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 Network Comparison Type Interaction Map Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 475 to 524 of 25824 in total

Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison	
60	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [source:swissprot;acc:q9uk08]	Ranked	Divided	266.864	336.184	1.25976	
60	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [source:swissprot;acc:p43360]	Squared	Divided	219048	129762	1.68808	
60	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [source:swissprot;acc:o60732]	Rooted	Subtracted	137.446	120.823	16.623	
60	protein phosphatase inhibitor 2 (ipp-2). [source:swissprot;acc:p41236]	Squared	Subtracted	192904	126167	66737	
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	Divided	35.6294	49.8119	1.39806	
60	ubiquitin activating enzyme e1-like protein. [source:refseq;acc:nm_006395]	Measured	Subtracted	16771.5	12889.1	3882.4	
61	beta-arrestin 2 (arrestin, beta 2). [source:swissprot;acc:p32121]	Measured	Subtracted	6475.5	10307.5	3832	
61	glycogen phosphorylase, brain form (ec 2.4.1.1). [source:swissprot;acc:p11216]	Measured	Divided	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	Divided	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	Divided	43.4291	31.7159	1.36932	
61	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [source:swissprot;acc:p43365]	Rooted	Subtracted	137.446	120.823	16.623	
61	necdin. [source:swissprot;acc:q99608]	Squared	Divided	219048	129762	1.68808	
61	potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [source:refseq;acc:nm_004980]	Ranked	Subtracted	269.248	327.642	58.394	
61	type 1 protein phosphatase inhibitor. [source:refseq;acc:nm_025210]	Squared	Subtracted	192779	126095	66684	
62	beta-arrestin 1 (arrestin, beta 1). [source:swissprot;acc:p49407]	Measured	Subtracted	6475.5	10307.5	3832	
62	glycogen phosphorylase, liver form (ec 2.4.1.1). [source:swissprot;acc:p06737]	Measured	Divided	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	Divided	266.865	336.181	1.25974	
62	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [source:swissprot;acc:p43355]	Rooted	Subtracted	137.446	120.823	16.623	
62	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [source:swissprot;acc:q9y5v3]	Squared	Divided	219048	129762	1.68808	
62	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [source:refseq;acc:nm_147183]	Rooted	Divided	43.4519	31.7522	1.36847	
62	potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [source:refseq;acc:nm_004979]	Ranked	Subtracted	269.23	327.601	58.371	
62	ribosome biogenesis regulatory protein homolog. [source:swissprot;acc:q15050]	Squared	Subtracted	189976	124480	65496	
63	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [source:swissprot;acc:q9y3k8]	Ranked	Divided	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	Divided	43.4554	31.7576	1.36835	
63	melanoma-associated antigen 10 (mage-10 antigen). [source:swissprot;acc:p43363]	Rooted	Subtracted	137.446	120.823	16.623	
63	melanoma-associated antigen f1 (mage-f1 antigen). [source:swissprot;acc:q9hay2]	Squared	Divided	219048	129762	1.68808	
63	myosin xv (unconventional myosin-15). [source:swissprot;acc:q9ukn7]	Measured	Divided	4489.19	2765.82	1.6231	
63	nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [source:swissprot;acc:q13952]	Ranked	Subtracted	260.532	204.309	56.223	
63	serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [source:swissprot;acc:p08129]	Squared	Subtracted	189976	124480	65496	
63	spermatogenesis associated 6. [source:refseq;acc:nm_019073]	Measured	Subtracted	6475.5	10307.5	3832	
64	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	Rooted	Divided	63.8686	47.2654	1.35128	
64	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [source:swissprot;acc:q01433]	Measured	Subtracted	6475.5	10307.5	3832	
64	ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [source:swissprot;acc:p23511]	Ranked	Subtracted	260.532	204.309	56.223	
64	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [source:refseq;acc:nm_052936]	Squared	Subtracted	144940	81169.7	63770.3	
64	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [source:swissprot;acc:p11217]	Measured	Divided	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	Divided	266.868	336.159	1.25965	
64	melanoma antigen, family b, 6. [source:refseq;acc:nm_173523]	Squared	Divided	219048	129762	1.68808	
64	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [source:swissprot;acc:p43366]	Rooted	Subtracted	137.446	120.823	16.623	
65	cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [source:refseq;acc:nm_001326]	Measured	Subtracted	22515.5	18702.6	3812.9	
65	glycogen phosphorylase, brain form (ec 2.4.1.1). [source:swissprot;acc:p11216]	Rooted	Divided	63.8686	47.2654	1.35128	
65	guanine nucleotide-binding protein g(q), alpha subunit. [source:swissprot;acc:p50148]	Ranked	Divided	267.136	336.077	1.25807	
65	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [source:swissprot;acc:p43358]	Squared	Divided	219048	129762	1.68808	
65	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [source:swissprot;acc:q9unf1]	Rooted	Subtracted	137.446	120.823	16.623	
65	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [source:swissprot;acc:q9gzq8]	Squared	Subtracted	144912	81155	63757	
65	neuralized-like. [source:refseq;acc:nm_004210]	Measured	Divided	1657.68	2690.25	1.6229	
65	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [source:swissprot;acc:q00007]	Ranked	Subtracted	187.457	243.678	56.221	
66	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [source:swissprot;acc:p10398]	Measured	Subtracted	17757.5	14008	3749.5	
66	glycogen phosphorylase, liver form (ec 2.4.1.1). [source:swissprot;acc:p06737]	Rooted	Divided	63.8686	47.2654	1.35128	
66	guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [source:swissprot;acc:p29992]	Ranked	Divided	267.136	336.077	1.25807	
66	melanoma-associated antigen 9 (mage-9 antigen). [source:swissprot;acc:p43362]	Squared	Divided	219048	129762	1.68808	

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/