Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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

Results: HTML CSV LaTeX

Showing element 651 to 700 of 77072 in total

Rank	description	Value Type	Network Comparison Type	Interaction Map	Filtered	green	red	network_comparison
21	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]	Squared	Divided	High confidence	1	823.69	108.641	7.58176
	gbp protein isoform a. [refseq;acc:nm_017870]	Ranked	Subtracted			256.492	325.586	69.094
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6]	Rooted	Divided			24.2744	40.3337	1.66157
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Squared	Subtracted	Low confidence		159767	122475	37292
	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	Ranked		High confidence	0	21113.7	14592	6521.7
	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Measured			1	18263	23693.7	5430.7
	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	Squared			1	129762	219048	89286
	myoglobin. [swissprot;acc:p02144]	Ranked		Low confidence	0	15983.3	11485.4	4497.9
	myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]	Ranked	Divided	High confidence	1	245.247	185.678	1.32082
	n33 protein. [swissprot;acc:q13454]	Rooted		Low confidence		71.1231	57.2538	1.24224
	phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326]	Ranked				163	198	1.21472
		Rooted	Subtracted			71.1231	57.2538	13.8693
	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	Measured	Divided		0	434.911	111.278	3.90833
	protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]	Squared	Subtracted		0	20593.3	12337.8	8255.5
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Squared	Divided		1	134787	189688	1.40732
	serpin b12. [swissprot;acc:q96p63]	Rooted	Subtracted		0	1.18697	10.2928	9.10583
	spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6]	Measured	Subtracted			3321.82	4088.01	766.19
	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]	Squared	Divided	High confidence		5.76	0.0236686	243.36
	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]	Measured	Subtracted			5690.63	6804.88	1114.25
		Squared	Subtracted			28034.4	40674.4	12640
	syntaxin 10 (syn10). [swissprot;acc:o60499]	Measured	Divided			17.6611	118.878	6.73106
	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	Ranked	Subtracted	Low confidence	1	258.33	296.837	38.507
22	adenomatous polyposis coli like. [refseq;acc:nm_005883]	Ranked	Subtracted		0	7597.61	12074.1	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			0.00001	37	3700000
	cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [swissprot;acc:q9ubr2]	Ranked	Divided			7867	11515	1.46371
	cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336]	Rooted	Subtracted	High confidence		13.5647	24.454	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	57685.7	80340.8	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	Divided			3997.02	3126.88	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			246.125	210.241	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	25.7294	12.3693	2.0801
	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]	Ranked	Divided	High confidence	1	245.247	185.678	1.32082
	glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488]	Squared	Subtracted		0	204096	192242	11854
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	Rooted	Divided		1	24.2915	40.3357	1.66049
	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	Measured	Subtracted		1	18263	23693.7	5430.7
	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	Rooted	Subtracted	Low confidence	0	1.2188	10.3085	9.0897
	implantation-associated protein. [refseq;acc:nm_032121]	Rooted	Divided		1	71.1231	57.2538	1.24224
	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]	Squared	Divided		0	0.697197	0.0435834	15.9968
	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	Measured	Subtracted		1	543.5	2399.5	1856
	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	Squared		High confidence		129762	219048	89286
	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	Rooted		High confidence		133.176	153.578	20.402
	n33 protein. [swissprot;acc:q13454]	Ranked	Divided	Low confidence		163	198	1.21472
	n33 protein. [swissprot;acc:q13454]	Rooted	Subtracted			71.1231	57.2538	13.8693
	probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185]	Squared			0	78378.5	70246.6	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	253	322	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			1865.5	677.5	2.75351
		Squared				823.69	108.641	7.58176
	protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]	Squared			0	0.0532544	0.000236686	225
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	Ranked			0	12479	20989	1.68195
	retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246]	Squared	Subtracted	Low confidence	1	159767	122475	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	0.00001	60	6000000

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.

- http://analysis.yellowcouch.org/