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

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Showing element 2862 to 2911 of 25824 in total

Interaction Map

: High confidence
Filtered

: 1

Rank	Hugo	description	Value Type	Network Comparison Type	red	green	network_comparison
358	PRKAG2	5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0]	Squared	Subtracted	34129.6	40434.5	6304.9
	RAB37	ras-related protein rab-37. [swissprot;acc:q96ax2]	Ranked	Subtracted	240.287	260.193	19.906
	RPL10L	ribosomal protein l10-like protein. [refseq;acc:nm_080746]	Ranked	Divided	243.12	266.662	1.09683
359	CDK3	cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526]	Measured	Divided	12798.9	10887.2	1.17559
	NDUFS4	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). [swissprot;acc:o43181]	Measured	Subtracted	1920.75	2907.43	986.68
	PES1	pescadillo homolog 1. [swissprot;acc:o00541]	Rooted	Divided	49.2488	54.4603	1.10582
	PPP2R2B	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). [swissprot;acc:q00005]	Squared	Divided	9812.34	7908.87	1.24068
	PRKAA1	5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131]	Squared	Subtracted	34129.4	40434.2	6304.8
	RAB26	ras-related protein rab-26. [swissprot;acc:q9ulw5]	Ranked	Subtracted	240.287	260.193	19.906
	RPL4	60s ribosomal protein l4 (l1). [swissprot;acc:p36578]	Ranked	Divided	239.277	262.434	1.09678
	SART1	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. [refseq;acc:nm_005146]	Rooted	Subtracted	57.6823	64.4212	6.7389
360	CCNB2	g2/mitotic-specific cyclin b2. [swissprot;acc:o95067]	Measured	Divided	12796.8	10886	1.17553
	DDX24	atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7]	Rooted	Subtracted	46.901	53.624	6.723
	GNL3	nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366]	Rooted	Divided	49.3771	54.5905	1.10558
	LSM8	u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777]	Measured	Subtracted	4590.18	5575.52	985.34
	POLR2C	dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387]	Ranked	Subtracted	240.287	260.193	19.906
	PPP2R2C	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). [swissprot;acc:q9y2t4]	Squared	Divided	9814.47	7911.48	1.24054
	SEC61G	protein transport protein sec61 gamma subunit. [swissprot;acc:p38384]	Ranked	Divided	243.072	266.559	1.09663
	VAV2	vav-2 protein. [swissprot;acc:p52735]	Squared	Subtracted	31377.3	37670.1	6292.8
361	CAPN2	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). [swissprot;acc:p17655]	Rooted		46.8525	53.5324	6.6799
	CBL	cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681]	Measured		6875.08	7858.38	983.3
	CDK2	cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941]	Measured	Divided	12787.6	10880.5	1.17528
	KATNA1	katanin p60 subunit a 1. [refseq;acc:nm_007044]	Ranked	Subtracted	232.431	252.238	19.807
	MRPL17	mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061]	Ranked	Divided	242.83	266.248	1.09644
	RPS4Y2	40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47]	Rooted		50.7801	45.9472	1.10518
	SFPQ	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). [swissprot;acc:p23246]	Squared		70694.1	56989.9	1.24047
	TPT1	translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [swissprot;acc:p13693]	Squared	Subtracted	42363.8	36083.8	6280
362	no value	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750]	Rooted	Divided	50.7803	45.9477	1.10518
	no value	nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594]	Squared	Subtracted	34071.5	40336.5	6265
	CAPN1	calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384]	Rooted	Subtracted	46.8525	53.5316	6.6791
	CCNB1	g2/mitotic-specific cyclin b1. [swissprot;acc:p14635]	Measured	Divided	12786.6	10879.9	1.17525
	DVL3	segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997]	Measured	Subtracted	4981.52	5964.58	983.06
	KATNB1	katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886]	Ranked	Subtracted	232.382	252.166	19.784
	SHROOM2	apical-like protein (apxl protein). [swissprot;acc:q13796]	Ranked	Divided	231.492	211.136	1.09641
	TAF7	transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545]	Squared	Divided	57808.9	46630.3	1.23973
363	no value	alpha-nac protein. [sptrembl;acc:q9h009]	Squared	Subtracted	34069.4	40333	6263.6
	BOP1	block of proliferation 1. [swissprot;acc:q14137]	Rooted	Divided	49.4884	54.6735	1.10477
	CBLB	signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191]	Measured	Subtracted	6856.71	7838.3	981.59
	CDC2	cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493]	Measured	Divided	12780.7	10876.4	1.17509
	LSM6	u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8]	Rooted	Subtracted	56.48	63.119	6.639
	SETMAR	set domain and mariner transposase fusion gene. [refseq;acc:nm_006515]	Ranked	Subtracted	233.539	253.197	19.658
	SHROOM3	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859]	Ranked	Divided	231.481	211.131	1.09639
	TAF7L	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. [refseq;acc:nm_024885]	Squared	Divided	57579.2	46497.2	1.23834
364	no value	dok-like protein. [refseq;acc:nm_024872]	Measured	Subtracted	6102.59	7081.46	978.87
	CLEC4M	cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257]	Ranked	Subtracted	233.539	253.197	19.658
	DDX31	dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779]	Rooted	Divided	50.0785	55.3215	1.1047
	DIRAS1	small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173]	Squared	Subtracted	34068.1	40330.8	6262.7
	GIPC1	rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908]	Rooted	Subtracted	60.594	67.2244	6.6304
	GULP1	ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315]	Measured	Divided	5189	6088.47	1.17334
	POLR2B	dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876]	Ranked	Divided	243.208	266.617	1.09625

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Hugo is the HGNC identifier if it exists
- 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/