MK5 Microarray Data

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	Gene	description	Value Type	Network Comparison Type	Interaction Map	Filtered	green	red	network_comparison

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Showing element 1751 to 1800 of 3228 in total

Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

Rank	description	green	red	network_comparison
1751	adaptor-related protein complex 1, mu 2 subunit (mu-adaptin 2) (adaptor protein complex ap-1 mu-2 subunit) (golgi adaptor ha1/ap1 adaptin mu-2 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 2) (ap-mu chain family member mu1b). [swissprot;acc:q9y6q5]	223.97	221.185	1.01259
1752	brca1-associated ring domain protein 1 (bard-1). [swissprot;acc:q99728]	218.991	216.271	1.01258
1753	peptide methionine sulfoxide reductase (ec 1.8.4.6) (protein- methionine-s-oxide reductase) (peptide met(o) reductase). [swissprot;acc:q9uj68]	217.362	220.091	1.01256
1754	phosphoserine aminotransferase (ec 2.6.1.52) (psat). [swissprot;acc:q9y617]
1755	ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812]	178.393	180.609	1.01242
1756	megf6 (fragment). [sptrembl;acc:o75095]	219.09	221.811
1757	cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857]	178.325	180.537	1.0124
1758	ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447]	230.595	233.45	1.01238
1759	ruvb-like 1 (ec 3.6.1.-) (49-kda tata box-binding protein-interacting protein) (49 kda tbp-interacting protein) (tip49a) (pontin 52) (nuclear matrix protein 238) (nmp 238) (54 kda erythrocyte cytosolic protein) (ecp-54) (tip60-associated protein 54-alpha) (tap54-alpha). [swissprot;acc:q9y265]	222.086	219.37
1760	myosin light chain 1, skeletal muscle isoform (mlc1f) (a1 catalytic) (alkali). [swissprot;acc:p05976]	230.595	233.45
1761	myosin light chain 1, slow-twitch muscle b/ventricular isoform (mlc1sb) (alkali). [swissprot;acc:p08590]
1762	nadh-ubiquinone oxidoreductase 13 kda-a subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-a) (ci-13kd-a). [swissprot;acc:o75380]
1763	myosin light chain 1, slow-twitch muscle a isoform (mlc1sa) (alkali). [swissprot;acc:p14649]
1764	myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829]
1765	isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252]	218.369	215.698
1766	c-1-tetrahydrofolate synthase, cytoplasmic (c1-thf synthase) [includes: methylenetetrahydrofolate dehydrogenase (ec 1.5.1.5); methenyltetrahydrofolate cyclohydrolase (ec 3.5.4.9); formyltetrahydrofolate synthetase (ec 6.3.4.3)]. [swissprot;acc:p11586]	231.732	228.932	1.01223
1767	60s ribosomal protein l24 (l30). [swissprot;acc:p38663]	198.86	201.288	1.01221
1768	estradiol 17 beta-dehydrogenase 4 (ec 1.1.1.62) (17-beta-hsd 4) (17-beta-hydroxysteroid dehydrogenase 4). [swissprot;acc:p51659]	187.534	185.276	1.01219
1769	5'-methylthioadenosine phosphorylase (ec 2.4.2.28) (mta phosphorylase) (mtapase). [swissprot;acc:q13126]	225.734	223.016
1770	adaptor-related protein complex 1, mu 1 subunit (mu-adaptin 1) (adaptor protein complex ap-1 mu-1 subunit) (golgi adaptor ha1/ap1 adaptin mu-1 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 1) (clathrin coat assembly protein ap47) (clathrin coat associated protein ap47) (ap-mu chain family member mu1a). [swissprot;acc:q9bxs5]	223.778	221.082
1771	putative ribosomal rna methyltransferase 1 (ec 2.1.1.-) (rrna (uridine-2'-o-)-methyltransferase) (jm23 protein). [swissprot;acc:q9uet6]	225.734	223.016
1772	spectrin beta chain, brain 2 (spectrin, non-erythroid beta chain 2) (beta-iii spectrin). [swissprot;acc:o15020]	225.739	223.032	1.01214
1773	spectrin beta chain, brain 1 (spectrin, non-erythroid beta chain 1) (beta-ii spectrin) (fodrin beta chain). [swissprot;acc:q01082]
1774	phosphoacetylglucosamine mutase (ec 5.4.2.3) (pagm) (acetylglucosamine phosphomutase) (n-acetylglucosamine-phosphate mutase) (phosphoglucomutase 3). [swissprot;acc:o95394]
1775	serine palmitoyltransferase 1 (ec 2.3.1.50) (long chain base biosynthesis protein 1) (lcb 1) (serine-palmitoyl-coa transferase 1) (spt 1) (spt1). [swissprot;acc:o15269]	210.274	207.757	1.01212
1776	nucleoporin like 1. [refseq;acc:nm_014089]	214.286	216.878	1.0121
1777	rho guanine nucleotide exchange factor 4 isoform a; apc-stimulated guanine nucleotide exchange factor. [refseq;acc:nm_015320]
1778	cdc42 guanine exchange factor 9; hpem-2 collybistin. [refseq;acc:nm_015185]
1779	pre-b-cell leukemia transcription factor-1 (homeobox protein pbx1) (homeobox protein prl). [swissprot;acc:p40424]	203.874	206.332	1.01206
1780	germ cell-less. [refseq;acc:nm_022471]	203.877	206.335
1781	pre-b-cell leukemia transcription factor-3 (homeobox protein pbx3). [swissprot;acc:p40426]	203.874	206.332
1782	hyporthetical protein mgc27169. [refseq;acc:nm_176782]
1783	homeobox protein meis1. [swissprot;acc:o00470]
1784	homeobox protein meis2 (meis1-related protein 1). [swissprot;acc:o14770]
1785	bag-family molecular chaperone regulator-2. [swissprot;acc:o95816]
1786	pre-b-cell leukemia transcription factor-2 (homeobox protein pbx2) (g17 protein). [swissprot;acc:p40425]
1787	pre-b-cell leukemia transcription factor 4. [refseq;acc:nm_025245]
1788	homeobox protein meis3 (meis1-related protein 2) (fragment). [swissprot;acc:q99687]
1789	ribonuclease hi large subunit (ec 3.1.26.-) (rnase hi large subunit) (rnase h(35)) (ribonuclease h2) (rnase h2). [swissprot;acc:o75792]	213.539	210.997	1.01205
1790	dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388]	201.349	203.759	1.01197
1791	elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576]	215.295	217.866	1.01194
1792	elav-like protein 4 (paraneoplastic encephalomyelitis antigen hud) (hu-antigen d). [swissprot;acc:p26378]	215.199	217.766	1.01193
1793	putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361]	190.823	193.1
1794	nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [swissprot;acc:p22392]	190.861	193.138
1795	elav-like protein 2 (hu-antigen b) (hub) (elav-like neuronal protein 1) (nervous system-specific rna binding protein hel-n1). [swissprot;acc:q12926]	215.158	217.724
1796	dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880]	201.357	203.759
1797	nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [swissprot;acc:p15531]	190.834	193.111
1798	elav-like protein 1 (hu-antigen r) (hur). [swissprot;acc:q15717]	215.242	217.807	1.01192
1799	alpha-actinin 2 (alpha actinin skeletal muscle isoform 2) (f-actin cross linking protein). [swissprot;acc:p35609]	214.481	217.016	1.01182
1800	dual-specificity tyrosine-phosphorylation regulated kinase 1a (ec 2.7.1.-) (protein kinase minibrain homolog) (mnbh) (hp86) (dual specificity yak1-related kinase). [swissprot;acc:q13627]		217.011	1.0118

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.