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	red	green	network_comparison

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Showing element 1780 to 1829 of 3228 in total

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

Rank	description	red	green	network_comparison
1780	germ cell-less. [refseq;acc:nm_022471]	206.335	203.877	1.01206
1781	pre-b-cell leukemia transcription factor-3 (homeobox protein pbx3). [swissprot;acc:p40426]	206.332	203.874
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]	210.997	213.539	1.01205
1790	dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388]	203.759	201.349	1.01197
1791	elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576]	217.866	215.295	1.01194
1792	elav-like protein 4 (paraneoplastic encephalomyelitis antigen hud) (hu-antigen d). [swissprot;acc:p26378]	217.766	215.199	1.01193
1793	putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361]	193.1	190.823
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]	193.138	190.861
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]	217.724	215.158
1796	dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880]	203.759	201.357
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]	193.111	190.834
1798	elav-like protein 1 (hu-antigen r) (hur). [swissprot;acc:q15717]	217.807	215.242	1.01192
1799	alpha-actinin 2 (alpha actinin skeletal muscle isoform 2) (f-actin cross linking protein). [swissprot;acc:p35609]	217.016	214.481	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
1801	cug triplet repeat rna-binding protein 1 (cug-bp1) (rna-binding protein brunol-2) (deadenylation factor cug-bp) (50 kda nuclear polyadenylated rna-binding protein) (eden-bp). [swissprot;acc:q92879]	217.984	215.441
1802	elongation protein 4 homolog; pax6 neighbor gene; chromosome 11 open reading frame 19. [refseq;acc:nm_019040]	217.011	214.481
1803	dual-specificity tyrosine-phosphorylation regulated kinase 1b (ec 2.7.1.-) (mirk protein kinase). [swissprot;acc:q9y463]
1804	cug triplet repeat, rna binding protein 2; elav-type rna-binding protein; cug triplet repeat,rna-binding protein 2; cug triplet repeat, rna-binding protein 2; neuroblastoma apoptosis-related rna-binding protein. [refseq;acc:nm_006561]	217.984	215.442
1805	alpha-actinin 4 (non-muscle alpha-actinin 4) (f-actin cross linking protein). [swissprot;acc:o43707]	217.008	214.482	1.01178
1806	alpha-actinin 1 (alpha-actinin cytoskeletal isoform) (non-muscle alpha-actinin 1) (f-actin cross linking protein). [swissprot;acc:p12814]	217.009
1807	ral guanine nucleotide exchange factor ralgps1a. [refseq;acc:nm_014636]	211.102	208.651	1.01175
1808	ral-a exchange factor ralgps2. [refseq;acc:nm_152663]
1809	stip1 homology and u-box containing protein 1; serologically defined colon cancer antigen 7; carboxy terminus of hsp70p-interacting protein; heat shock protein a binding protein 2 (c-terminal). [refseq;acc:nm_005861]
1810	lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [swissprot;acc:p36776]	223.214	225.827	1.01171
1811	polypeptide n-acetylgalactosaminyltransferase 2; udp-galnac transferase 2. [refseq;acc:nm_004481]	216.854	214.35	1.01168
1812	cyclin c. [swissprot;acc:p24863]	217.071	214.564
1813	similar to expressed sequence ai415388 (fragment). [sptrembl;acc:q8n428]	216.854	214.35
1814	serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873]	122.3	123.727	1.01167
1815	dpy-30-like protein. [swissprot;acc:q9c005]	220.462	217.926	1.01164
1816	rab coupling protein; rab-interacting recycling protein; rab effector protein; rab11-family interacting protein 1. [refseq;acc:nm_025151]
1817	gamma-snap-associated factor 1; rab11-interacting protein. [refseq;acc:nm_015470]
1818	neighbor of cox4. [swissprot;acc:o43402]
1819	protein c14orf122 (cgi-112). [swissprot;acc:q9y3b6]
1820	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]
1821	rna-binding region containing protein 1 (hsrnaseb) (ssdna binding protein seb4) (cll-associated antigen kw-5). [swissprot;acc:q9h0z9]	218.36	215.874	1.01152
1822	6-phosphofructokinase, liver type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme b) (pfk-b). [swissprot;acc:p17858]	240.32	243.085	1.01151
1823	fragile x mental retardation syndrome related protein 2. [swissprot;acc:p51116]	202.386	200.086	1.0115
1824	f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907]	214.722	212.281
1825	fragile x mental retardation syndrome related protein 1. [swissprot;acc:p51114]	202.386	200.086
1826	nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	202.393	200.094	1.01149
1827	nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232]	191.39	189.219	1.01147
1828	fragile x mental retardation 1 protein (protein fmr-1) (fmrp). [swissprot;acc:q06787]	202.41	200.115
1829	cad protein [includes: glutamine-dependent carbamoyl-phosphate synthase (ec 6.3.5.5); aspartate carbamoyltransferase (ec 2.1.3.2); dihydroorotase (ec 3.5.2.3)]. [swissprot;acc:p27708]	212.884	215.323	1.01146

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.