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 Interaction Map Network Comparison Type Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 2001 to 2050 of 29840 in total

Interaction Map	High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison	
126	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	Subtracted	1	71387.4	96033.4	24646	
126	associated molecule with the sh3 domain of stam (amsh) like protein. [source:refseq;acc:nm_020799]	Ranked	Divided	1	94	114	1.21277	
126	calcyphosine. [source:swissprot;acc:q13938]	Measured	Divided	0	472.524	635.875	1.3457	
126	cysteine endopeptidase aut-like isoform b. [source:refseq;acc:nm_178326]	Measured	Divided	1	24250	18164.9	1.33499	
126	cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [source:swissprot;acc:p78329]	Ranked	Subtracted	0	12314.9	10489.3	1825.6	
126	dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [source:swissprot;acc:p31513]	Squared	Divided	0	118.204	219.216	1.85456	
126	dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [source:swissprot;acc:p42658]	Squared	Subtracted	0	3339.18	2360.97	978.21	
126	dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [source:swissprot;acc:q02880]	Rooted	Divided	0	21.3244	25.9172	1.21538	
126	f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [source:refseq;acc:nm_018315]	Ranked	Subtracted	1	285.684	252.234	33.45	
126	high-mobility group 20a. [source:refseq;acc:nm_018200]	Rooted	Subtracted	1	60.9353	75.094	14.1587	
126	high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [source:refseq;acc:nm_006339]	Rooted	Divided	1	60.9342	75.1387	1.23311	
126	importin 7; ran-binding protein 7. [source:refseq;acc:nm_006391]	Rooted	Subtracted	0	11.0328	6.96286	4.06994	
126	pp3111 protein. [source:refseq;acc:nm_022156]	Measured	Subtracted	0	789	530	259	
126	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Measured	Subtracted	1	450.5	2394.5	1944	
126	ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [source:swissprot;acc:o60858]	Ranked	Divided	0	9722.71	11493.8	1.18216	
126	serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [source:swissprot;acc:p08129]	Squared	Divided	1	189976	124480	1.52616	
127	alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [source:swissprot;acc:p11766]	Measured	Subtracted	0	2017.91	1759.22	258.69	
127	alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [source:swissprot;acc:q9nvd7]	Rooted	Subtracted	0	25.8457	21.7945	4.0512	
127	ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [source:swissprot;acc:q9uiv1]	Ranked	Subtracted	0	11732	13530.6	1798.6	
127	cullin homolog 2 (cul-2). [source:swissprot;acc:q13617]	Ranked	Subtracted	1	285.684	252.234	33.45	
127	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [source:swissprot;acc:p33551]	Squared	Divided	1	88432.6	58423.3	1.51365	
127	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [source:refseq;acc:nm_021233]	Rooted	Subtracted	1	153.191	166.771	13.58	
127	glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [source:swissprot;acc:p49448]	Squared	Subtracted	0	25936.7	26909.5	972.8	
127	high-mobility group 20a. [source:refseq;acc:nm_018200]	Rooted	Divided	1	60.9353	75.094	1.23236	
127	lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [source:swissprot;acc:p30301]	Squared	Subtracted	1	71386.9	96032.5	24645.6	
127	lipopolysaccharide-binding protein precursor (lbp). [source:swissprot;acc:p18428]	Measured	Divided	0	86	64	1.34375	
127	putative breast adenocarcinoma marker (32kd). [source:refseq;acc:nm_014453]	Ranked	Divided	1	94	114	1.21277	
127	putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [source:swissprot;acc:q8n0y7]	Rooted	Divided	0	37.9737	31.257	1.21489	
127	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	Measured	Subtracted	1	450.5	2394.5	1944	
127	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [source:swissprot;acc:q15393]	Squared	Divided	0	799.337	432.882	1.84655	
127	trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [source:refseq;acc:nm_014317]	Ranked	Divided	0	9411.34	11119.7	1.18152	
127	transcription factor jun-d. [source:swissprot;acc:p17535]	Measured	Divided	1	5638.2	7523.39	1.33436	
128	60s ribosomal protein l12 like protein. [source:sptrembl;acc:o60886]	Squared	Subtracted	0	3687.69	4640.77	953.08	
128	60s ribosomal protein l39. [source:swissprot;acc:p02404]	Ranked	Divided	0	11564.4	9794.29	1.18073	
128	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	Subtracted	1	71346.6	95965.1	24618.5	
128	associated molecule with the sh3 domain of stam. [source:refseq;acc:nm_006463]	Ranked	Divided	1	94	114	1.21277	
128	dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [source:swissprot;acc:q12882]	Squared	Divided	0	166.774	90.363	1.8456	
128	importin 9. [source:refseq;acc:nm_018085]	Measured	Subtracted	0	1143.55	1397.66	254.11	
128	luc7-like 2; cgi-74 protein; cgi-59 protein. [source:refseq;acc:nm_016019]	Measured	Divided	1	4355.61	5810.82	1.3341	
128	mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [source:swissprot;acc:p82650]	Measured	Divided	0	81.504	60.8613	1.33918	
128	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [source:swissprot;acc:p31483]	Rooted	Subtracted	1	54.6527	67.9743	13.3216	
128	phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [source:swissprot;acc:p18669]	Rooted	Divided	0	37.9737	31.257	1.21489	
128	pnas-18. [source:sptrembl;acc:q9bzu3]	Squared	Divided	1	87787.3	58155.8	1.50952	
128	presenilin 1 (ps-1) (s182 protein). [source:swissprot;acc:p49768]	Ranked	Subtracted	1	285.684	252.234	33.45	
128	ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [source:swissprot;acc:o60858]	Ranked	Subtracted	0	9722.71	11493.8	1771.09	
128	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [source:swissprot;acc:p17987]	Measured	Subtracted	1	11004.2	12944.2	1940	
128	tar dna-binding protein-43 (tdp-43). [source:swissprot;acc:q13148]	Rooted	Divided	1	48.0515	39.0445	1.23069	
128	udp-glucuronosyltransferase 2b17 precursor, microsomal (ec 2.4.1.17) (udpgt) (c19-steroid specific udp-glucuronosyltransferase). [source:swissprot;acc:o75795]	Rooted	Subtracted	0	32.4121	28.377	4.0351	
129	60s ribosomal protein l39. [source:swissprot;acc:p02404]	Ranked	Subtracted	0	11564.4	9794.29	1770.11	
129	cullin homolog 1 (cul-1). [source:swissprot;acc:q13616]	Ranked	Subtracted	1	285.684	252.234	33.45	

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/