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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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

Results: HTML CSV LaTeX

Showing element 6436 to 6485 of 12912 in total

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

Rank	description	Value Type	red	green	network_comparison
1609	wilms' tumor 1-associating protein (wt1-associated protein). [swissprot;acc:q15007]	Squared	28992.5	32145.6	1.10876
1610	eif-5a2 protein. [refseq;acc:nm_020390]	Measured	6222.4	6665.83	1.07126
	hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043]	Squared	15639.2	17338.5	1.10866
	sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911]	Rooted	67.4766	69.831	1.03489
	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]	Ranked	208.122	204.886	1.01579
1611	cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642]	Measured	5497.73	5132.35	1.07119
	heat shock factor binding protein 1. [swissprot;acc:o75506]	Squared	27263.5	30225.7	1.10865
	kidney and liver proline oxidase 1. [refseq;acc:nm_021232]	Rooted	67.4958	69.8487	1.03486
	p10-binding protein. [refseq;acc:nm_024491]	Ranked	221.313	217.877	1.01577
1612	brain protein 16. [refseq;acc:nm_016458]	Squared	26202.2	29043.8	1.10845
	enthoprotin; epsin 4; clathrin interacting protein localized in the trans-golgi region. [refseq;acc:nm_014666]	Ranked	221.426	224.902	1.0157
	eukaryotic translation initiation factor 5a (eif-5a) (eif-4d) (rev- binding factor). [swissprot;acc:p10159]	Measured	6212.98	6655.12	1.07116
	solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [refseq;acc:nm_145913]	Rooted	67.5045	69.8568	1.03485
1613	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]	Ranked	182.378	185.241	1.0157
	mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650]	Measured	6035.6	6464.5	1.07106
	neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092]	Squared	15399.5	17067.9	1.10834
	sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [swissprot;acc:q9y289]	Rooted	67.511	69.8628	1.03484
1614	hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [swissprot;acc:q9y261]	Ranked	217.233	213.897	1.0156
	nefa-interacting nuclear protein nip30. [refseq;acc:nm_024946]	Measured	6035.6	6464.5	1.07106
	neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966]	Squared	15399.5	17067.9	1.10834
	trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317]	Rooted	54.1932	56.0802	1.03482
1615	dna polymerase epsilon subunit b (ec 2.7.7.7) (dna polymerase ii subunit b). [swissprot;acc:p56282]	Ranked	246.38	242.596	1.0156
	heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839]	Squared	15399.5	17067.9	1.10834
	lim homeobox transcription factor 1 alpha (lim/homeobox protein lmx1a) (lim-homeobox protein 1.1) (lmx-1.1). [swissprot;acc:q8te12]	Measured	6035.6	6464.5	1.07106
	monoglyceride lipase; lysophospholipase-like. [refseq;acc:nm_007283]	Rooted	67.8337	70.1815	1.03461
1616	mitochondrial precursor proteins import receptor (translocase of outer membrane tom70). [swissprot;acc:o94826]	Measured	6035.6	6464.5	1.07106
	n-acetylglutamate synthase. [refseq;acc:nm_153006]	Ranked	223.179	226.611	1.01538
	runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [swissprot;acc:q13950]	Squared	15399.5	17067.9	1.10834
	twinkle; likely ortholog of mouse t7 gp4-like protein with intramitochondrial nucleoid localization. [refseq;acc:nm_021830]	Rooted	62.3332	64.4896	1.03459
1617	e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040]	Squared	15399.5	17067.9	1.10834
	lim homeobox transcription factor 1 beta (lim/homeobox protein lmx1b) (lim-homeobox protein 1.2) (lmx-1.2). [swissprot;acc:o60663]	Measured	6035.6	6464.5	1.07106
	rabaptin, rab gtpase binding effector protein 1; rabaptin-5; neurocrescin. [refseq;acc:nm_004703]	Rooted	62.3332	64.4896	1.03459
	serine hydroxymethyltransferase, cytosolic (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34896]	Ranked	221.045	217.699	1.01537
1618	60s ribosomal protein l18. [swissprot;acc:q07020]	Squared	15399.5	17067.9	1.10834
	f-actin capping protein alpha-3 subunit (capz alpha-3) (germ cell- specific protein 3). [swissprot;acc:q96kx2]	Rooted	64.1847	66.4025	1.03455
	proteasome subunit beta type 2 (ec 3.4.25.1) (proteasome component c7-i) (macropain subunit c7-i) (multicatalytic endopeptidase complex subunit c7-i). [swissprot;acc:p49721]	Measured	6035.6	6464.5	1.07106
	transcription elongation factor a protein 2 (transcription elongation factor s-ii protein 2) (testis-specific s-ii) (transcription elongation factor tfiis.l). [swissprot;acc:q15560]	Ranked	227.768	231.246	1.01527
1619	adp-ribosylation factor-like protein 1. [swissprot;acc:p40616]	Measured	6035.6	6464.5	1.07106
	f-actin capping protein beta subunit (capz beta). [swissprot;acc:p47756]	Rooted	64.1847	66.4025	1.03455
	serine/threonine-protein kinase dcamkl1 (ec 2.7.1.-) (doublecortin- like and cam kinase-like 1). [swissprot;acc:o15075]	Squared	31022.4	34382.7	1.10832
	transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193]	Ranked	227.768	231.246	1.01527
1620	acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [swissprot;acc:p45954]	Measured	6296.52	6743.85	1.07104
	heat shock protein hsp 90-beta (hsp 84) (hsp 90). [swissprot;acc:p08238]	Squared	26833.7	29737.4	1.10821
	s-adenosylmethionine synthetase gamma form (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-ii). [swissprot;acc:p31153]	Rooted	64.4022	66.6218	1.03446
	transcription initiation factor iib (general transcription factor tfiib) (s300-ii). [swissprot;acc:q00403]	Ranked	228.611	225.185	1.01521
1621	calreticulin precursor (crp55) (calregulin) (hacbp) (erp60). [swissprot;acc:p27797]	Rooted	58.9585	60.9832	1.03434
	sterile alpha and tir motif containing 1; sterile alpha and heat/armadillo motif protein, ortholog of drosophila. [refseq;acc:nm_015077]	Measured	5520.36	5911.98	1.07094
	t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711]	Squared	14652.3	16236.8	1.10814
	thyroid receptor interacting protein 3 (trip-3) (fragment). [swissprot;acc:q15649]	Ranked	228.611	225.185	1.01521
1622	apurinic/apyrimidinic endonuclease 2; apurinic/apyrimidinic endonuclease-like 2; apex nuclease-like 2. [refseq;acc:nm_014481]	Rooted	61.6526	63.7646	1.03426

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.