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

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Showing element 2351 to 2400 of 12912 in total

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

Rank	description	Value Type	red	green	network_comparison
588	imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549]	Rooted	59.7294	64.6872	1.083
	shwachman-bodian-diamond syndrome protein (cgi-97). [swissprot;acc:q9y3a5]	Ranked	216.557	230.362	1.06375
589	microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378]	Rooted	59.7294	64.6872	1.083
	nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556]	Measured	6739.85	7644.63	1.13424
	rab acceptor 1 (prenylated); prenylated rab acceptor 1. [refseq;acc:nm_006423]	Squared	23526.4	27879.3	1.18502
	u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333]	Ranked	228.215	214.546	1.06371
590	oligoribonuclease, mitochondrial precursor (ec 3.1.-.-) (small fragment nuclease) (cgi-114). [swissprot;acc:q9y3b8]	Squared	23526.4	27879.3	1.18502
	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921]	Ranked	217.215	204.279	1.06333
	similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9]	Measured	6739.85	7644.63	1.13424
	transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116]	Rooted	108.671	100.365	1.08276
591	choline o-acetyltransferase (ec 2.3.1.6) (choactase) (choline acetylase) (chat). [swissprot;acc:p28329]	Squared	23526.5	27879.4	1.18502
	homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356]	Measured	6740.5	7644.76	1.13415
	leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13]	Rooted	108.659	100.356	1.08274
	ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [swissprot;acc:p78346]	Ranked	216.72	230.439	1.0633
592	histone h2b.c (h2b/c). [swissprot;acc:q99880]	Measured	3946.32	4475.47	1.13409
	protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]	Ranked	91.63	97.4011	1.06298
	ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211]	Rooted	108.659	100.356	1.08274
	voltage-gated potassium channel beta-2 subunit (k+ channel beta-2 subunit) (kv-beta-2) (hkvbeta2). [swissprot;acc:q13303]	Squared	23526.4	27879.3	1.18502
593	aflatoxin b1 aldehyde reductase 1 (ec 1.-.-.-) (afb1-ar 1) (aldoketoreductase 7). [swissprot;acc:o43488]
	histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778]	Measured	3946.32	4475.47	1.13409
	tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658]	Ranked	232.118	218.406	1.06278
	transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112]	Rooted	108.653	100.352	1.08272
594	histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106]	Measured	3946.32	4475.47	1.13409
	importin alpha-1 subunit (karyopherin alpha-1 subunit) (srp1-beta) (rag cohort protein 2) (nucleoprotein interactor 1) (npi-1). [swissprot;acc:p52294]	Squared	23517.1	27867.3	1.18498
	pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508]	Ranked	223.282	210.136	1.06256
	transforming protein n-ras. [swissprot;acc:p01111]	Rooted	108.65	100.35	1.08271
595	5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646]	Squared	34129.7	40434.8	1.18474
	fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087]	Rooted	51.2427	55.468	1.08246
	histone h2b. [refseq;acc:nm_175055]	Measured	3946.32	4475.47	1.13409
	vav proto-oncogene. [swissprot;acc:p15498]	Ranked	212.2	199.849	1.0618
596	5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619]	Squared	34129.6	40434.5	1.18473
	cbf1 interacting corepressor. [refseq;acc:nm_004882]	Rooted	60.0587	65.0057	1.08237
	histone h2b.s (h2b/s). [swissprot;acc:p57053]	Measured	3946.32	4475.47	1.13409
	vav-3 protein. [swissprot;acc:q9ukw4]	Ranked	212.253	199.908	1.06175
597	5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131]	Squared	34129.4	40434.2	1.18473
	evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025]	Rooted	60.0587	65.0057	1.08237
	histone h2b.d (h2b/d). [swissprot;acc:q99877]	Measured	3946.32	4475.47	1.13409
	vav-2 protein. [swissprot;acc:p52735]	Ranked	212.526	200.212	1.0615
598	5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741]	Squared	34129.6	40434.5	1.18473
	histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695]	Measured	3946.32	4475.47	1.13409
	methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192]	Rooted	61.2527	66.2644	1.08182
	rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749]	Ranked	248.463	234.095	1.06138
599	5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9]	Squared	34129.6	40434.5	1.18473
	cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693]	Rooted	138.375	127.926	1.08168
	rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [swissprot;acc:q9y243]	Ranked	248.463	234.095	1.06138
	testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610]	Measured	3946.32	4475.47	1.13409
600	5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478]	Squared	34129.6	40434.5	1.18473
	histone h2b.e (h2b/e). [swissprot;acc:q99879]	Measured	3946.32	4475.47	1.13409
	rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [swissprot;acc:p31751]	Ranked	248.463	234.095	1.06138
	trs85 homolog. [swissprot;acc:q9y2l5]	Rooted	138.375	127.926	1.08168

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.