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 2563 to 2612 of 25824 in total

Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison	
321	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	putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [source:swissprot;acc:o60361]	Squared	Divided	33526	42390.2	1.2644	
321	ras-related gtp binding b short isoform; gtp-binding protein ragb. [source:refseq;acc:nm_006064]	Measured	Divided	20911	24908.5	1.19117	
321	signal transducing adaptor molecule 1; signal transducing adaptor molecule. [source:refseq;acc:nm_003473]	Measured	Subtracted	11797.1	10750.2	1046.9	
321	trophinin. [source:swissprot;acc:q12816]	Ranked	Subtracted	88.2482	110.265	22.0168	
321	u6 snrna-associated sm-like protein lsm7. [source:swissprot;acc:q9uk45]	Rooted	Divided	55.9231	62.0565	1.10968	
322	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	carboxypeptidase b precursor. [source:refseq;acc:nm_020361]	Squared	Subtracted	25326.4	18354.1	6972.3	
322	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	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	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	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	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	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	40s ribosomal protein s14 (pro2640). [source:swissprot;acc:p06366]	Ranked	Subtracted	242.238	264.11	21.872	
323	60s ribosomal protein l23a. [source:swissprot;acc:p29316]	Ranked	Divided	241.884	265.945	1.09947	
323	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	heterogeneous nuclear ribonucleoprotein l (hnrnp l). [source:swissprot;acc:p14866]	Measured	Subtracted	10247.8	11289	1041.2	
323	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	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	protein phosphatase inhibitor 2 (ipp-2). [source:swissprot;acc:p41236]	Rooted	Subtracted	125.493	117.944	7.549	
323	u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [source:swissprot;acc:q9y4z0]	Measured	Divided	4620.76	5501.94	1.1907	
324	40s ribosomal protein s18 (ke-3) (ke3). [source:swissprot;acc:p25232]	Ranked	Subtracted	242.238	264.11	21.872	
324	40s ribosomal protein s23. [source:swissprot;acc:p39028]	Ranked	Divided	243.944	268.195	1.09941	
324	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	fad synthetase. [source:refseq;acc:nm_025207]	Rooted	Divided	50.3803	45.4193	1.10923	
324	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	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	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	type 1 protein phosphatase inhibitor. [source:refseq;acc:nm_025210]	Rooted	Subtracted	125.447	117.906	7.541	
325	28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [source:swissprot;acc:o15235]	Ranked	Divided	243.944	268.195	1.09941	
325	60s ribosomal protein l13, mitochondrial (l13mt). [source:swissprot;acc:q9byd1]	Ranked	Subtracted	241.828	263.62	21.792	
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	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	hira-interacting protein 5 (cgi-33). [source:swissprot;acc:q9ums0]	Rooted	Subtracted	100.684	108.135	7.451	
325	histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [source:swissprot;acc:p12081]	Squared	Divided	34506.3	43476	1.25994	
325	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [source:swissprot;acc:p13533]	Squared	Subtracted	19321	12542.6	6778.4	
325	septin-like protein kiaa0202 (fragment). [source:swissprot;acc:q92599]	Measured	Divided	16177.9	19235.4	1.18899	
326	40s ribosomal protein s16. [source:swissprot;acc:p17008]	Ranked	Subtracted	241.828	263.62	21.792	
326	60s ribosomal protein l5. [source:swissprot;acc:p46777]	Ranked	Divided	241.899	265.924	1.09932	
326	anaphase-promoting complex subunit 2; anaphase-promoting complex 2. [source:refseq;acc:nm_013366]	Squared	Divided	69124.3	54897.4	1.25915	
326	atp-dependent rna helicase ddx24 (dead-box protein 24). [source:swissprot;acc:q9gzr7]	Measured	Divided	3432.96	4081.21	1.18883	
326	ligatin (hepatocellular carcinoma-associated antigen 56). [source:swissprot;acc:p41214]	Rooted	Divided	50.3803	45.4193	1.10923	
326	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [source:swissprot;acc:q9y623]	Squared	Subtracted	19321	12542.6	6778.4	
326	protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [source:swissprot;acc:q02156]	Measured	Subtracted	11773	10733.2	1039.8	
326	u6 snrna-associated sm-like protein lsm5. [source:swissprot;acc:q9y4y9]	Rooted	Subtracted	56.0466	63.4808	7.4342	
327	60s ribosomal protein l13a (23 kda highly basic protein). [source:swissprot;acc:p40429]	Ranked	Subtracted	241.83	263.615	21.785	
327	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [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:o43252]	Rooted	Divided	50.3803	45.4193	1.10923	
327	dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [source:swissprot;acc:p24928]	Ranked	Divided	243.817	267.962	1.09903	
327	luc7-like 2; cgi-74 protein; cgi-59 protein. [source:refseq;acc:nm_016019]	Squared	Divided	16424.1	20645.8	1.25704	

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/