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 980 to 1029 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
123	probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185]	Rooted	0	27.4843	22.4483	1.22434
	protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]	Squared	1	192904	126167	1.52896
	ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858]	Measured	0	2285.62	1681.3	1.35944
	secreted modular calcium-binding protein 1. [refseq;acc:nm_022137]	Squared		31.8185	16.8625	1.88694
	zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58]	Ranked		11522.8	13684.9	1.18764
124	f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755]	Rooted		10.6611	13.034	1.22258
	high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339]	Ranked	1	208.52	171.595	1.21519
	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	Measured		24255.7	18168.9	1.33501
	nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085]	Rooted		54.6625	67.9477	1.24304
	regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754]	Measured	0	3248.95	2399.76	1.35386
	sh2-b homolog; likely ortholog of mouse sh2 domain-containing putative adapter sh2-b; sh2-b gamma signaling protein; sh2-b alpha signaling protein. [refseq;acc:nm_015503]	Squared	0	2.70982	1.44	1.88182
	type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210]	Squared	1	192779	126095	1.52884
	zinc finger imprinted 2. [swissprot;acc:q9nzv7]	Ranked	0	11520.7	13680.4	1.18746
125	high-mobility group 20a. [refseq;acc:nm_018200]	Ranked	1	208.588	171.778	1.21429
	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]	Measured	1	24255.7	18168.9	1.33501
	pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790]	Squared	0	10.3503	19.2071	1.8557
	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). [swissprot;acc:o00750]	Ranked		22038	18578	1.18624
	pp3111 protein. [refseq;acc:nm_022156]	Rooted		28.0891	23.0217	1.22011
	probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185]	Measured		1095.42	812.166	1.34876
	ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050]	Squared	1	189976	124480	1.52616
	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641]	Rooted		54.8203	67.934	1.23921
126	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	Ranked		94	114	1.21277
	calcyphosine. [swissprot;acc:q13938]	Measured	0	472.524	635.875	1.3457
	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	Measured	1	24250	18164.9	1.33499
	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). [swissprot;acc:p31513]	Squared	0	118.204	219.216	1.85456
	dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880]	Rooted	0	21.3244	25.9172	1.21538
	high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339]	Rooted	1	60.9342	75.1387	1.23311
	ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858]	Ranked	0	9722.71	11493.8	1.18216
	serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129]	Squared	1	189976	124480	1.52616
127	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]	Squared		88432.6	58423.3	1.51365
	high-mobility group 20a. [refseq;acc:nm_018200]	Rooted		60.9353	75.094	1.23236
	lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428]	Measured	0	86	64	1.34375
	putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453]	Ranked	1	94	114	1.21277
	putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7]	Rooted	0	37.9737	31.257	1.21489
	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]	Squared		799.337	432.882	1.84655
	trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317]	Ranked		9411.34	11119.7	1.18152
	transcription factor jun-d. [swissprot;acc:p17535]	Measured	1	5638.2	7523.39	1.33436
128	60s ribosomal protein l39. [swissprot;acc:p02404]	Ranked	0	11564.4	9794.29	1.18073
	associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]	Ranked	1	94	114	1.21277
	dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882]	Squared	0	166.774	90.363	1.8456
	luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019]	Measured	1	4355.61	5810.82	1.3341
	mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650]	Measured	0	81.504	60.8613	1.33918
	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). [swissprot;acc:p18669]	Rooted	0	37.9737	31.257	1.21489
	pnas-18. [sptrembl;acc:q9bzu3]	Squared	1	87787.3	58155.8	1.50952
	tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148]	Rooted	1	48.0515	39.0445	1.23069
129	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	Squared	0	21723.1	39570.4	1.82158
	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	Rooted	1	54.2343	66.7323	1.23044
	isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252]	Ranked	0	14222.5	12058.6	1.17945
	luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032]	Measured	1	4358.13	5811.49	1.33348
	neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079]	Ranked	1	94	114	1.21277

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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/