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

Results: HTML CSV LaTeX

Showing element 51 to 100 of 3730 in total

Value Type	Measured
Network Comparison Type	Divided
Interaction Map	High confidence

Rank	description	Filtered	green	red	network_comparison	
26	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [source:refseq;acc:nm_013402]	0	662	153	4.3268	
26	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [source:swissprot;acc:q9ubi6]	1	892.67	1833.01	2.0534	
27	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [source:swissprot;acc:p50150]	1	895.134	1834.33	2.04922	
27	phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [source:swissprot;acc:p11086]	0	139	570	4.10072	
28	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [source:refseq;acc:nm_031938]	0	139	570	4.10072	
28	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [source:swissprot;acc:p29798]	1	895.194	1834.36	2.04912	
29	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [source:swissprot;acc:q9uk08]	1	895.507	1834.52	2.04858	
29	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [source:refseq;acc:nm_012281]	0	434.911	111.278	3.90833	
30	dystrophin. [source:swissprot;acc:p11532]	0	111.739	427.217	3.82335	
30	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [source:swissprot;acc:p30670]	1	895.633	1834.59	2.04837	
31	dok-like protein. [source:refseq;acc:nm_024872]	0	0.00001	35	3500000	
31	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [source:swissprot;acc:p50151]	1	895.697	1834.63	2.04827	
32	cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [source:swissprot;acc:p49336]	0	184	598	3.25	
32	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [source:swissprot;acc:q9y3k8]	1	895.893	1834.73	2.04793	
33	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [source:swissprot;acc:p50152]	1	896.972	1835.3	2.04611	
33	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [source:refseq;acc:nm_003893]	0	39.8063	12.6208	3.15402	
34	glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [source:swissprot;acc:p46926]	0	47	143	3.04255	
34	guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [source:swissprot;acc:p29992]	1	907.546	1836.71	2.02382	
35	adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [source:swissprot;acc:p12236]	0	1377	459.5	2.99674	
35	guanine nucleotide-binding protein g(q), alpha subunit. [source:swissprot;acc:p50148]	1	907.564	1836.71	2.02378	
36	guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [source:swissprot;acc:p19086]	1	907.741	1836.76	2.02344	
36	heparan sulfate 6-o-sulfotransferase 2. [source:refseq;acc:nm_147174]	0	56	157	2.80357	
37	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	0	934.348	334.401	2.79409	
37	guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [source:swissprot;acc:p11488]	1	907.763	1836.76	2.02339	
38	guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [source:swissprot;acc:p19087]	1	907.774	1836.76	2.02337	
38	zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [source:swissprot;acc:o43623]	0	120.429	320.012	2.65727	
39	guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [source:swissprot;acc:p04899]	1	907.903	1836.8	2.02312	
39	microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [source:refseq;acc:nm_014268]	0	192.295	482.426	2.50878	
40	guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [source:swissprot;acc:p04898]	1	907.978	1836.81	2.02297	
40	nanos (fragment). [source:sptrembl;acc:q8wy41]	0	151	377	2.49669	
41	guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [source:swissprot;acc:p08754]	1	907.978	1836.81	2.02297	
41	nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [source:swissprot;acc:q16718]	0	645	266	2.42481	
42	guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [source:swissprot;acc:o14775]	1	958.237	1857.32	1.93827	
42	presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [source:refseq;acc:nm_172341]	0	86.9525	205.439	2.36266	
43	elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [source:swissprot;acc:p43897]	0	587.988	263.66	2.2301	
43	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [source:swissprot;acc:p16520]	1	1027.36	1881.02	1.83093	
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). [source:swissprot;acc:p45954]	0	98.5074	45.4292	2.16837	
44	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [source:swissprot;acc:p04901]	1	1057.39	1931.34	1.82652	
45	guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [source:swissprot;acc:q9hav0]	1	1056.02	1926.69	1.82448	
45	tigger transposable element derived 6. [source:refseq;acc:nm_030953]	0	438.605	202.374	2.1673	
46	neurogenic differentiation factor 2 (neurod2). [source:swissprot;acc:q15784]	1	1390.33	779.167	1.78438	
46	tigger transposable element derived 7; jerky (mouse) homolog-like. [source:refseq;acc:nm_033208]	0	438.035	202.163	2.16674	
47	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [source:swissprot;acc:q12873]	1	1390.33	779.167	1.78438	
47	tigger transposable element derived 1; jerky (mouse) homolog-like. [source:refseq;acc:nm_145702]	0	438.016	202.156	2.16672	
48	deltex homolog 1; hdx-1. [source:refseq;acc:nm_004416]	0	403.196	870.482	2.15895	
48	doc-1 related protein (doc-1r). [source:swissprot;acc:o75956]	1	1390.33	779.167	1.78438	
49	neurogenic differentiation factor 6 (neurod6) (my051 protein). [source:swissprot;acc:q96nk8]	1	1390.33	779.167	1.78438	
49	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [source:swissprot;acc:q99611]	0	151	72	2.09722	
50	neurogenic differentiation factor 1 (neurod1) (neurod). [source:swissprot;acc:q13562]	1	1390.33	779.167	1.78438	
50	transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [source:swissprot;acc:p15884]	0	21	44	2.09524	

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/