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 7764 to 7813 of 12912 in total

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

Rank	description	Value Type	red	green	network_comparison
1941	rac gtpase activating protein 1; gtpase activating protein. [refseq;acc:nm_013277]	Measured	5521.07	5856.93	1.06083
1942	j domain protein c21orf55. [swissprot;acc:q9nx36]	Ranked	198.257	196.319	1.00987
	mitochondrial ribosomal protein l30 isoform a. [refseq;acc:nm_145212]	Rooted	62.7515	64.5421	1.02853
	pre-mrna cleavage factor i, 59 kda subunit. [refseq;acc:nm_024811]	Measured	5805.06	6158.16	1.06083
	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]	Squared	28751.1	31432.6	1.09327
1943	14-3-3 protein beta/alpha (protein kinase c inhibitor protein-1) (kcip-1) (protein 1054). [swissprot;acc:p31946]	Rooted	61.3337	63.0838	1.02853
	dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928]	Squared	12346.3	13497.1	1.09321
	megf11 protein. [refseq;acc:nm_032445]	Ranked	224.34	222.147	1.00987
	p300/cbp-associated factor (ec 2.3.1.-) (p/caf) (histone acetylase pcaf). [swissprot;acc:q92831]	Measured	7210.87	7649.23	1.06079
1944	26s protease regulatory subunit s10b (proteasome subunit p42) (p44) (conserved atpase domain protein 44) (cadp44). [swissprot;acc:q92524]	Rooted	62.7515	64.5421	1.02853
	general control of amino acid synthesis protein 5-like 2 (ec 2.3.1.-) (histone acetyltransferase gcn5) (hsgcn5). [swissprot;acc:q92830]	Measured	7210.64	7648.94	1.06079
	megf10 protein. [refseq;acc:nm_032446]	Ranked	224.341	222.148	1.00987
	proteasome subunit alpha type 2 (ec 3.4.25.1) (proteasome component c3) (macropain subunit c3) (multicatalytic endopeptidase complex subunit c3). [swissprot;acc:p25787]	Squared	30581.7	33431.1	1.09317
1945	beta adducin (erythrocyte adducin beta subunit). [swissprot;acc:p35612]	Ranked	224.343	222.151	1.00987
	cofilin, non-muscle isoform (18 kda phosphoprotein) (p18). [swissprot;acc:p23528]	Measured	6230.21	6608.64	1.06074
	junction plakoglobin (desmoplakin iii). [swissprot;acc:p14923]	Squared	27812.9	30401.4	1.09307
	lamin b2. [swissprot;acc:q03252]	Rooted	61.8915	63.6572	1.02853
1946	cofilin, muscle isoform (cofilin 2). [swissprot;acc:q9y281]	Measured	6230.21	6608.64	1.06074
	nuclear factor, interleukin 3 regulated. [refseq;acc:nm_005384]	Ranked	214.234	212.142	1.00986
	tax interaction protein 1. [refseq;acc:nm_014604]	Squared	27812.9	30401.4	1.09307
	transcription initiation factor tfiid 100 kda subunit (tafii-100) (tafii100). [swissprot;acc:q15542]	Rooted	69.7815	71.7716	1.02852
1947	adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819]	Squared	13166.7	14390.7	1.09296
	meiotic recombination protein dmc1/lim15 homolog. [swissprot;acc:q14565]	Rooted	63.5764	65.3899	1.02852
	protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]	Ranked	125.845	127.083	1.00984
	transcription initiation factor tfiid 100 kda subunit (tafii-100) (tafii100). [swissprot;acc:q15542]	Measured	7195.76	7632.83	1.06074
1948	15 kda selenoprotein precursor. [swissprot;acc:o60613]	Ranked	214.522	212.432	1.00984
	destrin (actin-depolymerizing factor) (adf). [swissprot;acc:p18282]	Measured	6230.21	6608.64	1.06074
	glycogenin-1 (ec 2.4.1.186). [swissprot;acc:p46976]	Rooted	65.9292	67.8076	1.02849
	methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582]	Squared	12197.6	13331.2	1.09294
1949	adenosine kinase (ec 2.7.1.20) (ak) (adenosine 5'-phosphotransferase). [swissprot;acc:p55263]	Rooted	65.9292	67.8076	1.02849
	methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [swissprot;acc:p50579]	Squared	12197.6	13331.2	1.09294
	rna-binding protein with multiple splicing (rbp-ms). [swissprot;acc:q93062]	Ranked	218.794	216.663	1.00984
	ubiquitin fusion degradation protein 1 homolog (ub fusion protein 1). [swissprot;acc:q92890]	Measured	6230.21	6608.64	1.06074
1950	60s ribosomal protein l23a. [swissprot;acc:p29316]	Squared	12632.4	13806.3	1.09293
	glutaminyl-trna synthase (glutamine-hydrolyzing)-like 1. [refseq;acc:nm_018292]	Measured	5888.32	6245.89	1.06073
	protein x 0001. [refseq;acc:nm_016302]	Rooted	65.9292	67.8076	1.02849
	vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253]	Ranked	215.847	213.747	1.00982
1951	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]	Squared	12628.2	13801.5	1.09291
	fatty-acid amide hydrolase (ec 3.1.-.-) (oleamide hydrolase) (anandamide amidohydrolase). [swissprot;acc:o00519]	Measured	5888.32	6245.89	1.06073
	glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488]	Rooted	65.9292	67.8076	1.02849
	trna isopentenylpyrophosphate transferase. [refseq;acc:nm_017646]	Ranked	205.876	203.873	1.00982
1952	basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811]	Rooted	63.7832	65.5999	1.02848
	coactosin-like protein. [swissprot;acc:q14019]	Measured	5888.32	6245.89	1.06073
	epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830]	Squared	12627.9	13801.1	1.09291
	importin alpha-1 subunit (karyopherin alpha-1 subunit) (srp1-beta) (rag cohort protein 2) (nucleoprotein interactor 1) (npi-1). [swissprot;acc:p52294]	Ranked	211.647	213.724	1.00981
1953	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678]	Squared	12789.3	13977.2	1.09288
	salivary proline-rich protein po (allele k) [contains: peptide p-d] (fragment). [swissprot;acc:p10162]	Rooted	63.7832	65.5999	1.02848
	type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210]	Ranked	125.912	127.146	1.0098
	uracil-dna glycosylase, mitochondrial precursor (ec 3.2.2.-) (udg). [swissprot;acc:p13051]	Measured	5888.32	6245.89	1.06073
1954	40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]	Squared	12789.3	13977.2	1.09288

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.