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

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Showing element 3180 to 3229 of 77072 in total

Filtered  : 0
Value Type  : Ranked
Network Comparison Type  : Divided

Interaction Map	Rank	network_comparison	description	green	red
High confidence	490	1.00484	dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0]	10338.7	10388.7
	491	1.00411	rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952]	21880	21970
	492	1.00394	swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5]	6829.74	6802.96
	493	1.00355	dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6]	12041.7	11999.1
	494	1.00218	signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240]	11959.4	11985.5
	495	1.00195	26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232]	11748.1	11725.2
	496	1.00186	vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670]	9411.49	9394
	497		sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633]	13718.2	13692.7
	498	1.00161	adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144]	10248.3	10231.8
	499	1.00123	inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268]	9069.58	9080.73
	500	1	huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]	394	394
	501		homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	0.00001	0.00001
	502		brca1 associated protein. [refseq;acc:nm_006768]
Low confidence	1	2.55362	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	14977	5865
	2	2.45711	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	21883	8906
	3	2.14604	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	20617	9607
	4		neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]
	5	1.82499	ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]	19873	10889.4
	6	1.71877	trinucleotide repeat containing 15. [refseq;acc:nm_015575]	9583.37	5575.71
	7	1.69451	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	6812	11543
	8	1.68629	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	13216	22286
	9		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]
	10		homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]
	11	1.66289	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	8257	13730.5
	12	1.65028	anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801]	1933	3190
	13	1.63963	sorbitol dehydrogenase (ec 1.1.1.14) (l-iditol 2-dehydrogenase). [swissprot;acc:q00796]	12191.6	7435.56
	14	1.60673	ptd016 protein. [refseq;acc:nm_016125]	11234	18050
	15	1.5892	adenomatous polyposis coli like. [refseq;acc:nm_005883]	7597.61	12074.1
	16	1.57201	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	11625	7395
	17	1.53462	leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735]	5266.67	8082.33
	18	1.52187	early hematopoietic zinc finger. [refseq;acc:nm_015461]	8903.28	5850.23
	19	1.5182	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	4871.6	3208.8
	20	1.4984	guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4]	14964	22422
	21	1.49458	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]	2582	3859
	22	1.46371	cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [swissprot;acc:q9ubr2]	7867	11515
	23	1.44743	serpin b12. [swissprot;acc:q96p63]	21138.6	14604.2
	24	1.44694	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	21113.7	14592
	25	1.42278	nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718]	6909	9830
	26	1.42223	folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932]	6526.57	9282.29
	27	1.41246	camp-regulated phosphoprotein 19 (arpp-19) [contains: camp-regulated phosphoprotein 16 (arpp-16)]. [swissprot;acc:p56211]	18516	13109
	28	1.40082	elongation of very long chain fatty acids protein 2. [swissprot;acc:q9nxb9]	11505	16116.4
	29	1.39628	solute carrier family 12 (potassium/chloride transporters), member 9; cation-chloride cotransporter-interacting protein. [refseq;acc:nm_020246]	8687.07	12129.6
	30	1.39185	alpha 2 globin. [refseq;acc:nm_000517]	15987.1	11486.2
	31	1.39168	hemoglobin gamma-a and gamma-g chains. [swissprot;acc:p02096]	15984.3	11485.6
	32	1.39162	myoglobin. [swissprot;acc:p02144]	15983.3	11485.4
	33	1.37827	fk506-binding protein 6 (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (36 kda fk506 binding protein) (fkbp- 36) (immunophilin fkbp36). [swissprot;acc:o75344]	14746.1	20324.1
	34	1.37724	fibrillin 3. [refseq;acc:nm_032447]	7506.66	5450.5
	35	1.37553	protein tyrosine phosphatase type iva, member 2 isoform 1; protein tyrosine phosphatase iva2; protein tyrosine phosphatase iva; phosphatase of regenerating liver 2. [refseq;acc:nm_003479]	16243	11808.5
	36	1.37097	sam-domain protein samsn-1 (sam domain, sh3 domain and nuclear localisation signals protein 1). [swissprot;acc:q9nsi8]	9520.8	13052.7
	37	1.36786	myotubularin related protein 8. [refseq;acc:nm_017677]	8993.6	12302

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.