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 1458 to 1507 of 3228 in total

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

red	green	Rank	description	network_comparison
5473.09	5887.45	1470	ornithine aminotransferase, mitochondrial precursor (ec 2.6.1.13) (ornithine--oxo-acid aminotransferase). [swissprot;acc:p04181]	1.07571
5475.44	5127.66	1728	ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6]	1.06782
5475.74	5800.97	1978	uv excision repair protein rad23 homolog a (hhr23a). [swissprot;acc:p54725]	1.05939
		1979	26s proteasome non-atpase regulatory subunit 4 (26s proteasome regulatory subunit s5a) (rpn10) (multiubiquitin chain binding protein) (antisecretory factor-1) (af) (asf). [swissprot;acc:p55036]
		1981	inositol polyphosphate 5-phosphatase ocrl-1 (ec 3.1.3.36) (lowe's oculocerebrorenal syndrome protein). [swissprot;acc:q01968]
		1982	uv excision repair protein rad23 homolog b (hhr23b) (xp-c repair complementing complex 58 kda protein) (p58). [swissprot;acc:p54727]
		1983	myosin vi. [swissprot;acc:q9um54]
5480.24	6222.04	560	cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520]	1.13536
		561	transforming protein rhoc (h9). [swissprot;acc:p08134]
		562	thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762]
		563	3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325]
		564	transforming protein rhoa (h12). [swissprot;acc:p06749]
5488.7	5131.89	1655	40s ribosomal protein s26. [swissprot;acc:p02383]	1.06953
		1656	mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584]
		1657	atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691]
		1659	ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [swissprot;acc:p14927]
5489.18	5972.09	1158	delta-aminolevulinic acid dehydratase (ec 4.2.1.24) (porphobilinogen synthase) (aladh). [swissprot;acc:p13716]	1.08797
5489.99	5986.63	1106	peptide methionine sulfoxide reductase (ec 1.8.4.6) (protein- methionine-s-oxide reductase) (peptide met(o) reductase). [swissprot;acc:q9uj68]	1.09046
		1107	phosphoserine aminotransferase (ec 2.6.1.52) (psat). [swissprot;acc:q9y617]
5490.24	5838.67	1882	eukaryotic translation initiation factor 2 subunit 3 (eukaryotic translation initiation factor 2 gamma subunit) (eif-2-gamma). [swissprot;acc:p41091]	1.06346
5493.1	6350.19	418	breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872]	1.15603
		419	cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253]
5494.73	6001.08	1069	elongation factor 2 (ef-2). [swissprot;acc:p13639]	1.09215
		1070	metabotropic glutamate receptor 2 precursor (mglur2). [swissprot;acc:q14416]
		1071	metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832]
5497.73	5132.35	1611	cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642]	1.07119
5500.92	5949.26	1305	glutaminyl-trna synthetase (ec 6.1.1.18) (glutamine--trna ligase) (glnrs). [swissprot;acc:p47897]	1.0815
		1306	spermidine synthase (ec 2.5.1.16) (putrescine aminopropyltransferase) (spdsy). [swissprot;acc:p19623]
		1307	glycyl-trna synthetase (ec 6.1.1.14) (glycine--trna ligase) (glyrs). [swissprot;acc:p41250]
		1308	glutamyl trna synthetase. [sptrembl;acc:o14563]
5501.3	5866.02	1795	dna-directed rna polymerases iii 12.5 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c11 subunit) (hsc11p) (hrpc11) (my010 protein). [swissprot;acc:q9y2y1]	1.0663
5502.5	5721.43	2394	trifunctional purine biosynthetic protein adenosine-3 [includes: phosphoribosylamine--glycine ligase (ec 6.3.4.13) (gars) (glycinamide ribonucleotide synthetase) (phosphoribosylglycinamide synthetase); phosphoribosylformylglycinamidine cyclo-ligase (ec 6.3.3.1) (airs) (phosphoribosyl-aminoimidazole synthetase) (air synthase); phosphoribosylglycinamide formyltransferase (ec 2.1.2.2) (gart) (gar transformylase) (5'-phosphoribosylglycinamide transformylase)]. [swissprot;acc:p22102]	1.03979
5509.89	6029.29	1026	phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871]	1.09427
5511.2	6054.71	922	tubulin-tyrosine ligase. [refseq;acc:nm_153712]	1.09862
5511.96	6031.95	1025	phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [swissprot;acc:o15305]	1.09434
5514.19	5871.64	1812	hrd1 protein isoform a; synoviolin1. [refseq;acc:nm_032431]	1.06482
5514.81	5755.1	2359	signal transducer and activator of transcription 1-alpha/beta (transcription factor isgf-3 components p91/p84). [swissprot;acc:p42224]	1.04357
5514.83	5755.14	2358	signal transducer and activator of transcription 4. [swissprot;acc:q14765]	1.04358
5514.85	5755.17	2357	signal transducer and activator of transcription 3 (acute-phase response factor). [swissprot;acc:p40763]
5515.12	5755.63	2356	signal transducer and activator of transcription 6 (il-4 stat). [swissprot;acc:p42226]	1.04361
5516.67	5758.22	2354	signal transducer and activator of transcription 5a. [swissprot;acc:p42229]	1.04379
5516.82	5758.48	2353	signal transducer and activator of transcription 5b. [swissprot;acc:p51692]	1.0438
5516.89	5844.37	1985	scribble. [refseq;acc:nm_015356]	1.05936
5517.24	5844.68	1986	lap (leucine-rich repeats and pdz) and no pdz protein. [refseq;acc:nm_018214]	1.05935
5520.26	5841.16	2022	enthoprotin; epsin 4; clathrin interacting protein localized in the trans-golgi region. [refseq;acc:nm_014666]	1.05813
5520.36	5911.98	1621	sterile alpha and tir motif containing 1; sterile alpha and heat/armadillo motif protein, ortholog of drosophila. [refseq;acc:nm_015077]	1.07094
5521.07	5856.93	1941	rac gtpase activating protein 1; gtpase activating protein. [refseq;acc:nm_013277]	1.06083
5528.65	5985.58	1271	mitotic checkpoint serine/threonine-protein kinase bub1 beta (ec 2.7.1.-) (hbubr1) (mad3/bub1-related protein kinase) (mitotic checkpoint kinase mad3l). [swissprot;acc:o60566]	1.08265
		1272	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]
5534.46	5684.97	2496	solute carrier family 35, member b1; udp-galactose transporter related. [refseq;acc:nm_005827]	1.0272

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.