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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

  • value_type as 'ranked' since this provides a very robust analysis method.
  • intercation map as 'high confidence'
  • network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins
  • filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

    • Navigation/Query Panel:
    Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
    Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2380 to 2429 of 3228 in total 
    Value Type	Measured
    Network Comparison Type	Divided
    Interaction Map	High confidence
    Filtered	1
    
Rank	description	red	green	network_comparison	
2380	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [source:refseq;acc:nm_003169]	3690.79	3543.33	1.04162	
2381	dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [source:swissprot;acc:o95602]	3667.94	3521.41	1.04161	
2382	hydroxyacid oxidase 2 (ec 1.1.3.15) (haox2) ((s)-2-hydroxy-acid oxidase, peroxisomal) (long chain alpha-hydroxy acid oxidase) (long- chain l-2-hydroxy acid oxidase). [source:swissprot;acc:q9nyq3]	4457.6	4642.72	1.04153	
2383	calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [source:swissprot;acc:p17655]	4164.76	4337.01	1.04136	
2384	calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [source:swissprot;acc:p07384]	4164.96	4336.92	1.04129	
2385	adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [source:swissprot;acc:p54819]	3716.43	3569.68	1.04111	
2386	60s ribosomal protein l30. [source:swissprot;acc:p04645]	3674.02	3529.35	1.04099	
2387	cell division cycle protein 23; anaphase-promoting complex subunit 8. [source:refseq;acc:nm_004661]	8265.85	7940.87	1.04092	
2388	diphosphomevalonate decarboxylase (ec 4.1.1.33) (mevalonate pyrophosphate decarboxylase) (mevalonate (diphospho)decarboxylase). [source:swissprot;acc:p53602]	4418.21	4594.87	1.03998	
2389	lipoate-protein ligase, mitochondrial precursor (ec 6.-.-.-) (lipoate biosynthesis protein) (lipoyl ligase) (lipoyltransferase). [source:swissprot;acc:q9y234]	6327.14	6579.38	1.03987	
2390	tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [source:swissprot;acc:p23258]	6327.14	6579.38	1.03987	
2391	defender against cell death 1 (dad-1). [source:swissprot;acc:p46966]	6327.14	6579.38	1.03987	
2392	t-complex 11. [source:refseq;acc:nm_018679]	6327.14	6579.38	1.03987	
2393	tubulin gamma-2 chain (gamma-2 tubulin). [source:swissprot;acc:q9nrh3]	6327.14	6579.38	1.03987	
2394	trifunctional purine biosynthetic protein adenosine-3 [includes: phosphoribosylamine--glycine ligase (ec 6.3.4.13) (gars) (glycinamide ribonucleotide synthetase) (phosphoribosylglycinamide synthetase); phosphoribosylformylglycinamidine cyclo-ligase (ec 6.3.3.1) (airs) (phosphoribosyl-aminoimidazole synthetase) (air synthase); phosphoribosylglycinamide formyltransferase (ec 2.1.2.2) (gart) (gar transformylase) (5'-phosphoribosylglycinamide transformylase)]. [source:swissprot;acc:p22102]	5502.5	5721.43	1.03979	
2395	homeobox protein otx2. [source:swissprot;acc:p32243]	5682	5905.08	1.03926	
2396	myofibrillogenesis regulator 1; trans-activated by hepatitis c virus core protein 2; likely ortholog of mouse brain protein 17. [source:refseq;acc:nm_022572]	6711.27	6974.49	1.03922	
2397	yl-1 protein (transcription factor-like 1). [source:swissprot;acc:q15906]	6707.29	6970.07	1.03918	
2398	hydroxyacylglutathione hydrolase (ec 3.1.2.6) (glyoxalase ii) (glx ii). [source:swissprot;acc:q16775]	6707.29	6970.07	1.03918	
2399	homeobox protein otx1. [source:swissprot;acc:p32242]	5691.1	5913.92	1.03915	
2400	malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [source:swissprot;acc:p40926]	4368.44	4539.34	1.03912	
2401	cone-rod homeobox protein. [source:swissprot;acc:o43186]	5694.04	5916.78	1.03912	
2402	40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [source:swissprot;acc:p08865]	5078.5	5275.76	1.03884	
2403	40s ribosomal protein s21. [source:swissprot;acc:p35265]	5078.5	5275.76	1.03884	
2404	cytoplasmic antiproteinase 3 (cap3) (cap-3) (protease inhibitor 9) (serpin b9). [source:swissprot;acc:p50453]	5078.5	5275.76	1.03884	
2405	maspin precursor (protease inhibitor 5). [source:swissprot;acc:p36952]	5078.5	5275.76	1.03884	
2406	bomapin (protease inhibitor 10) (serpin b10). [source:swissprot;acc:p48595]	5078.5	5275.76	1.03884	
2407	plasminogen activator inhibitor-2 precursor (pai-2) (placental plasminogen activator inhibitor) (monocyte arg-serpin) (urokinase inhibitor). [source:swissprot;acc:p05120]	5078.5	5275.76	1.03884	
2408	serpin b11. [source:swissprot;acc:q96p15]	5078.5	5275.76	1.03884	
2409	placental thrombin inhibitor (cytoplasmic antiproteinase) (cap) (protease inhibitor 6) (pi-6). [source:swissprot;acc:p35237]	5078.5	5275.76	1.03884	
2410	cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [source:swissprot;acc:p50452]	5078.5	5275.76	1.03884	
2411	leukocyte elastase inhibitor (lei) (monocyte/neutrophil elastase inhibitor) (m/nei) (ei). [source:swissprot;acc:p30740]	5078.5	5275.76	1.03884	
2412	dynactin 4. [source:refseq;acc:nm_032486]	4644.04	4470.47	1.03883	
2413	cytoplasmic cysteine conjugate-beta lyase; glutamine-phenylpyruvate aminotransferase. [source:refseq;acc:nm_004059]	6956.32	7223.14	1.03836	
2414	alanine aminotransferase 2; glutamic-pyruvate transaminase 2. [source:refseq;acc:nm_133443]	6956.32	7223.14	1.03836	
2415	alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [source:swissprot;acc:p24298]	6956.62	7223.09	1.0383	
2416	dr1-associated protein 1; negative cofactor 2 alpha; dr1-associated corepressor. [source:refseq;acc:nm_006442]	8048.38	7752.09	1.03822	
2417	60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [source:swissprot;acc:q9y3b7]	3598.55	3467.65	1.03775	
2418	60s acidic ribosomal protein p1. [source:swissprot;acc:p05386]	4857.03	5039.78	1.03763	
2419	thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [source:refseq;acc:nm_032243]	4857.03	5039.78	1.03763	
2420	thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [source:swissprot;acc:p10599]	4857.03	5039.78	1.03763	
2421	c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [source:sptrembl;acc:q96qi5]	7355.46	7088.93	1.0376	
2422	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [source:refseq;acc:nm_006042]	7355.46	7088.93	1.0376	
2423	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [source:refseq;acc:nm_006041]	7355.46	7088.93	1.0376	
2424	heparan sulfate d-glucosaminyl  3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [source:refseq;acc:nm_006043]	7355.46	7088.93	1.0376	
2425	mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [source:refseq;acc:nm_014026]	7355.46	7088.93	1.0376	
2426	tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [source:swissprot;acc:q01658]	6123.47	6351.84	1.03729	
2427	mitochondrial 28s ribosomal protein s2 (mrp-s2) (cgi-91). [source:swissprot;acc:q9y399]	5333.6	5531.41	1.03709	
2428	fragile x mental retardation syndrome related protein 2. [source:swissprot;acc:p51116]	7243.19	7509.81	1.03681	
2429	fragile x mental retardation syndrome related protein 1. [source:swissprot;acc:p51114]	7243.19	7509.81	1.03681	

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/