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	network_comparison	red	green

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Showing element 101 to 150 of 3228 in total

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

Rank	description	network_comparison	red	green
101	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]	1.24949	88.2482	110.265
102	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1]
103	trophinin. [swissprot;acc:q12816]
104	homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839]	1.24926	252.371	202.016
105	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901]	1.24914	266.716	333.165
106	ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807]	1.24913	252.329	202.004
107	homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272]	1.24907	252.309	201.998
108	homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838]	1.24902	252.296	201.995
109	guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0]	1.24856	266.933	333.281
110	deltex 2. [refseq;acc:nm_020892]	1.2459	333.144	267.393
111	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]	1.24563	332.925	267.274
112	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]	1.24557	332.874	267.246
113	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558]
114	kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559]
115	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688]
116	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520]	1.24545	268.565	334.483
117	neuralized-like. [refseq;acc:nm_004210]	1.24491	332.326	266.948
118	nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09]	1.24382	284.753	228.934
119	nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181]	1.23157	318.982	259.004
120	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	1.21699	269.278	327.709
121	cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929]	1.2169	269.254	327.655
122	potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980]	1.21688	269.248	327.642
123	potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979]	1.21681	269.23	327.601
124	high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339]	1.21519	208.52	171.595
125	high-mobility group 20a. [refseq;acc:nm_018200]	1.21429	208.588	171.778
126	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	1.21277	94	114
127	putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453]
128	associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]
129	neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079]
130	protein hspc134 (protein cda04). [swissprot;acc:q9by43]
131	son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583]	1.21228	294.053	242.562
132	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	1.2069	350	290
133	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]
134	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]
135	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]
136	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]
137	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]
138	serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323]	1.20493	194.372	234.204
139	amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410]	1.20415	271.752	225.68
140	ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570]	1.20408	59	49
141	ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157]
142	ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]
143	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685]
144	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592]	1.20312	265.686	319.651
145	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183]	1.20293	265.639	319.546
146	kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193]	1.20291	265.632	319.531
147	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	1.2009	50.7983	42.3003
148	sad1/unc-84 protein-like 1. [swissprot;acc:o94901]	1.19841	296.677	247.559
149	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	1.19718	142	170
150	myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]	1.19565	55	46

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.