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

Results: HTML CSV LaTeX

Showing element 475 to 524 of 14920 in total

Interaction Map	High confidence
Network Comparison Type	Divided

Rank	description	Value Type	Filtered	red	green	network_comparison	
60	glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [source:swissprot;acc:p46926]	Ranked	0	11761	15924	1.35397	
60	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [source:swissprot;acc:q9uk08]	Ranked	1	266.864	336.184	1.25976	
60	inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [source:swissprot;acc:p12268]	Squared	0	219.839	59.1928	3.71395	
60	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [source:swissprot;acc:p43360]	Squared	1	219048	129762	1.68808	
60	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [source:swissprot;acc:q99611]	Rooted	0	8.48528	12.2882	1.44818	
60	son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [source:swissprot;acc:p18583]	Rooted	1	35.6294	49.8119	1.39806	
61	adp-ribosylation factor 3. [source:swissprot;acc:p16587]	Squared	0	33.5285	123.56	3.68522	
61	glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [source:swissprot;acc:p30712]	Measured	0	324.442	593.094	1.82804	
61	glycogen phosphorylase, brain form (ec 2.4.1.1). [source:swissprot;acc:p11216]	Measured	1	4489.19	2765.82	1.6231	
61	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [source:swissprot;acc:p30670]	Ranked	1	266.864	336.182	1.25975	
61	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [source:refseq;acc:nm_014592]	Rooted	1	43.4291	31.7159	1.36932	
61	necdin. [source:swissprot;acc:q99608]	Squared	1	219048	129762	1.68808	
61	testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [source:swissprot;acc:p16562]	Ranked	0	15352	11346.5	1.35302	
61	transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [source:swissprot;acc:p15884]	Rooted	0	6.63325	4.58258	1.44749	
62	bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [source:swissprot;acc:p34820]	Rooted	0	15.0883	21.8314	1.44691	
62	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [source:refseq;acc:nm_017743]	Measured	0	210.767	384.407	1.82385	
62	elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [source:swissprot;acc:p04720]	Squared	0	21.2079	6.15501	3.44563	
62	glycine receptor alpha-3 chain precursor. [source:swissprot;acc:o75311]	Ranked	0	9418.7	12695.6	1.34791	
62	glycogen phosphorylase, liver form (ec 2.4.1.1). [source:swissprot;acc:p06737]	Measured	1	4489.19	2765.82	1.6231	
62	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [source:swissprot;acc:p50151]	Ranked	1	266.865	336.181	1.25974	
62	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [source:swissprot;acc:q9y5v3]	Squared	1	219048	129762	1.68808	
62	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [source:refseq;acc:nm_147183]	Rooted	1	43.4519	31.7522	1.36847	
63	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [source:sptrembl;acc:q8wwk2]	Rooted	0	18.1049	12.6095	1.43581	
63	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [source:swissprot;acc:q9y3k8]	Ranked	1	266.865	336.178	1.25973	
63	kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [source:refseq;acc:nm_173193]	Rooted	1	43.4554	31.7576	1.36835	
63	melanoma-associated antigen f1 (mage-f1 antigen). [source:swissprot;acc:q9hay2]	Squared	1	219048	129762	1.68808	
63	myosin xv (unconventional myosin-15). [source:swissprot;acc:q9ukn7]	Measured	1	4489.19	2765.82	1.6231	
63	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [source:swissprot;acc:p46977]	Ranked	0	8519.83	11453	1.34428	
63	protein phosphatase inhibitor 2 (ipp-2). [source:swissprot;acc:p41236]	Squared	0	1.24091	0.365145	3.3984	
63	spir-2 protein (fragment). [source:sptrembl;acc:q8wwl2]	Measured	0	31.1429	56.278	1.80709	
64	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	Rooted	1	63.8686	47.2654	1.35128	
64	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [source:swissprot;acc:p11217]	Measured	1	4489.19	2765.82	1.6231	
64	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [source:swissprot;acc:p50152]	Ranked	1	266.868	336.159	1.25965	
64	melanoma antigen, family b, 6. [source:refseq;acc:nm_173523]	Squared	1	219048	129762	1.68808	
64	muscle-specific beta 1 integrin binding protein. [source:refseq;acc:nm_014446]	Rooted	0	15.7225	22.5496	1.43422	
64	phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [source:swissprot;acc:o00750]	Measured	0	0.00001	18	1800000	
64	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [source:refseq;acc:nm_032517]	Ranked	0	15264	20387	1.33563	
64	tyrosinase-related gene segment, exon 5 (fragment). [source:sptrembl;acc:q15677]	Squared	0	50.8715	15.2519	3.33542	
65	5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [source:swissprot;acc:p17643]	Squared	0	50.642	15.1833	3.33538	
65	60s ribosomal protein l21. [source:swissprot;acc:p46778]	Rooted	0	20.5734	29.2291	1.42072	
65	e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [source:refseq;acc:nm_015409]	Ranked	0	7853.67	10406.3	1.32502	
65	glycogen phosphorylase, brain form (ec 2.4.1.1). [source:swissprot;acc:p11216]	Rooted	1	63.8686	47.2654	1.35128	
65	guanine nucleotide-binding protein g(q), alpha subunit. [source:swissprot;acc:p50148]	Ranked	1	267.136	336.077	1.25807	
65	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [source:swissprot;acc:p43358]	Squared	1	219048	129762	1.68808	
65	neuralized-like. [source:refseq;acc:nm_004210]	Measured	1	1657.68	2690.25	1.6229	
65	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [source:refseq;acc:nm_007372]	Measured	0	18	0.00001	1800000	
66	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [source:sptrembl;acc:q8wwk2]	Squared	0	1797.76	558.241	3.2204	
66	glycogen phosphorylase, liver form (ec 2.4.1.1). [source:swissprot;acc:p06737]	Rooted	1	63.8686	47.2654	1.35128	
66	guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [source:swissprot;acc:p29992]	Ranked	1	267.136	336.077	1.25807	
66	heparan sulfate 6-o-sulfotransferase 2. [source:refseq;acc:nm_147174]	Ranked	0	11461	15180	1.32449	

Legend:
- Rank is the rank after comparing the two networks
- 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/