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 975 to 1024 of 14920 in total

Interaction Map	High confidence
Network Comparison Type	Divided

Rank	description	Value Type	Filtered	red	green	network_comparison	
122	ubiquitin-conjugating enzyme e2-17 kda 3 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 3). [source:swissprot;acc:p47986]	Squared	0	34.1583	18.0543	1.89198	
122	zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [source:swissprot;acc:p17028]	Ranked	0	11523	13685.4	1.18766	
123	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [source:refseq;acc:nm_052936]	Measured	1	24260.3	18172.1	1.33503	
123	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [source:swissprot;acc:p31483]	Rooted	1	54.6527	67.9743	1.24375	
123	potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [source:refseq;acc:nm_004979]	Ranked	1	269.23	327.601	1.21681	
123	probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [source:swissprot;acc:o75185]	Rooted	0	27.4843	22.4483	1.22434	
123	protein phosphatase inhibitor 2 (ipp-2). [source:swissprot;acc:p41236]	Squared	1	192904	126167	1.52896	
123	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]	Measured	0	2285.62	1681.3	1.35944	
123	secreted modular calcium-binding protein 1. [source:refseq;acc:nm_022137]	Squared	0	31.8185	16.8625	1.88694	
123	zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [source:swissprot;acc:q9ul58]	Ranked	0	11522.8	13684.9	1.18764	
124	f-actin capping protein alpha-2 subunit (capz alpha-2). [source:swissprot;acc:p47755]	Rooted	0	10.6611	13.034	1.22258	
124	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]	Ranked	1	208.52	171.595	1.21519	
124	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [source:swissprot;acc:q9gzq8]	Measured	1	24255.7	18168.9	1.33501	
124	nucleolysin tiar (tia-1 related protein). [source:swissprot;acc:q01085]	Rooted	1	54.6625	67.9477	1.24304	
124	regulator of chromosome condensation (cell cycle regulatory protein). [source:swissprot;acc:p18754]	Measured	0	3248.95	2399.76	1.35386	
124	sh2-b homolog; likely ortholog of mouse sh2 domain-containing putative adapter sh2-b; sh2-b gamma signaling protein; sh2-b alpha signaling protein. [source:refseq;acc:nm_015503]	Squared	0	2.70982	1.44	1.88182	
124	type 1 protein phosphatase inhibitor. [source:refseq;acc:nm_025210]	Squared	1	192779	126095	1.52884	
124	zinc finger imprinted 2. [source:swissprot;acc:q9nzv7]	Ranked	0	11520.7	13680.4	1.18746	
125	high-mobility group 20a. [source:refseq;acc:nm_018200]	Ranked	1	208.588	171.778	1.21429	
125	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [source:swissprot;acc:q9h492]	Measured	1	24255.7	18168.9	1.33501	
125	pepsin a precursor (ec 3.4.23.1). [source:swissprot;acc:p00790]	Squared	0	10.3503	19.2071	1.8557	
125	phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [source:swissprot;acc:o00750]	Ranked	0	22038	18578	1.18624	
125	pp3111 protein. [source:refseq;acc:nm_022156]	Rooted	0	28.0891	23.0217	1.22011	
125	probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [source:swissprot;acc:o75185]	Measured	0	1095.42	812.166	1.34876	
125	ribosome biogenesis regulatory protein homolog. [source:swissprot;acc:q15050]	Squared	1	189976	124480	1.52616	
125	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [source:swissprot;acc:p13641]	Rooted	1	54.8203	67.934	1.23921	
126	associated molecule with the sh3 domain of stam (amsh) like protein. [source:refseq;acc:nm_020799]	Ranked	1	94	114	1.21277	
126	calcyphosine. [source:swissprot;acc:q13938]	Measured	0	472.524	635.875	1.3457	
126	cysteine endopeptidase aut-like isoform b. [source:refseq;acc:nm_178326]	Measured	1	24250	18164.9	1.33499	
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	0	118.204	219.216	1.85456	
126	dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [source:swissprot;acc:q02880]	Rooted	0	21.3244	25.9172	1.21538	
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	1	60.9342	75.1387	1.23311	
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	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	1	189976	124480	1.52616	
127	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [source:swissprot;acc:p33551]	Squared	1	88432.6	58423.3	1.51365	
127	high-mobility group 20a. [source:refseq;acc:nm_018200]	Rooted	1	60.9353	75.094	1.23236	
127	lipopolysaccharide-binding protein precursor (lbp). [source:swissprot;acc:p18428]	Measured	0	86	64	1.34375	
127	putative breast adenocarcinoma marker (32kd). [source:refseq;acc:nm_014453]	Ranked	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	0	37.9737	31.257	1.21489	
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	0	799.337	432.882	1.84655	
127	trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [source:refseq;acc:nm_014317]	Ranked	0	9411.34	11119.7	1.18152	
127	transcription factor jun-d. [source:swissprot;acc:p17535]	Measured	1	5638.2	7523.39	1.33436	
128	60s ribosomal protein l39. [source:swissprot;acc:p02404]	Ranked	0	11564.4	9794.29	1.18073	
128	associated molecule with the sh3 domain of stam. [source:refseq;acc:nm_006463]	Ranked	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	0	166.774	90.363	1.8456	
128	luc7-like 2; cgi-74 protein; cgi-59 protein. [source:refseq;acc:nm_016019]	Measured	1	4355.61	5810.82	1.3341	
128	mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [source:swissprot;acc:p82650]	Measured	0	81.504	60.8613	1.33918	
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	0	37.9737	31.257	1.21489	
128	pnas-18. [source:sptrembl;acc:q9bzu3]	Squared	1	87787.3	58155.8	1.50952	
128	tar dna-binding protein-43 (tdp-43). [source:swissprot;acc:q13148]	Rooted	1	48.0515	39.0445	1.23069	

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/