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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 1775 to 1824 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
111	voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359]	Rooted	Divided	1	49.2923	62.3969	1.26585
	williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158]	Squared		0	16.4056	33.4891	2.04132
112	40s ribosomal protein s26. [swissprot;acc:p02383]	Ranked			14269.7	17098	1.1982
	autophagy protein 12-like (apg12-like). [swissprot;acc:o94817]	Measured	Subtracted	1	11757.8	9352.11	2405.69
	ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1]	Rooted	Divided	0	22.4608	17.665	1.27149
	cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857]	Squared	Subtracted	1	96730.5	69286.7	27443.8
	dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33]	Ranked			275.754	235.908	39.846
	guanine nucleotide-binding protein beta subunit-like protein 12.3 (p205) (receptor of activated protein kinase c 1) (rack1) (receptor for activated c kinase). [swissprot;acc:p25388]	Rooted		0	31.1565	35.6653	4.5088
	imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549]	Ranked			8335.82	10228.3	1892.48
	lats homolog 1. [refseq;acc:nm_004690]	Measured	Divided		160	112.25	1.42539
	microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268]	Squared			138.269	68.9705	2.00476
	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055]			1	19321	12542.6	1.54043
	pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152]		Subtracted	0	12235.5	13399.2	1163.7
	probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185]	Measured			1095.42	812.166	283.254
	sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906]	Rooted		1	33.9632	18.4255	15.5377
	t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492]	Ranked	Divided		332.874	267.246	1.24557
	u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621]	Measured			4366.44	5899.76	1.35116
	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02]	Rooted			49.3267	62.4167	1.26537
113	60s ribosomal protein l7. [swissprot;acc:p18124]	Squared	Subtracted	0	5826.27	6955.21	1128.94
	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	Rooted	Divided	1	80.4705	101.526	1.26165
	ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812]	Squared	Subtracted		96602.7	69211.2	27391.5
	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]	Measured			4800.81	7132.71	2331.9
	db83 protein. [swissprot;acc:p57088]	Rooted			33.9632	18.4255	15.5377
	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]	Measured	Divided		4366.44	5899.76	1.35116
	fos-related antigen 2. [swissprot;acc:p15408]	Rooted	Subtracted	0	44.3292	39.9005	4.4287
	glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434]	Squared	Divided		387.336	770.962	1.99042
	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558]	Ranked		1	332.874	267.246	1.24557
	microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378]		Subtracted	0	8335.82	10228.3	1892.48
	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882]	Squared	Divided	1	19321	12542.6	1.54043
	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	Rooted		0	72.1137	56.7758	1.27015
	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640]	Ranked			5673.33	6797.56	1.19816
	serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323]		Subtracted	1	194.372	234.204	39.832
	sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]	Measured	Divided	0	160	112.25	1.42539
	transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653]		Subtracted		3117.17	2833.94	283.23
114	60s ribosomal protein l37a. [swissprot;acc:p12751]				305.45	26.1599	279.29
	autophagy protein 12-like (apg12-like). [swissprot;acc:o94817]	Squared		1	67438.6	40697	26741.6
	b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681]	Ranked			229.818	267.265	37.447
	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	Rooted	Divided		80.4705	101.526	1.26165
	bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132]	Ranked		0	8871.11	10603.2	1.19525
	cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526]	Squared	Subtracted		5868.74	4797.35	1071.39
	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]	Measured		1	13768.2	11466	2302.2
	daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959]		Divided	0	671.769	472.945	1.4204
	guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775]	Rooted	Subtracted	1	40.225	24.7051	15.5199
	huntingtin interacting protein c. [refseq;acc:nm_012272]	Measured	Divided		4300.47	5807.72	1.35048
	isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252]	Rooted	Subtracted	0	11.0051	15.3166	4.3115
	kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559]	Ranked	Divided	1	332.874	267.246	1.24557
	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]		Subtracted	0	19355	17469.2	1885.8
	myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883]	Squared	Divided	1	19321	12542.6	1.54043
	polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393]	Rooted		0	14.7363	18.7165	1.27009
	zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782]	Squared			35.0828	69.7867	1.9892

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.