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 2863 to 2912 of 25824 in total

Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison	
358	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]	Squared	Divided	9811.73	7908.13	1.24071	
358	serine/threonine-protein kinase nek2 (ec 2.7.1.37) (nima-related protein kinase 2) (nima-like protein kinase 1) (hspk 21). [source:swissprot;acc:p51955]	Rooted	Divided	61.2684	67.755	1.10587	
359	5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [source:swissprot;acc:q13131]	Squared	Subtracted	34129.4	40434.2	6304.8	
359	60s ribosomal protein l4 (l1). [source:swissprot;acc:p36578]	Ranked	Divided	239.277	262.434	1.09678	
359	cell division protein kinase 3 (ec 2.7.1.-). [source:swissprot;acc:q00526]	Measured	Divided	12798.9	10887.2	1.17559	
359	nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [source:swissprot;acc:o43181]	Measured	Subtracted	1920.75	2907.43	986.68	
359	pescadillo homolog 1. [source:swissprot;acc:o00541]	Rooted	Divided	49.2488	54.4603	1.10582	
359	ras-related protein rab-26. [source:swissprot;acc:q9ulw5]	Ranked	Subtracted	240.287	260.193	19.906	
359	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [source:swissprot;acc:q00005]	Squared	Divided	9812.34	7908.87	1.24068	
359	squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [source:refseq;acc:nm_005146]	Rooted	Subtracted	57.6823	64.4212	6.7389	
360	atp-dependent rna helicase ddx24 (dead-box protein 24). [source:swissprot;acc:q9gzr7]	Rooted	Subtracted	46.901	53.624	6.723	
360	dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [source:swissprot;acc:p19387]	Ranked	Subtracted	240.287	260.193	19.906	
360	g2/mitotic-specific cyclin b2. [source:swissprot;acc:o95067]	Measured	Divided	12796.8	10886	1.17553	
360	nucleostemin; putative nucleotide binding protein, estradiol-induced. [source:refseq;acc:nm_014366]	Rooted	Divided	49.3771	54.5905	1.10558	
360	protein transport protein sec61 gamma subunit. [source:swissprot;acc:p38384]	Ranked	Divided	243.072	266.559	1.09663	
360	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [source:swissprot;acc:q9y2t4]	Squared	Divided	9814.47	7911.48	1.24054	
360	u6 snrna-associated sm-like protein lsm8. [source:swissprot;acc:o95777]	Measured	Subtracted	4590.18	5575.52	985.34	
360	vav-2 protein. [source:swissprot;acc:p52735]	Squared	Subtracted	31377.3	37670.1	6292.8	
361	40s ribosomal protein s4, y isoform 2. [source:swissprot;acc:q8td47]	Rooted	Divided	50.7801	45.9472	1.10518	
361	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]	Rooted	Subtracted	46.8525	53.5324	6.6799	
361	cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [source:swissprot;acc:p22681]	Measured	Subtracted	6875.08	7858.38	983.3	
361	cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [source:swissprot;acc:p24941]	Measured	Divided	12787.6	10880.5	1.17528	
361	katanin p60 subunit a 1. [source:refseq;acc:nm_007044]	Ranked	Subtracted	232.431	252.238	19.807	
361	mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [source:refseq;acc:nm_022061]	Ranked	Divided	242.83	266.248	1.09644	
361	splicing factor, proline-and glutamine-rich (polypyrimidine tract- binding protein-associated splicing factor) (ptb-associated splicing factor) (psf) (dna-binding p52/p100 complex, 100 kda subunit). [source:swissprot;acc:p23246]	Squared	Divided	70694.1	56989.9	1.24047	
361	translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [source:swissprot;acc:p13693]	Squared	Subtracted	42363.8	36083.8	6280	
362	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [source:swissprot;acc:p12750]	Rooted	Divided	50.7803	45.9477	1.10518	
362	apical-like protein (apxl protein). [source:swissprot;acc:q13796]	Ranked	Divided	231.492	211.136	1.09641	
362	calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [source:swissprot;acc:p07384]	Rooted	Subtracted	46.8525	53.5316	6.6791	
362	g2/mitotic-specific cyclin b1. [source:swissprot;acc:p14635]	Measured	Divided	12786.6	10879.9	1.17525	
362	katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [source:refseq;acc:nm_005886]	Ranked	Subtracted	232.382	252.166	19.784	
362	nascent-polypeptide-associated complex alpha polypeptide. [source:refseq;acc:nm_005594]	Squared	Subtracted	34071.5	40336.5	6265	
362	segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [source:swissprot;acc:q92997]	Measured	Subtracted	4981.52	5964.58	983.06	
362	transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [source:swissprot;acc:q15545]	Squared	Divided	57808.9	46630.3	1.23973	
363	alpha-nac protein. [source:sptrembl;acc:q9h009]	Squared	Subtracted	34069.4	40333	6263.6	
363	block of proliferation 1. [source:swissprot;acc:q14137]	Rooted	Divided	49.4884	54.6735	1.10477	
363	cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [source:swissprot;acc:p06493]	Measured	Divided	12780.7	10876.4	1.17509	
363	set domain and mariner transposase fusion gene. [source:refseq;acc:nm_006515]	Ranked	Subtracted	233.539	253.197	19.658	
363	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [source:refseq;acc:nm_020859]	Ranked	Divided	231.481	211.131	1.09639	
363	signal transduction protein cbl-b (sh3-binding protein cbl-b). [source:swissprot;acc:q13191]	Measured	Subtracted	6856.71	7838.3	981.59	
363	tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [source:refseq;acc:nm_024885]	Squared	Divided	57579.2	46497.2	1.23834	
363	u6 snrna-associated sm-like protein lsm6 (sm protein f). [source:swissprot;acc:q9y4y8]	Rooted	Subtracted	56.48	63.119	6.639	
364	cd209 antigen-like; putative type ii membrane protein. [source:refseq;acc:nm_014257]	Ranked	Subtracted	233.539	253.197	19.658	
364	dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [source:refseq;acc:nm_022779]	Rooted	Divided	50.0785	55.3215	1.1047	
364	dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [source:swissprot;acc:p30876]	Ranked	Divided	243.208	266.617	1.09625	
364	dok-like protein. [source:refseq;acc:nm_024872]	Measured	Subtracted	6102.59	7081.46	978.87	
364	ptb domain adaptor protein ced-6; engulfment adapter protein. [source:refseq;acc:nm_016315]	Measured	Divided	5189	6088.47	1.17334	
364	rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [source:swissprot;acc:o14908]	Rooted	Subtracted	60.594	67.2244	6.6304	
364	sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [source:refseq;acc:nm_005489]	Squared	Divided	17957.2	22234.1	1.23817	
364	small gtp-binding tumor suppressor 1. [source:refseq;acc:nm_145173]	Squared	Subtracted	34068.1	40330.8	6262.7	

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/