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

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

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.