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

Results: HTML CSV LaTeX

Showing element 1 to 32 of 32 in total

Rank  : 22

description	Value Type	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison
adenomatous polyposis coli like. [refseq;acc:nm_005883]	Ranked	Subtracted	Low confidence	0	12074.1	7597.61	4476.49
carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615]	Measured	Divided			37	0.00001	3700000
cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [swissprot;acc:q9ubr2]	Ranked				11515	7867	1.46371
cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336]	Rooted	Subtracted	High confidence		24.454	13.5647	10.8893
cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	Squared	Divided	Low confidence	1	80340.8	57685.7	1.39273
cytochrome p450 24a1, mitochondrial precursor (ec 1.14.-.-) (p450- cc24) (vitamin d(3) 24-hydroxylase) (1,25-dihydroxyvitamin d(3) 24- hydroxylase) (24-ohase). [swissprot;acc:q07973]	Measured				3126.88	3997.02	1.27828
dual specificity mitogen-activated protein kinase kinase 4 (ec 2.7.1.-) (map kinase kinase 4) (jnk activating kinase 1) (c-jun n- terminal kinase kinase 1) (jnkk) (sapk/erk kinase 1) (sek1). [swissprot;acc:p45985]	Ranked	Subtracted			210.241	246.125	35.884
fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	Rooted	Divided		0	12.3693	25.7294	2.0801
glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]	Ranked		High confidence	1	185.678	245.247	1.32082
glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488]	Squared	Subtracted		0	192242	204096	11854
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	Rooted	Divided		1	40.3357	24.2915	1.66049
hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	Measured	Subtracted			23693.7	18263	5430.7
hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	Rooted		Low confidence	0	10.3085	1.2188	9.0897
implantation-associated protein. [refseq;acc:nm_032121]		Divided		1	57.2538	71.1231	1.24224
lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]	Squared			0	0.0435834	0.697197	15.9968
lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	Measured	Subtracted		1	2399.5	543.5	1856
melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	Squared		High confidence		219048	129762	89286
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	Rooted				153.578	133.176	20.402
n33 protein. [swissprot;acc:q13454]	Ranked	Divided	Low confidence		198	163	1.21472
	Rooted	Subtracted			57.2538	71.1231	13.8693
probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185]	Squared			0	70246.6	78378.5	8131.9
protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	Ranked		High confidence	1	322	253	69
protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	Measured	Divided			677.5	1865.5	2.75351
	Squared				108.641	823.69	7.58176
protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]				0	0.000236686	0.0532544	225
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	Ranked				20989	12479	1.68195
retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246]	Squared	Subtracted	Low confidence	1	122475	159767	37292
similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	Measured	Divided	High confidence	0	60	0.00001	6000000
sorbitol dehydrogenase (ec 1.1.1.14) (l-iditol 2-dehydrogenase). [swissprot;acc:q00796]		Subtracted	Low confidence		4821.65	4100.24	721.41
succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521]	Rooted	Divided	High confidence		3.16228	12.49	3.94968
transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268]	Measured	Subtracted			31122	30022.4	1099.6
ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	Ranked				5510.5	11965.7	6455.2

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.