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	Network Comparison Type	Value Type	Filtered	Interaction Map	green	red	network_comparison

Results: HTML CSV LaTeX

Showing element 12864 to 12913 of 25824 in total

Filtered  : 1
Interaction Map  : High confidence

Rank	description	Network Comparison Type	Value Type	green	red	network_comparison
1608	ubiquitin. [swissprot;acc:p02248]	Divided	Measured	6597.55	6158.22	1.07134
1609	26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832]			6242.44	5826.74
	apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772]	Subtracted	Ranked	204.662	207.916	3.254
	eukaryotic translation initiation factor 2 subunit 3 (eukaryotic translation initiation factor 2 gamma subunit) (eif-2-gamma). [swissprot;acc:p41091]		Squared	26802.4	24291.6	2510.8
	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]	Divided	Rooted	67.884	65.5919	1.03494
	sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4]	Subtracted		64.1935	61.9701	2.2234
	serine/threonine-protein kinase dcamkl1 (ec 2.7.1.-) (doublecortin- like and cam kinase-like 1). [swissprot;acc:o15075]		Measured	6721.08	6297.05	424.03
	utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851]	Divided	Ranked	204.876	208.113	1.0158
	wilms' tumor 1-associating protein (wt1-associated protein). [swissprot;acc:q15007]		Squared	32145.6	28992.5	1.10876
1610	c18b11 homolog (44.9kd). [refseq;acc:nm_152260]	Subtracted	Ranked	214.2	217.446	3.246
	clathrin coat assembly protein ap180 (clathrin coat associated protein ap180) (91 kda synaptosomal-associated protein). [swissprot;acc:o60641]		Rooted	64.1935	61.9701	2.2234
	eif-5a2 protein. [refseq;acc:nm_020390]	Divided	Measured	6665.83	6222.4	1.07126
	hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043]		Squared	17338.5	15639.2	1.10866
	proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [swissprot;acc:p07332]	Subtracted	Measured	6503.12	6079.19	423.93
	sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911]	Divided	Rooted	69.831	67.4766	1.03489
	tata element modulatory factor (tmf). [swissprot;acc:p82094]	Subtracted	Squared	26223.8	23713.7	2510.1
	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]	Divided	Ranked	204.886	208.122	1.01579
1611	arginine-glutamic acid dipeptide (re) repeats; atrophin 1-like; arginine glutamic acid dipeptide re repeats. [refseq;acc:nm_012102]	Subtracted	Rooted	64.1938	61.9705	2.2233
	cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642]	Divided	Measured	5132.35	5497.73	1.07119
	heat shock factor binding protein 1. [swissprot;acc:o75506]		Squared	30225.7	27263.5	1.10865
	kidney and liver proline oxidase 1. [refseq;acc:nm_021232]		Rooted	69.8487	67.4958	1.03486
	molybdenum cofactor synthesis protein 2 large subunit (molybdopterin synthase large subunit) (mpt synthase large subunit) (mocs2b) (moco1- b). [swissprot;acc:o96007]	Subtracted	Measured	6503.12	6079.19	423.93
	p10-binding protein. [refseq;acc:nm_024491]	Divided	Ranked	217.877	221.313	1.01577
	scy1-like 1; telomerase regulation-associated protein; ht019 protein; telomerase regulation-associated protein; n-terminal kinase-like protein; teratoma-associated tyrosine kinase; n-terminal kinase-like. [refseq;acc:nm_020680]	Subtracted	Squared	26223.8	23713.7	2510.1
	z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24]		Ranked	214.2	217.446	3.246
1612	anaphase-promoting complex subunit 10; anaphase-promoting complex 10. [refseq;acc:nm_014885]		Measured	6503.12	6079.19	423.93
	brain protein 16. [refseq;acc:nm_016458]	Divided	Squared	29043.8	26202.2	1.10845
	enthoprotin; epsin 4; clathrin interacting protein localized in the trans-golgi region. [refseq;acc:nm_014666]		Ranked	224.902	221.426	1.0157
	eukaryotic translation initiation factor 5a (eif-5a) (eif-4d) (rev- binding factor). [swissprot;acc:p10159]		Measured	6655.12	6212.98	1.07116
	nuclear pore complex protein nup98 (nucleoporin nup98) (98 kda nucleoporin). [swissprot;acc:p52948]	Subtracted	Squared	26223.8	23713.7	2510.1
	pp1201 protein. [refseq;acc:nm_022152]		Ranked	214.2	217.446	3.246
	solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [refseq;acc:nm_145913]	Divided	Rooted	69.8568	67.5045	1.03485
	ubiquitin carboxyl-terminal hydrolase 8 (ec 3.1.2.15) (ubiquitin thiolesterase 8) (ubiquitin-specific processing protease 8) (deubiquitinating enzyme 8). [swissprot;acc:p40818]	Subtracted		64.1936	61.9703	2.2233
1613	60s ribosomal protein l29 (cell surface heparin binding protein hip). [swissprot;acc:p47914]		Measured	6503.12	6079.19	423.93
	ammecr1 protein. [refseq;acc:nm_015365]		Squared	26223.8	23713.7	2510.1
	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]	Divided	Ranked	185.241	182.378	1.0157
	lifeguard; kiaa0950 protein. [refseq;acc:nm_012306]	Subtracted		214.2	217.446	3.246
	mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650]	Divided	Measured	6464.5	6035.6	1.07106
	neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092]		Squared	17067.9	15399.5	1.10834
	rod1 regulator of differentiation 1; fission yeast differentiation regulator; regulator of differentiation (in s. pombi) 1; regulator of differentiation (in s. pombe) 1. [refseq;acc:nm_005156]	Subtracted	Rooted	64.1936	61.9703	2.2233
	sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [swissprot;acc:q9y289]	Divided		69.8628	67.511	1.03484
1614	hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [swissprot;acc:q9y261]		Ranked	213.897	217.233	1.0156
	mrna-associated protein mrnp 41 (rae1 protein homolog). [swissprot;acc:p78406]	Subtracted	Squared	26223.8	23713.7	2510.1
	nefa-interacting nuclear protein nip30. [refseq;acc:nm_024946]	Divided	Measured	6464.5	6035.6	1.07106
	neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966]		Squared	17067.9	15399.5	1.10834
	polypyrimidine tract binding protein 2; neural polypyrimidine tract binding protein; ptb-like protein. [refseq;acc:nm_021190]	Subtracted	Rooted	64.1936	61.9703	2.2233
	proto-oncogene tyrosine-protein kinase fer (ec 2.7.1.112) (p94-fer) (c-fer). [swissprot;acc:p16591]		Measured	6503.12	6079.19	423.93
	sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772]		Ranked	214.2	217.446	3.246
	trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317]	Divided	Rooted	56.0802	54.1932	1.03482
1615	adaptor-associated kinase 1. [refseq;acc:nm_014911]	Subtracted		64.1936	61.9703	2.2233

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.