 1.18.1.2) (adrenodoxin reductase) (ar) (ferredoxin-nadp(+) reductase). [swissprot;acc:p22570] 1.08979
5948.26 1794 6342.84 epsin 2 isoform b; eps15 binding protein. [refseq;acc:nm_014964] 1.06634
5949.31 1934 6313.1 transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3] 1.06115
5950.27 1200 6465.72 xylulokinase homolog; xylulokinase (h. influenzae) homolog. [refseq;acc:nm_005108] 1.08663
5958.23 604 6743.37 vinculin (metavinculin). [swissprot;acc:p18206] 1.13177
5961.97 1318 6443.07 serine/threonine-protein kinase nek1 (ec 2.7.1.37) (nima-related protein kinase 1) (ny-ren-55 antigen). [swissprot;acc:q96py6] 1.08069
1319 serine/threonine-protein kinase nek3 (ec 2.7.1.37) (nima-related protein kinase 3) (hspk 36). [swissprot;acc:p51956]
1320 glyceraldehyde 3-phosphate dehydrogenase, liver (ec 1.2.1.12) (gapdh). [swissprot;acc:p04406]
5964.17 2519 6113.96 adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741] 1.02511
2520 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]
2521 17 beta-hydroxysteroid dehydrogenase. [sptrembl;acc:q13034]
2522 retinol dehydrogenase 8 (all-trans); photoreceptor outer segment all-trans retinol dehydrogenase. [refseq;acc:nm_015725]

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/