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

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Showing element 1775 to 1824 of 3228 in total

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

red	green	Rank	description	network_comparison
5774.02	6133.01	1923	brain protein 16. [refseq;acc:nm_016458]	1.06217
5775.22	6094.89	2089	putative gtp-binding protein ptd004 (pro2455). [swissprot;acc:q9ntk5]	1.05535
5775.55	6171.79	1709	homeobox protein six2 (sine oculis homeobox homolog 2). [swissprot;acc:q9npc8]	1.06861
5776.79	6092.77	2113	rna-binding protein 9 (rna binding motif protein 9) (hexaribonucleotide binding protein 2) (repressor of tamoxifen transcriptional activity). [swissprot;acc:o43251]	1.0547
5776.96	6049.61	2243	inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268]	1.0472
		2244	gmp synthase [glutamine-hydrolyzing] (ec 6.3.5.2) (glutamine amidotransferase) (gmp synthetase). [swissprot;acc:p49915]
		2245	inosine-5'-monophosphate dehydrogenase 1 (ec 1.1.1.205) (imp dehydrogenase 1) (impdh-i) (impd 1). [swissprot;acc:p20839]
5777.1	6174.15	1707	proliferation-associated protein 2g4 (cell cycle protein p38-2g4 homolog) (hg4-1). [swissprot;acc:q9uq80]	1.06873
5778.16	6093.65	2117	ataxin 2-binding protein. [swissprot;acc:q9nwb1]	1.0546
5778.4	6176.13	1704	homeobox protein six1 (sine oculis homeobox homolog 1). [swissprot;acc:q15475]	1.06883
5778.62	6086.03	2149	importin beta-2 subunit (karyopherin beta-2 subunit) (transportin) (m9 region interaction protein) (mip). [swissprot;acc:q92973]	1.0532
5778.65	6328.56	995	annexin a11 (annexin xi) (calcyclin-associated annexin 50) (cap-50) (56 kda autoantigen). [swissprot;acc:p50995]	1.09516
5779.66	6044.78	2274	eyes absent homolog 3. [swissprot;acc:q99504]	1.04587
5779.82	6086.64	2150	karyopherin beta 2b, transportin; importin 3. [refseq;acc:nm_013433]	1.05308
5779.83	6244.56	1330	isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252]	1.08041
5780.34	6329.3	1005	annexin a7 (annexin vii) (synexin). [swissprot;acc:p20073]	1.09497
5781.8	6173.1	1732	proteasome subunit beta type 7 precursor (ec 3.4.25.1) (proteasome subunit z) (macropain chain z) (multicatalytic endopeptidase complex chain z). [swissprot;acc:q99436]	1.06768
5782.86	6126.69	1977	lim domain only 7; zinc-finger domain-containing protein; lomp protein; f-box only protein 20; f-box protein fbx20. [refseq;acc:nm_005358]	1.05946
5782.92	6186.39	1641	ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9]	1.06977
		1642	40s ribosomal protein s7 (s8). [swissprot;acc:p23821]
		1643	26s proteasome-associated pad1 homolog. [refseq;acc:nm_005805]
		1644	apolipoprotein b-100 precursor (apo b-100) [contains: apolipoprotein b-48 (apo b-48)]. [swissprot;acc:p04114]
5783.69	6048.87	2276	sal-like protein 2 (zinc finger protein sall2) (hsal2). [swissprot;acc:q9y467]	1.04585
5783.7	6048.88	2283	atrophin-1 (dentatorubral-pallidoluysian atrophy protein). [swissprot;acc:p54259]
		2287	sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4]
5783.71	6048.89	2291	clathrin coat assembly protein ap180 (clathrin coat associated protein ap180) (91 kda synaptosomal-associated protein). [swissprot;acc:o60641]
5783.72	6048.9	2277	sal-like protein 3 (zinc finger protein sall3) (hsall3). [swissprot;acc:q9bxa9]
5783.73	6048.91	2279	ubiquitin carboxyl-terminal hydrolase 8 (ec 3.1.2.15) (ubiquitin thiolesterase 8) (ubiquitin-specific processing protease 8) (deubiquitinating enzyme 8). [swissprot;acc:p40818]
		2280	rod1 regulator of differentiation 1; fission yeast differentiation regulator; regulator of differentiation (in s. pombi) 1; regulator of differentiation (in s. pombe) 1. [refseq;acc:nm_005156]
		2281	polypyrimidine tract binding protein 2; neural polypyrimidine tract binding protein; ptb-like protein. [refseq;acc:nm_021190]
		2282	adaptor-associated kinase 1. [refseq;acc:nm_014911]
		2284	dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355]
		2285	rho-gtpase activating protein 10. [refseq;acc:nm_020824]
		2294	growth-arrest-specific protein 7 (gas-7). [swissprot;acc:o60861]
5783.75	6048.93	2290	phosphatidylinositol-binding clathrin assembly protein (clathrin assembly lymphoid myeloid leukemia protein). [swissprot;acc:q13492]
5783.76	6048.94	2278	arginine-glutamic acid dipeptide (re) repeats; atrophin 1-like; arginine glutamic acid dipeptide re repeats. [refseq;acc:nm_012102]
		2286	sal-like protein 1 (zinc finger protein sall1) (spalt-like transcription factor 1) (hsal1). [swissprot;acc:q9nsc2]
		2288	2-oxoisovalerate dehydrogenase beta subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component beta chain) (bckdh e1-beta). [swissprot;acc:p21953]
		2289	ccr4-not transcription complex, subunit 4; not4 (negative regulator of transcription 4, yeast) homolog; ccr4-not transcription complex, subunit. [refseq;acc:nm_013316]
		2292	membrane-associated nucleic acid binding protein. [refseq;acc:nm_018835]
		2293	polypyrimidine tract-binding protein 1 (ptb) (heterogeneous nuclear ribonucleoprotein i) (hnrnp i) (57 kda rna-binding protein pptb-1). [swissprot;acc:p26599]
5783.9	6240.19	1355	ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [swissprot;acc:p00480]	1.07889
5783.97	6207.5	1539	26s protease regulatory subunit 7 (mss1 protein). [swissprot;acc:p35998]	1.07322
5784.06	6141.48	1930	p28 ing5. [refseq;acc:nm_032329]	1.06179
5784.36	6198.73	1586	ubiquitin-like protein smt3c precursor (ubiquitin-homology domain protein pic1) (ubiquitin-like protein ubl1) (ubiquitin-related protein sumo-1) (gap modifying protein 1) (gmp1) (sentrin). [swissprot;acc:q93068]	1.07164
		1587	udp-glucose 6-dehydrogenase (ec 1.1.1.22) (udp-glc dehydrogenase) (udp-glcdh) (udpgdh). [swissprot;acc:o60701]
5784.9	6049.99	2296	eyes absent homolog 4. [swissprot;acc:o95677]	1.04582
5785.08	6051.03	2268	eyes absent homolog 1. [swissprot;acc:q99502]	1.04597
5786.15	6050.71	2299	eyes absent homolog 2. [swissprot;acc:o00167]	1.04572
5786.36	6149.1	1899	ruvb-like 2 (ec 3.6.1.-) (48-kda tata box-binding protein-interacting protein) (48-kda tbp-interacting protein) (tip49b) (repressing pontin 52) (reptin 52) (51 kda erythrocyte cytosolic protein) (ecp-51) (tip60-associated protein 54-beta) (tap54-beta) (cgi-46). [swissprot;acc:q9y230]	1.06269

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.