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

Results: HTML CSV LaTeX

Showing element 2551 to 2600 of 25824 in total

Interaction Map	High confidence
Filtered	1

Rank	Hugo	description	Value Type	Network Comparison Type	red	green	network_comparison	
319	RPL19	60s ribosomal protein l19. [source:swissprot;acc:p14118]	Ranked	Divided	240.73	264.729	1.09969	
319	RRAGA	ras-related gtp binding a; ras-related gtp-binding protein. [source:refseq;acc:nm_006570]	Measured	Divided	20911	24908.5	1.19117	
320		40s ribosomal protein s29. [source:swissprot;acc:p30054]	Rooted	Divided	50.2784	45.294	1.11005	
320	CDH1	epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [source:swissprot;acc:p12830]	Ranked	Divided	241.892	265.96	1.0995	
320	COPA	coatomer alpha subunit (alpha-coat protein) (alpha-cop) (hepcop) (hep-cop) [contains: xenin (xenopsin-related peptide); proxenin]. [source:swissprot;acc:p53621]	Squared	Subtracted	49280.5	42272.7	7007.8	
320	CPA6	carboxypeptidase b precursor. [source:refseq;acc:nm_020361]	Rooted	Subtracted	77.5801	70.0182	7.5619	
320	EPHX1	epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [source:swissprot;acc:p07099]	Squared	Divided	87971.9	69563.1	1.26463	
320	ESRRB	steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [source:swissprot;acc:o95718]	Measured	Subtracted	10263.8	11318.6	1054.8	
320	MAGED2	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]	Ranked	Subtracted	88.2482	110.265	22.0168	
320	RRAGC	ras-related gtp binding c; rag c protein. [source:refseq;acc:nm_022157]	Measured	Divided	20911	24908.5	1.19117	
321		c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [source:sptrembl;acc:q9br02]	Ranked	Divided	241.892	265.959	1.09949	
321		u6 snrna-associated sm-like protein lsm7. [source:swissprot;acc:q9uk45]	Rooted	Divided	55.9231	62.0565	1.10968	
321	CPA3	mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [source:swissprot;acc:p15088]	Rooted	Subtracted	77.58	70.0181	7.5619	
321	FBLN1	fibulin-1 precursor. [source:swissprot;acc:p23142]	Squared	Subtracted	44407.1	51387.4	6980.3	
321	NME2P1	putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [source:swissprot;acc:o60361]	Squared	Divided	33526	42390.2	1.2644	
321	RRAGB	ras-related gtp binding b short isoform; gtp-binding protein ragb. [source:refseq;acc:nm_006064]	Measured	Divided	20911	24908.5	1.19117	
321	STAM	signal transducing adaptor molecule 1; signal transducing adaptor molecule. [source:refseq;acc:nm_003473]	Measured	Subtracted	11797.1	10750.2	1046.9	
321	TRO	trophinin. [source:swissprot;acc:q12816]	Ranked	Subtracted	88.2482	110.265	22.0168	
322	ANLN	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [source:refseq;acc:nm_018685]	Measured	Divided	20911	24908.5	1.19117	
322	CPA6	carboxypeptidase b precursor. [source:refseq;acc:nm_020361]	Squared	Subtracted	25326.4	18354.1	6972.3	
322	CPB2	plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [source:refseq;acc:nm_001872]	Rooted	Subtracted	77.5797	70.0179	7.5618	
322	DNASE2B	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [source:refseq;acc:nm_021233]	Ranked	Divided	86.7483	78.8995	1.09948	
322	GIPC1	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	Divided	60.594	67.2244	1.10942	
322	NME2	nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [source:swissprot;acc:p15531]	Squared	Divided	33522.8	42384.8	1.26436	
322	PC	pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [source:swissprot;acc:p11498]	Measured	Subtracted	9304.83	10347.3	1042.47	
322	RRM2	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [source:swissprot;acc:p31350]	Ranked	Subtracted	231.969	210.064	21.905	
323		60s ribosomal protein l23a. [source:swissprot;acc:p29316]	Ranked	Divided	241.884	265.945	1.09947	
323		nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [source:swissprot;acc:p22392]	Squared	Divided	33514.4	42370.8	1.26426	
323	CPA3	mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [source:swissprot;acc:p15088]	Squared	Subtracted	25326.3	18354.1	6972.2	
323	HNRNPL	heterogeneous nuclear ribonucleoprotein l (hnrnp l). [source:swissprot;acc:p14866]	Measured	Subtracted	10247.8	11289	1041.2	
323	LSM4	u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [source:swissprot;acc:q9y4z0]	Measured	Divided	4620.76	5501.94	1.1907	
323	PCYT1A	cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [source:swissprot;acc:p49585]	Rooted	Divided	50.3803	45.4193	1.10923	
323	PPP1R2	protein phosphatase inhibitor 2 (ipp-2). [source:swissprot;acc:p41236]	Rooted	Subtracted	125.493	117.944	7.549	
323	RPS14	40s ribosomal protein s14 (pro2640). [source:swissprot;acc:p06366]	Ranked	Subtracted	242.238	264.11	21.872	
324		40s ribosomal protein s18 (ke-3) (ke3). [source:swissprot;acc:p25232]	Ranked	Subtracted	242.238	264.11	21.872	
324	CPB2	plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [source:refseq;acc:nm_001872]	Squared	Subtracted	25326.2	18354.1	6972.1	
324	DNASE2B	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [source:refseq;acc:nm_021233]	Measured	Divided	28136.5	33457.6	1.18912	
324	FLAD1	fad synthetase. [source:refseq;acc:nm_025207]	Rooted	Divided	50.3803	45.4193	1.10923	
324	HARS2	histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [source:swissprot;acc:p49590]	Squared	Divided	34527.9	43507.9	1.26008	
324	PPP1R2P9	type 1 protein phosphatase inhibitor. [source:refseq;acc:nm_025210]	Rooted	Subtracted	125.447	117.906	7.541	
324	PRKCH	protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [source:swissprot;acc:p24723]	Measured	Subtracted	11773.7	10733.8	1039.9	
324	RPS23	40s ribosomal protein s23. [source:swissprot;acc:p39028]	Ranked	Divided	243.944	268.195	1.09941	
325		bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [source:swissprot;acc:o95340]	Rooted	Divided	50.3803	45.4193	1.10923	
325		myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [source:swissprot;acc:p13533]	Squared	Subtracted	19321	12542.6	6778.4	
325	GORASP2	golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [source:refseq;acc:nm_015530]	Measured	Subtracted	8362.81	9402.7	1039.89	
325	HARS	histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [source:swissprot;acc:p12081]	Squared	Divided	34506.3	43476	1.25994	
325	MRPL13	60s ribosomal protein l13, mitochondrial (l13mt). [source:swissprot;acc:q9byd1]	Ranked	Subtracted	241.828	263.62	21.792	
325	MRPS12	28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [source:swissprot;acc:o15235]	Ranked	Divided	243.944	268.195	1.09941	
325	NFU1	hira-interacting protein 5 (cgi-33). [source:swissprot;acc:q9ums0]	Rooted	Subtracted	100.684	108.135	7.451	
325	SEPT8	septin-like protein kiaa0202 (fragment). [source:swissprot;acc:q92599]	Measured	Divided	16177.9	19235.4	1.18899	

Legend:
- Rank is the rank after comparing the two networks
- 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/