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 2401 to 2450 of 3228 in total

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

red	green	Rank	description	network_comparison
6228.97	7013.53	635	ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8]	1.12595
6229.16	6742.79	1283	orphan nuclear receptor nurr1 (immediate-early response protein not) (transcriptionally inducible nuclear receptor). [swissprot;acc:p43354]	1.08246
6229.69	6829.58	988	ubiquitin-conjugating enzyme e2 n (ec 6.3.2.19) (ubiquitin-protein ligase n) (ubiquitin carrier protein n) (ubc13) (bendless-like ubiquitin conjugating enzyme). [swissprot;acc:q16781]	1.0963
6230.21	6608.64	1945	cofilin, non-muscle isoform (18 kda phosphoprotein) (p18). [swissprot;acc:p23528]	1.06074
		1946	cofilin, muscle isoform (cofilin 2). [swissprot;acc:q9y281]
		1948	destrin (actin-depolymerizing factor) (adf). [swissprot;acc:p18282]
		1949	ubiquitin fusion degradation protein 1 homolog (ub fusion protein 1). [swissprot;acc:q92890]
6230.38	6744.35	1282	nuclear hormone receptor nor-1 (neuron-derived orphan receptor 1) (mitogen induced nuclear orphan receptor). [swissprot;acc:q92570]	1.08249
6230.49	6744.5	1281	orphan nuclear receptor hmr (early response protein nak1) (tr3 orphan receptor). [swissprot;acc:p22736]	1.0825
6230.94	7168.2	436	arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069]	1.15042
6231.31	6933.9	762	pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278]	1.11275
6237.83	6400.74	2505	succinate dehydrogenase [ubiquinone] iron-sulfur protein, mitochondrial precursor (ec 1.3.5.1) (ip) (iron-sulfur subunit of complex ii). [swissprot;acc:p21912]	1.02612
6239.69	6378.35	2544	peroxiredoxin 5, mitochondrial precursor (prx-v) (peroxisomal antioxidant enzyme) (plp) (thioredoxin peroxidase pmp20) (antioxidant enzyme b166) (aoeb166) (tpx type vi) (liver tissue 2d-page spot 71b) (alu co-repressor 1) (sbbi10). [swissprot;acc:p30044]	1.02222
6245.32	6534.23	2257	sr rich protein. [refseq;acc:nm_032870]	1.04626
6251.32	6774.12	1258	glutamate carboxypeptidase-like protein 2 precursor. [swissprot;acc:q96kn2]	1.08363
6251.91	7192.08	440	calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632]	1.15038
6251.96	7192.13	441	grancalcin. [swissprot;acc:p28676]
6251.99	7192.17	442	sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626]
6252.27	7192.51	443	brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732]
6252.58	7192.88	438	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	6415.04	2511	integral membrane protein cii-3b. [sptrembl;acc:o75609]	1.02535
6256.49	6415.21	2510	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	6711.4	1564	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	6932.95	821	trna isopentenylpyrophosphate transferase. [refseq;acc:nm_017646]	1.10786
6259.3	7190.91	448	ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385]	1.14884
6259.8	6684.3	1730	phospholipid scramblase 4 (pl scramblase 4) (ca(2+)-dependent phospholipid scramblase 4). [swissprot;acc:q9nrq2]	1.06781
	6684.31	1729	phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6]	1.06782
6260.43	6685.05	1727	phospholipid scramblase 2 (pl scramblase 2) (ca(2+)-dependent phospholipid scramblase 2). [swissprot;acc:q9nry7]	1.06783
6262.66	6652.85	1920	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	6668.72	1849	arginase ii, mitochondrial precursor (ec 3.5.3.1) (non-hepatic arginase) (kidney-type arginase). [swissprot;acc:p78540]	1.06394
6268.94	6755.57	1408	serologically defined colon cancer antigen 16. [refseq;acc:nm_006649]	1.07763
6270.67	6823.73	1155	transducin-like enhancer protein 4. [swissprot;acc:q04727]	1.0882
6271.17	6670.97	1852	arginase 1 (ec 3.5.3.1) (liver-type arginase). [swissprot;acc:p05089]	1.06375
6272.91	7226.06	429	vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504]	1.15195
6274.62	6760.78	1410	delta-interacting protein a (hepatitis delta antigen interacting protein a). [swissprot;acc:q15834]	1.07748
6275.86	6803.95	1248	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	6934.8	844	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	6807.51	1247	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	6837.01	1149	transducin-like enhancer protein 3 (esg3). [swissprot;acc:q04726]	1.08857
6281.21	6837.61	1143	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	6845.28	1125	transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724]	1.08879
6288.27	6846.97	1124	transducin-like enhancer protein 2 (esg2). [swissprot;acc:q04725]	1.08885
6289.72	6911.96	915	cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229]	1.09893

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.