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

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Showing element 2418 to 2467 of 3228 in total

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

red	Rank	green	description	network_comparison
6251.99	442	7192.17	sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626]	1.15038
6252.27	443	7192.51	brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732]
6252.58	438	7192.88	swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497]	1.15039
	439		programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340]
6256.42	2511	6415.04	integral membrane protein cii-3b. [sptrembl;acc:o75609]	1.02535
6256.49	2510	6415.21	succinate dehydrogenase cytochrome b560 subunit, mitochondrial precursor (integral membrane protein cii-3) (qps1) (qps-1) (succinate dehydrogenase complex subunit c) (succinate-ubiquinone oxidoreductase cytochrome b large subunit) (cybl). [swissprot;acc:q99643]	1.02537
6257.62	1564	6711.4	proteasome subunit beta type 9 precursor (ec 3.4.25.1) (proteasome chain 7) (macropain chain 7) (multicatalytic endopeptidase complex chain 7) (ring12 protein) (low molecular mass protein 2). [swissprot;acc:p28065]	1.07252
6257.99	821	6932.95	trna isopentenylpyrophosphate transferase. [refseq;acc:nm_017646]	1.10786
6259.3	448	7190.91	ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385]	1.14884
6259.8	1729	6684.31	phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6]	1.06782
	1730	6684.3	phospholipid scramblase 4 (pl scramblase 4) (ca(2+)-dependent phospholipid scramblase 4). [swissprot;acc:q9nrq2]	1.06781
6260.43	1727	6685.05	phospholipid scramblase 2 (pl scramblase 2) (ca(2+)-dependent phospholipid scramblase 2). [swissprot;acc:q9nry7]	1.06783
6262.66	1920	6652.85	basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811]	1.0623
	1921		salivary proline-rich protein po (allele k) [contains: peptide p-d] (fragment). [swissprot;acc:p10162]
6267.93	1849	6668.72	arginase ii, mitochondrial precursor (ec 3.5.3.1) (non-hepatic arginase) (kidney-type arginase). [swissprot;acc:p78540]	1.06394
6268.94	1408	6755.57	serologically defined colon cancer antigen 16. [refseq;acc:nm_006649]	1.07763
6270.67	1155	6823.73	transducin-like enhancer protein 4. [swissprot;acc:q04727]	1.0882
6271.17	1852	6670.97	arginase 1 (ec 3.5.3.1) (liver-type arginase). [swissprot;acc:p05089]	1.06375
6272.91	429	7226.06	vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504]	1.15195
6274.62	1410	6760.78	delta-interacting protein a (hepatitis delta antigen interacting protein a). [swissprot;acc:q15834]	1.07748
6275.86	1248	6803.95	protein-tyrosine phosphatase, non-receptor type 2 (ec 3.1.3.48) (t- cell protein-tyrosine phosphatase) (tcptp). [swissprot;acc:p17706]	1.08415
6276.97	844	6934.8	preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387]	1.1048
	845		dnaj homolog subfamily b member 11 precursor (er-associated dnaj protein 3) (erj3) (er-associated hsp40 co-chaperone) (hdj9) (pwp1- interacting protein 4). [swissprot;acc:q9ubs4]
6278.76	1247	6807.51	protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031]	1.08421
6280.74	1149	6837.01	transducin-like enhancer protein 3 (esg3). [swissprot;acc:q04726]	1.08857
6281.21	1143	6837.61	homeobox protein engrailed-2 (hu-en-2). [swissprot;acc:p19622]	1.08858
	1144		cpg binding protein (protein containing phd finger and cxxc domain 1). [swissprot;acc:q9p0u4]
	1146		activator of basal transcription 1; tata-binding protein-binding protein; basal transcriptional activator. [refseq;acc:nm_013375]
	1147		cytokine-like nuclear factor n-pac. [refseq;acc:nm_032569]
	1148		hect type e3 ubiquitin ligase. [refseq;acc:nm_015052]
6287.07	1125	6845.28	transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724]	1.08879
6288.27	1124	6846.97	transducin-like enhancer protein 2 (esg2). [swissprot;acc:q04725]	1.08885
6289.72	915	6911.96	cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229]	1.09893
	916		cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243]
	917		nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387]
6291.2	2464	6486.07	dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.12) (e2) (pdc-e2) (70 kda mitochondrial autoantigen of primary biliary cirrhosis) (pbc) (m2 antigen complex 70 kda subunit). [swissprot;acc:p10515]	1.03098
6291.89	1404	6781.6	mesoderm induction early response 1. [refseq;acc:nm_020948]	1.07783
	1405		proteasome subunit alpha type 3 (ec 3.4.25.1) (proteasome component c8) (macropain subunit c8) (multicatalytic endopeptidase complex subunit c8). [swissprot;acc:p25788]
6294.37	2490	6472.9	glutathione reductase, mitochondrial precursor (ec 1.8.1.7) (gr) (grase). [swissprot;acc:p00390]	1.02836
6296.52	1620	6743.85	acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [swissprot;acc:p45954]	1.07104
6297.05	1741	6721.08	serine/threonine-protein kinase dcamkl1 (ec 2.7.1.-) (doublecortin- like and cam kinase-like 1). [swissprot;acc:o15075]	1.06734
6298.76	1742	6722.61	microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268]	1.06729
6298.77	1745	6722.62	microtubule-associated protein rp/eb family member 3 (protein eb3). [swissprot;acc:q9upy8]
6298.81	1743	6722.65	histidine-rich membrane protein ke4. [swissprot;acc:q92504]
	1744		microtubule-associated protein rp/eb family member 1 (apc-binding protein eb1). [swissprot;acc:q15691]
6301.03	1748	6724.63	doublecortin (lissencephalin-x) (lis-x) (doublin). [swissprot;acc:o43602]	1.06723
6304.21	1697	6738.77	wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6]	1.06893
	1699		rest corepressor. [refseq;acc:nm_015156]
6304.22	1696		wiskott-aldrich syndrome protein family member 2 (wasp-family protein member 2) (verprolin homology domain-containing protein 2). [swissprot;acc:q9y6w5]
	1698		wiskott-aldrich syndrome protein family member 1 (wasp-family protein member 1) (verprolin homology domain-containing protein 1). [swissprot;acc:q92558]

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.