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

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Showing element 2580 to 2629 of 25824 in total

Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison	
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	
327	max protein. [source:swissprot;acc:p25912]	Rooted	Subtracted	56.3054	63.7148	7.4094	
327	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [source:swissprot;acc:p13535]	Squared	Subtracted	19321	12542.6	6778.4	
327	peptidyl-prolyl cis-trans isomerase b precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin b) (s-cyclophilin) (scylp) (cyp-s1). [source:swissprot;acc:p23284]	Measured	Subtracted	11773	10733.2	1039.8	
327	septin 10 isoform 1. [source:refseq;acc:nm_144710]	Measured	Divided	16067.4	19094.4	1.18839	
328	atp-dependent rna helicase ddx24 (dead-box protein 24). [source:swissprot;acc:q9gzr7]	Ranked	Divided	258.437	235.183	1.09888	
328	brain protein 44. [source:swissprot;acc:o95563]	Measured	Divided	15999.1	19007.1	1.18801	
328	luc7-like; sarcoplasmic reticulum protein luc7b1. [source:refseq;acc:nm_018032]	Squared	Divided	16442.8	20662.7	1.25664	
328	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [source:swissprot;acc:q9ukx2]	Squared	Subtracted	19321	12542.6	6778.4	
328	nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [source:swissprot;acc:p16435]	Rooted	Divided	50.3803	45.4193	1.10923	
328	putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [source:swissprot;acc:o75642]	Ranked	Subtracted	240.801	262.34	21.539	
328	ribosome biogenesis regulatory protein homolog. [source:swissprot;acc:q15050]	Rooted	Subtracted	124.41	117.043	7.367	
328	udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [source:swissprot;acc:o15294]	Measured	Subtracted	11773	10733.2	1039.8	
329	cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [source:swissprot;acc:q9y5k3]	Rooted	Divided	50.3803	45.4193	1.10923	
329	cytochrome c oxidase subunit iv isoform 1, mitochondrial precursor (ec 1.9.3.1) (cox iv-1) (cytochrome c oxidase polypeptide iv). [source:swissprot;acc:p13073]	Measured	Subtracted	11773	10733.2	1039.8	
329	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [source:refseq;acc:nm_022075]	Ranked	Subtracted	191.644	170.192	21.452	
329	metaxin 2. [source:swissprot;acc:o75431]	Squared	Divided	41236	51807	1.25635	
329	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [source:swissprot;acc:p11055]	Squared	Subtracted	19321	12542.6	6778.4	

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/