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	Value Type	Gene	red	Rank	description	green	Interaction Map	network_comparison	Filtered

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Showing element 501 to 550 of 29840 in total

Network Comparison Type  : Divided
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 0

red	Rank	description	green	network_comparison
30	81	transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084]	50	1.66667
31	118	methyltransferase like 2. [refseq;acc:nm_018396]	43	1.3871
31.1429	63	spir-2 protein (fragment). [sptrembl;acc:q8wwl2]	56.278	1.80709
34.6667	90	metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832]	54.6667	1.57692
35	31	dok-like protein. [refseq;acc:nm_024872]	0.00001	3500000
39.7924	91	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931]	62.2106	1.56338
42	130	maspin precursor (protease inhibitor 5). [swissprot;acc:p36952]	56	1.33333
	131	serpin b11. [swissprot;acc:q96p15]
	132	cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452]
44	50	transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884]	21	2.09524
45.4292	44	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]	98.5074	2.16837
47.4756	60	adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377]	87.5499	1.8441
48	350	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	51	1.0625
	351	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]
	352	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]
	353	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]
	354	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]
	355	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]
	356	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]
	357	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]
	358	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]
	359	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]
	360	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]
	361	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]
	362	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]
	363	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]
	364	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]
	365	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]
	366	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1]
55.3059	86	alpha crystallin a chain. [swissprot;acc:p02489]	89.2447	1.61366
60	22	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	0.00001	6000000
65.2968	73	protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]	37.693	1.73233
72	49	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]	151	2.09722
81.504	128	mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650]	60.8613	1.33918
82	20	ero1-like. [refseq;acc:nm_014584]	0.00001	8200000
85	9	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	6410	75.4118
	10	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]
86	127	lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428]	64	1.34375
93.5	209	small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [swissprot;acc:p14678]	111	1.18717
100	109	dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9]	144	1.44
100.5	432	high-glucose-regulated protein 8 (ny-ren-2 antigen). [swissprot;acc:q9y5a9]	103.25	1.02736
	433	sh3 adapter protein spin90 (sh3 protein interacting with nck, 90 kda) (vaca-interacting protein, 54 kda) (vip54) (af3p21) (diaphanous protein interacting protein) (dia interacting protein-1) (dip-1). [swissprot;acc:q9nzq3]
107	122	sh2-b homolog; likely ortholog of mouse sh2 domain-containing putative adapter sh2-b; sh2-b gamma signaling protein; sh2-b alpha signaling protein. [refseq;acc:nm_015503]	78	1.37179
111.278	29	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	434.911	3.90833
112.666	170	williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645]	141.702	1.25772
	171	williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [refseq;acc:nm_018044]
	172	williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158]
118.878	21	syntaxin 10 (syn10). [swissprot;acc:o60499]	17.6611	6.73106
125.5	194	transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193]	103.5	1.21256
130.512	14	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	6.50325	20.0687

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.