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

Results: HTML CSV LaTeX

Showing element 51 to 100 of 38536 in total

Filtered	0
Value Type	Measured
Network Comparison Type	Divided

Rank	description	green	Interaction Map	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]	662	High confidence	153	4.3268	
26	glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [source:swissprot;acc:p46926]	47	Low confidence	143	3.04255	
27	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [source:refseq;acc:nm_030801]	35.5	Low confidence	105.5	2.97183	
27	phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [source:swissprot;acc:p11086]	139	High confidence	570	4.10072	
28	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [source:refseq;acc:nm_031938]	139	High confidence	570	4.10072	
28	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [source:swissprot;acc:p43357]	35.5	Low confidence	105.5	2.97183	
29	melanoma-associated antigen 11 (mage-11 antigen). [source:swissprot;acc:p43364]	35.5	Low confidence	105.5	2.97183	
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]	434.911	High confidence	111.278	3.90833	
30	dystrophin. [source:swissprot;acc:p11532]	111.739	High confidence	427.217	3.82335	
30	melanoma-associated antigen 2 (mage-2 antigen). [source:swissprot;acc:p43356]	35.5	Low confidence	105.5	2.97183	
31	dok-like protein. [source:refseq;acc:nm_024872]	0.00001	High confidence	35	3500000	
31	hepatocellular carcinoma-associated protein hca1. [source:refseq;acc:nm_020932]	35.5	Low confidence	105.5	2.97183	
32	cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [source:swissprot;acc:p49336]	184	High confidence	598	3.25	
32	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [source:swissprot;acc:p43360]	35.5	Low confidence	105.5	2.97183	
33	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [source:refseq;acc:nm_003893]	39.8063	High confidence	12.6208	3.15402	
33	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [source:swissprot;acc:q9y5v3]	35.5	Low confidence	105.5	2.97183	
34	glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [source:swissprot;acc:p46926]	47	High confidence	143	3.04255	
34	melanoma-associated antigen f1 (mage-f1 antigen). [source:swissprot;acc:q9hay2]	35.5	Low confidence	105.5	2.97183	
35	adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [source:swissprot;acc:p12236]	1377	High confidence	459.5	2.99674	
35	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [source:swissprot;acc:p43358]	35.5	Low confidence	105.5	2.97183	
36	heparan sulfate 6-o-sulfotransferase 2. [source:refseq;acc:nm_147174]	56	High confidence	157	2.80357	
36	melanoma-associated antigen 9 (mage-9 antigen). [source:swissprot;acc:p43362]	35.5	Low confidence	105.5	2.97183	
37	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	934.348	High confidence	334.401	2.79409	
37	melanoma-associated antigen 8 (mage-8 antigen). [source:swissprot;acc:p43361]	35.5	Low confidence	105.5	2.97183	
38	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [source:swissprot;acc:o60732]	35.5	Low confidence	105.5	2.97183	
38	zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [source:swissprot;acc:o43623]	120.429	High confidence	320.012	2.65727	
39	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [source:swissprot;acc:p43365]	35.5	Low confidence	105.5	2.97183	
39	microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [source:refseq;acc:nm_014268]	192.295	High confidence	482.426	2.50878	
40	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [source:swissprot;acc:p43355]	35.5	Low confidence	105.5	2.97183	
40	nanos (fragment). [source:sptrembl;acc:q8wy41]	151	High confidence	377	2.49669	
41	melanoma-associated antigen 10 (mage-10 antigen). [source:swissprot;acc:p43363]	35.5	Low confidence	105.5	2.97183	
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]	645	High confidence	266	2.42481	
42	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [source:swissprot;acc:p43366]	35.5	Low confidence	105.5	2.97183	
42	presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [source:refseq;acc:nm_172341]	86.9525	High confidence	205.439	2.36266	
43	elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [source:swissprot;acc:p43897]	587.988	High confidence	263.66	2.2301	
43	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]	35.5	Low confidence	105.5	2.97183	
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]	98.5074	High confidence	45.4292	2.16837	
44	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [source:swissprot;acc:p46531]	0.00001	Low confidence	286	28600000	
45	neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [source:swissprot;acc:q04721]	0.00001	Low confidence	286	28600000	
45	tigger transposable element derived 6. [source:refseq;acc:nm_030953]	438.605	High confidence	202.374	2.1673	
46	ephrin type-b receptor 4 precursor (ec 2.7.1.112) (tyrosine-protein kinase receptor htk). [source:swissprot;acc:p54760]	67	Low confidence	24	2.79167	
46	tigger transposable element derived 7; jerky (mouse) homolog-like. [source:refseq;acc:nm_033208]	438.035	High confidence	202.163	2.16674	
47	tenascin-x precursor (tn-x) (hexabrachion-like). [source:swissprot;acc:p22105]	776.89	Low confidence	310.103	2.50526	
47	tigger transposable element derived 1; jerky (mouse) homolog-like. [source:refseq;acc:nm_145702]	438.016	High confidence	202.156	2.16672	
48	deltex homolog 1; hdx-1. [source:refseq;acc:nm_004416]	403.196	High confidence	870.482	2.15895	
48	pnas-129. [source:sptrembl;acc:q9bxv8]	151.073	Low confidence	366.666	2.42708	
49	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]	645	Low confidence	266	2.42481	
49	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [source:swissprot;acc:q99611]	151	High confidence	72	2.09722	
50	latrophilin 2; lectomedin-1; latrophilin homolog 2 (cow). [source:refseq;acc:nm_012302]	111	Low confidence	262	2.36036	
50	transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [source:swissprot;acc:p15884]	21	High confidence	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/