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 1508 to 1557 of 25824 in total

Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison	
189	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [source:swissprot;acc:p46977]	Measured	Divided	4571.89	5864.86	1.28281	
189	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [source:swissprot;acc:q9nr22]	Measured	Subtracted	4366.44	5899.76	1533.32	
189	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [source:swissprot;acc:q9nr22]	Ranked	Divided	226.582	198.444	1.14179	
189	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	Subtracted	70694.1	56989.9	13704.2	
189	transcription factor e2f2 (e2f-2). [source:swissprot;acc:q14209]	Rooted	Divided	46.0352	53.0192	1.15171	
190	aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [source:swissprot;acc:p55087]	Squared	Divided	71389.9	96037.6	1.34525	
190	dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [source:swissprot;acc:p39656]	Measured	Divided	4571.89	5864.86	1.28281	
190	fad synthetase. [source:refseq;acc:nm_025207]	Ranked	Subtracted	241.373	267.352	25.979	
190	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [source:refseq;acc:nm_007278]	Rooted	Divided	149.165	129.699	1.15009	
190	mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [source:swissprot;acc:p53778]	Squared	Subtracted	42411.6	55802.1	13390.5	
190	rap1 gtpase-activating protein 1 (rap1gap). [source:swissprot;acc:p47736]	Rooted	Subtracted	47.6504	36.9304	10.72	
190	u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [source:swissprot;acc:p08621]	Measured	Subtracted	4366.44	5899.76	1533.32	
190	u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [source:swissprot;acc:p08621]	Ranked	Divided	226.582	198.444	1.14179	
191	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [source:swissprot;acc:p10398]	Rooted	Subtracted	116.797	106.111	10.686	
191	aquaporin 5. [source:swissprot;acc:p55064]	Squared	Divided	71388.5	96035.2	1.34525	
191	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]	Ranked	Subtracted	241.373	267.352	25.979	
191	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [source:swissprot;acc:p21333]	Measured	Subtracted	4366.44	5899.76	1533.32	
191	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [source:swissprot;acc:p21333]	Ranked	Divided	226.582	198.444	1.14179	
191	pallidin; pallid (mouse) homolog, pallidin. [source:refseq;acc:nm_012388]	Rooted	Divided	63.1192	72.584	1.14995	
191	sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [source:swissprot;acc:q9nya1]	Squared	Subtracted	42411.6	55802.1	13390.5	
191	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [source:swissprot;acc:o75533]	Measured	Divided	4638.1	5923.4	1.27712	
192	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [source:swissprot;acc:p10398]	Measured	Divided	17757.5	14008	1.26767	
192	aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [source:swissprot;acc:p41181]	Squared	Divided	71387.4	96033.4	1.34524	
192	ligatin (hepatocellular carcinoma-associated antigen 56). [source:swissprot;acc:p41214]	Ranked	Subtracted	241.373	267.352	25.979	
192	musashi 2 isoform a. [source:refseq;acc:nm_138962]	Ranked	Divided	227.491	199.458	1.14055	
192	raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [source:swissprot;acc:p04049]	Rooted	Subtracted	116.792	106.107	10.685	
192	small glutamine rich protein with tetratricopeptide repeats 2. [source:refseq;acc:nm_019072]	Measured	Subtracted	10807.4	12338.5	1531.1	
192	splicing factor 4 isoform b; rna-binding protein. [source:refseq;acc:nm_021164]	Rooted	Divided	53.6107	61.5862	1.14877	
192	udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [source:swissprot;acc:q9h3h5]	Squared	Subtracted	42411.6	55802.1	13390.5	
193	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]	Ranked	Subtracted	241.373	267.352	25.979	
193	lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [source:swissprot;acc:p30301]	Squared	Divided	71386.9	96032.5	1.34524	
193	musashi 1. [source:refseq;acc:nm_002442]	Ranked	Divided	227.491	199.458	1.14055	
193	nostrin. [source:refseq;acc:nm_052946]	Rooted	Divided	59.6399	51.9242	1.1486	
193	raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [source:swissprot;acc:p04049]	Measured	Divided	17756.5	14007.3	1.26766	
193	rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [source:swissprot;acc:q96qb1]	Squared	Subtracted	42411.6	55802.1	13390.5	
193	serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [source:swissprot;acc:q16537]	Rooted	Subtracted	116.707	106.044	10.663	
193	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [source:swissprot;acc:p30153]	Measured	Subtracted	4612.39	3093.6	1518.79	
194	aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [source:swissprot;acc:p29972]	Squared	Divided	71346.6	95965.1	1.34505	
194	cyclin g2. [source:swissprot;acc:q16589]	Measured	Divided	17738.6	13995.7	1.26743	
194	cyclin g2. [source:swissprot;acc:q16589]	Rooted	Subtracted	116.707	106.044	10.663	
194	eap30 subunit of ell complex. [source:refseq;acc:nm_007241]	Rooted	Divided	59.6399	51.9242	1.1486	
194	huntingtin interacting protein c. [source:refseq;acc:nm_012272]	Measured	Subtracted	4300.47	5807.72	1507.25	
194	map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [source:swissprot;acc:p49137]	Squared	Subtracted	42411.6	55802.1	13390.5	
194	nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [source:swissprot;acc:p16435]	Ranked	Subtracted	241.373	267.352	25.979	
194	nuclear protein ukp68. [source:refseq;acc:nm_024824]	Ranked	Divided	227.491	199.458	1.14055	
195	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]	Ranked	Subtracted	241.373	267.352	25.979	
195	cyclin g1 (cyclin g). [source:swissprot;acc:p51959]	Measured	Divided	17738.5	13995.6	1.26743	
195	cyclin g1 (cyclin g). [source:swissprot;acc:p51959]	Rooted	Subtracted	116.707	106.044	10.663	
195	huntingtin interacting protein c. [source:refseq;acc:nm_012272]	Ranked	Divided	227.971	200.417	1.13748	
195	liv-1 protein, estrogen regulated. [source:refseq;acc:nm_012319]	Rooted	Divided	59.6399	51.9242	1.1486	

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/