MK5 Microarray Data

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	Hugo	description	Value Type	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison

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Showing element 2575 to 2624 of 3228 in total

Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

Rank	Hugo	description	red	green	network_comparison
2575	PTPN2	protein-tyrosine phosphatase, non-receptor type 2 (ec 3.1.3.48) (t- cell protein-tyrosine phosphatase) (tcptp). [swissprot;acc:p17706]	209.583	209.255	1.00157
2576	SNTB1	beta-1-syntrophin (59 kda dystrophin-associated protein a1, basic component 1) (dapa1b) (tax interaction protein 43) (tip-43) (syntrophin 2) (bsyn2). [swissprot;acc:q13884]	213.422	213.75	1.00154
2577	CANT1	ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793]	192.625	192.922
2578	SNTB2	beta-2-syntrophin (59 kda dystrophin-associated protein a1, basic component 2) (syntrophin 3) (snt3) (syntrophin-like) (sntl). [swissprot;acc:q13425]	213.422	213.75
2579	NIT1	nitrilase 1. [refseq;acc:nm_005600]
2580	UTRN	utrophin (dystrophin-related protein 1) (drp1) (drp). [swissprot;acc:p46939]
2581	DTNB	dystrobrevin beta (beta-dystrobrevin) (dtn-b). [swissprot;acc:o60941]	213.428	213.756
2582	DBT	lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial precursor (ec 2.3.1.-) (e2) (dihydrolipoamide branched chain transacylase) (bckad e2 subunit). [swissprot;acc:p11182]	213.422	213.75
2583	DTNA	dystrobrevin alpha (dystrobrevin-alpha). [swissprot;acc:q9y4j8]	213.415	213.743
2584	no value	dystrophin. [swissprot;acc:p11532]	213.422	213.75
2585	AMOT	angiomotin. [refseq;acc:nm_133265]
2586	AMOTL2	angiomotin like 2; leman coiled-coil protein; angiomotin-like protein 2. [refseq;acc:nm_016201]
2587	SNTA1	alpha-1-syntrophin (59 kda dystrophin-associated protein a1, acidic component 1) (pro-tgf-alpha cytoplasmic domain-interacting protein 1) (tacip1) (syntrophin 1). [swissprot;acc:q13424]
2588	HSPD1	60 kda heat shock protein, mitochondrial precursor (hsp60) (60 kda chaperonin) (cpn60) (heat shock protein 60) (hsp-60) (mitochondrial matrix protein p1) (p60 lymphocyte protein) (hucha60). [swissprot;acc:p10809]	222.305	222.64	1.00151
2589	FAM57A	membrane protein expressed in epithelial-like lung adenocarcinoma. [refseq;acc:nm_024792]	212.74	212.422	1.0015
2590	PSMA6	proteasome subunit alpha type 6 (ec 3.4.25.1) (proteasome iota chain) (macropain iota chain) (multicatalytic endopeptidase complex iota chain) (27 kda prosomal protein) (pros-27) (p27k). [swissprot;acc:p34062]	214.605	214.287	1.00148
2591	PBRM1	polybromo 1. [refseq;acc:nm_018165]	220.02	219.696	1.00147
2592	SMARCA5	swi/snf-related matrix-associated actin-dependent regulator of chromatin a5; sucrose nonfermenting-like 5. [refseq;acc:nm_003601]
2593	SMARCA4	possible global transcription activator snf2l4 (snf2-beta) (brg-1 protein) (mitotic growth and transcription activator) (brahma protein homolog 1). [swissprot;acc:p51532]
2594	SMARCA1	possible global transcription activator snf2l1. [swissprot;acc:p28370]
2595	BTAF1	tbp-associated factor 172 (taf-172) (taf(ii)170). [swissprot;acc:o14981]
2596	SMARCA2	possible global transcription activator snf2l2 (snf2-alpha). [swissprot;acc:p51531]
2597	IPO11	ran binding protein 11. [refseq;acc:nm_016338]	212.711	212.401	1.00146
2598	TAF5	transcription initiation factor tfiid 100 kda subunit (tafii-100) (tafii100). [swissprot;acc:q15542]	202.142	202.436	1.00145
2599	KIAA1432	ba207c16.2 (fragment). [sptrembl;acc:q9nql7]	211.662	211.361	1.00142
2600	HYAL3	interferon-related developmental regulator 2 (skmc15 protein). [swissprot;acc:q12894]	224.877	225.193	1.00141
2601	CNNM3	cyclin m3; ancient conserved domain protein 3. [refseq;acc:nm_017623]	214.502	214.2
2602	ARPC5	arp2/3 complex 16 kda subunit (p16-arc) (actin-related protein 2/3 complex subunit 5). [swissprot;acc:o15511]	224.875	225.192
2603	CNNM4	cyclin m4; ancient conserved domain protein 4. [refseq;acc:nm_020184]	214.494	214.192
2604	CNNM2	cyclin m2; ancient conserved domain protein 2. [refseq;acc:nm_017649]	214.486	214.184
2605	PRUNE	tcd37 homolog; prune. [refseq;acc:nm_021222]	214.495	214.193
2606	CNNM1	cyclin m1; ancient conserved domain protein 1. [refseq;acc:nm_020348]	214.5	214.198
2607	MRPS22	mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650]	215.497	215.799	1.0014
2608	no value	nefa-interacting nuclear protein nip30. [refseq;acc:nm_024946]
2609	LMX1A	lim homeobox transcription factor 1 alpha (lim/homeobox protein lmx1a) (lim-homeobox protein 1.1) (lmx-1.1). [swissprot;acc:q8te12]
2610	TOMM70A	mitochondrial precursor proteins import receptor (translocase of outer membrane tom70). [swissprot;acc:o94826]
2611	LMX1B	lim homeobox transcription factor 1 beta (lim/homeobox protein lmx1b) (lim-homeobox protein 1.2) (lmx-1.2). [swissprot;acc:o60663]
2612	PSMB2	proteasome subunit beta type 2 (ec 3.4.25.1) (proteasome component c7-i) (macropain subunit c7-i) (multicatalytic endopeptidase complex subunit c7-i). [swissprot;acc:p49721]
2613	ARL1	adp-ribosylation factor-like protein 1. [swissprot;acc:p40616]
2614	RELA	transcription factor p65 (nuclear factor nf-kappa-b p65 subunit). [swissprot;acc:q04206]	202.821	202.54	1.00139
2615	RELB	transcription factor relb (i-rel). [swissprot;acc:q01201]
2616	NFKBIA	nf-kappab inhibitor alpha (major histocompatibility complex enhancer- binding protein mad3) (i-kappa-b-alpha) (ikappabalpha) (ikb-alpha). [swissprot;acc:p25963]
2617	CPOX	coproporphyrinogen iii oxidase, mitochondrial precursor (ec 1.3.3.3) (coproporphyrinogenase) (coprogen oxidase) (cox). [swissprot;acc:p36551]
2618	IDH2	isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [swissprot;acc:p48735]	190.166	190.429	1.00138
2619	SMARCC2	swi/snf-related matrix-associated actin-dependent regulator of chromatin c2 isoform a; mammalian chromatin remodeling complex brg1-associated factor 170; chromatin remodeling complex baf170 subunit; swi3-like protein; swi/snf complex 170 kda subunit. [refseq;acc:nm_003075]	220.024	219.722	1.00137
2620	PSMD9	26s proteasome non-atpase regulatory subunit 9 (26s proteasome regulatory subunit p27). [swissprot;acc:o00233]	215.615	215.91
2621	no value	dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6]	224.891	225.195	1.00135
2622	ZMYM6	zinc finger protein 258. [refseq;acc:nm_145310]
2623	ZMYM3	zinc finger protein 261 (dxs6673e protein). [swissprot;acc:q14202]
2624	ZMYM4	zinc finger protein 262; cell death inhibiting rna. [refseq;acc:nm_005095]

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
- Hugo is the HGNC identifier if it exists
- 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.