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

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Showing element 6408 to 6457 of 25824 in total

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

Rank	Value Type	description	green	red	network_comparison
1602	Rooted	dna topoisomerase iii alpha (ec 5.99.1.2). [swissprot;acc:q13472]	64.0396	61.8653	1.03515
1603	Measured	phosphoacetylglucosamine mutase (ec 5.4.2.3) (pagm) (acetylglucosamine phosphomutase) (n-acetylglucosamine-phosphate mutase) (phosphoglucomutase 3). [swissprot;acc:o95394]	5605.8	5232.14	1.07142
	Ranked	heat shock factor binding protein 1. [swissprot;acc:o75506]	213.22	216.62	1.01595
	Squared	casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784]	18947.6	17081.4	1.10925
	Rooted	fibulin-1 precursor. [swissprot;acc:p23142]	78.6278	75.958	1.03515
1604	Measured	malonyl-coa decarboxylase, mitochondrial precursor (ec 4.1.1.9) (mcd). [swissprot;acc:o95822]	6617.91	6176.82	1.07141
	Ranked	protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760]	211.614	214.984	1.01593
	Squared	lin-7 homolog a; vertebrate lin7 homolog 1; tax interaction protein 33; mammalian lin-7 1. [refseq;acc:nm_004664]	32458.3	29262.5	1.10921
	Rooted	phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing gamma polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-gamma) (ptdins-3-kinase c2 gamma) (pi3k-c2gamma). [swissprot;acc:o75747]	66.254	64.0052	1.03513
1605	Measured	itchy homolog e3 ubiquitin protein ligase; atrophin-1 interacting protein 4; itchy (mouse homolog) e3 ubiquitin protein ligase; nfe2-associated polypeptide 1; ubiquitin protein ligase itch. [refseq;acc:nm_031483]	6617.91	6176.82	1.07141
	Ranked	hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [swissprot;acc:p55317]	213.916	217.322	1.01592
	Squared	peroxisomal membrane protein 2 (22 kda peroxisomal membrane protein). [swissprot;acc:q9nr77]	34282.7	30908.9	1.10915
	Rooted	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]	66.254	64.0052	1.03513
1606	Measured	5'-methylthioadenosine phosphorylase (ec 2.4.2.28) (mta phosphorylase) (mtapase). [swissprot;acc:q13126]	5606.53	5232.99	1.07138
	Ranked	apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772]	204.662	207.916	1.0159
	Squared	heat shock-related 70 kda protein 2 (heat shock 70 kda protein 2). [swissprot;acc:p54652]	34282.7	30908.9	1.10915
	Rooted	dynamin 1-like protein isoform 3; dynamin-like protein. [refseq;acc:nm_005690]	66.254	64.0052	1.03513
1607	Measured	putative ribosomal rna methyltransferase 1 (ec 2.1.1.-) (rrna (uridine-2'-o-)-methyltransferase) (jm23 protein). [swissprot;acc:q9uet6]	5606.53	5232.99	1.07138
	Ranked	protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761]	211.622	214.982	1.01588
	Squared	heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107]	34282.7	30908.9	1.10915
	Rooted	phosphoinositide-3-kinase, class 2, alpha polypeptide; c2-containing phosphatidylinositol kinase. [refseq;acc:nm_002645]	66.254	64.0052	1.03513
1608	Measured	ubiquitin. [swissprot;acc:p02248]	6597.55	6158.22	1.07134
	Ranked	ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [refseq;acc:nm_003349]	204.867	208.106	1.01581
	Squared	heat shock cognate 71 kda protein. [swissprot;acc:p11142]	34282.7	30908.9	1.10915
	Rooted	likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235]	95.6982	99.0527	1.03505
1609	Measured	26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832]	6242.44	5826.74	1.07134
	Ranked	utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851]	204.876	208.113	1.0158
	Squared	wilms' tumor 1-associating protein (wt1-associated protein). [swissprot;acc:q15007]	32145.6	28992.5	1.10876
	Rooted	proteasome subunit beta type 5 precursor (ec 3.4.25.1) (proteasome epsilon chain) (macropain epsilon chain) (multicatalytic endopeptidase complex epsilon chain) (proteasome subunit x) (proteasome chain 6) (proteasome subunit mb1). [swissprot;acc:p28074]	67.884	65.5919	1.03494
1610	Measured	eif-5a2 protein. [refseq;acc:nm_020390]	6665.83	6222.4	1.07126
	Ranked	ubiquitin-conjugating enzyme e2 variant 2; 1 alpha,25-dihydroxyvitamin d3-inducible; enterocyte differentiation promoting factor; methyl methanesulfonate sensitive 2, s. cerevisiae, homolog of. [refseq;acc:nm_003350]	204.886	208.122	1.01579
	Squared	hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043]	17338.5	15639.2	1.10866
	Rooted	sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911]	69.831	67.4766	1.03489
1611	Measured	cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642]	5132.35	5497.73	1.07119
	Ranked	p10-binding protein. [refseq;acc:nm_024491]	217.877	221.313	1.01577
	Squared	heat shock factor binding protein 1. [swissprot;acc:o75506]	30225.7	27263.5	1.10865
	Rooted	kidney and liver proline oxidase 1. [refseq;acc:nm_021232]	69.8487	67.4958	1.03486
1612	Measured	eukaryotic translation initiation factor 5a (eif-5a) (eif-4d) (rev- binding factor). [swissprot;acc:p10159]	6655.12	6212.98	1.07116
	Ranked	enthoprotin; epsin 4; clathrin interacting protein localized in the trans-golgi region. [refseq;acc:nm_014666]	224.902	221.426	1.0157
	Squared	brain protein 16. [refseq;acc:nm_016458]	29043.8	26202.2	1.10845
	Rooted	solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [refseq;acc:nm_145913]	69.8568	67.5045	1.03485
1613	Measured	mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650]	6464.5	6035.6	1.07106
	Ranked	hiv-1 tat interactive protein 2, 30kda; tat-interacting protein (30kd); hiv-1 tat interactive protein 2, 30 kda; hiv-1 tat interactive protein 2, 30 kd. [refseq;acc:nm_006410]	185.241	182.378	1.0157
	Squared	neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092]	17067.9	15399.5	1.10834
	Rooted	sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [swissprot;acc:q9y289]	69.8628	67.511	1.03484
1614	Measured	nefa-interacting nuclear protein nip30. [refseq;acc:nm_024946]	6464.5	6035.6	1.07106
	Ranked	hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [swissprot;acc:q9y261]	213.897	217.233	1.0156
	Squared	neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966]	17067.9	15399.5	1.10834
	Rooted	trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317]	56.0802	54.1932	1.03482
1615	Measured	lim homeobox transcription factor 1 alpha (lim/homeobox protein lmx1a) (lim-homeobox protein 1.1) (lmx-1.1). [swissprot;acc:q8te12]	6464.5	6035.6	1.07106

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.