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

Results: HTML CSV LaTeX

Showing element 2951 to 3000 of 14920 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
369	ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658]	Squared	0	346.699	309.317	1.12085
	uncharacterized bone marrow protein bm033. [refseq;acc:nm_018452]	Rooted		17.8274	17.1002	1.04253
370	26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832]			30.7424	32.0298	1.04188
	dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959]	Measured		1049.21	989.438	1.06041
	lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455]		1	4108.15	4808.93	1.17058
	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]	Rooted		49.7435	45.0586	1.10397
	nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438]	Ranked		242.159	265.104	1.09475
	protein 4.1 (band 4.1) (p4.1) (epb4.1) (4.1r). [swissprot;acc:p11171]	Squared		45986	56776.1	1.23464
	pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803]	Ranked	0	13652.7	13061	1.0453
	survival motor neuron protein (component of gems 1) (gemin1). [swissprot;acc:q16637]	Squared		1039.56	927.649	1.12064
371	band 4.1-like protein 1 (neuronal protein 4.1) (4.1n). [swissprot;acc:q9h4g0]		1	45985.9	56776	1.23464
	dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9]		0	18585	20796.3	1.11898
	phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6]	Measured		1631.97	1542.23	1.05819
	protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [swissprot;acc:p07237]	Rooted		20.9428	21.8063	1.04123
	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424]	Ranked	1	186.52	170.42	1.09447
	serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [swissprot;acc:o43464]	Measured		5067.02	5926.46	1.16961
	swi/snf-related matrix-associated actin-dependent regulator of chromatin c2 isoform a; mammalian chromatin remodeling complex brg1-associated factor 170; chromatin remodeling complex baf170 subunit; swi3-like protein; swi/snf complex 170 kda subunit. [refseq;acc:nm_003075]	Ranked	0	13247.9	12674.2	1.04527
	zinc finger-like protein 9. [refseq;acc:nm_033414]	Rooted	1	49.3451	54.4606	1.10367
372	band 4.1-like protein 3 (4.1b) (differentially expressed in adenocarcinoma of the lung protein 1) (dal-1). [swissprot;acc:q9y2j2]	Squared		45986.7	56776.8	1.23464
	coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606]	Measured	0	5427.25	5130.58	1.05782
	dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355]	Ranked		11869.9	12402.7	1.04489
	enigma protein; lim domain protein. [refseq;acc:nm_005451]	Squared		21.836	19.5177	1.11878
	membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9]	Rooted	1	49.3451	54.4606	1.10367
	probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105]	Measured		5067	5926.17	1.16956
	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]	Ranked		186.52	170.42	1.09447
	secreted modular calcium-binding protein 1. [refseq;acc:nm_022137]	Rooted	0	11.9476	12.4394	1.04116
373	60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7]	Ranked	1	242.37	265.255	1.09442
	band 4.1-like protein 2 (generally expressed protein 4.1) (4.1g). [swissprot;acc:o43491]	Squared		45986	56776.1	1.23464
	guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915]	Rooted		49.3451	54.4606	1.10367
	kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719]	Measured	0	2713.5	2864.68	1.05571
	mitogen-activated protein kinase kinase kinase 5 (ec 2.7.1.-) (mapk/erk kinase kinase 5) (mek kinase 5) (mekk 5) (apoptosis signal- regulating kinase 1) (ask-1). [swissprot;acc:q99683]	Ranked		10598.2	11061.5	1.04371
	probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110]	Measured	1	5066.99	5926.1	1.16955
	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260]	Rooted	0	30.3054	31.5389	1.0407
	sprouty homolog 4 (spry-4). [swissprot;acc:q9c004]	Squared		215.107	192.635	1.11666
374	60s ribosomal protein l26. [swissprot;acc:q02877]	Rooted	1	50.2549	45.5599	1.10305
	adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741]	Measured	0	2323.8	2452.23	1.05527
	alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298]	Squared		2572.14	2869.96	1.11579
	calcyphosine. [swissprot;acc:q13938]	Ranked		9874.54	9478.1	1.04183
	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260]	Rooted		30.2858	31.5117	1.04048
	serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743]	Measured	1	5066.93	5925.38	1.16942
	spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6]	Squared		45987	56777.1	1.23463
	transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188]	Ranked		267.208	244.168	1.09436
375	45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [swissprot;acc:q9brk5]	Squared		45987	56777.1	1.23463
	60s ribosomal protein l35. [swissprot;acc:p42766]	Rooted		50.2545	45.5637	1.10295
	dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802]	Ranked		242.686	265.516	1.09407
	estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [swissprot;acc:p14061]	Measured	0	2323.8	2452.23	1.05527
	germ cell-less. [refseq;acc:nm_022471]	Rooted		27.8491	26.7806	1.0399
	importin 9. [refseq;acc:nm_018085]	Squared		1062.18	952.74	1.11487
	tbp-associated factor 9l; neuronal cell death-related protein; taf9-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 31 kd; neuronal cell death-related gene in neuron-7; transcription associated factor tafii31l; transcription initiation factor iid, 31kd subunit. [refseq;acc:nm_015975]	Ranked		14247.6	13686.9	1.04097
	u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116]	Measured	1	4700.42	5492.63	1.16854

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.