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

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Showing element 501 to 550 of 9634 in total

Value Type  : Ranked
Filtered  : 0
Network Comparison Type  : Divided

description	Rank	network_comparison	Interaction Map	green	red
hemoglobin gamma-a and gamma-g chains. [swissprot;acc:p02096]	31	1.39168	Low confidence	15984.3	11485.6
heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174]	66	1.32449	High confidence	15180	11461
	377	1.08754	Low confidence	9800.48	9011.64
hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934]	206	1.11361	High confidence	6716	7479
	307		Low confidence
hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	83	1.23109		17020.5	13825.5
	352	1.04776	High confidence	15577	16321
hepatocellularcarcinoma-associated antigen hca557a. [refseq;acc:nm_015433]	450	1.07276	Low confidence	2772	2584
hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712]	23	1.67148	High confidence	9285.44	15520.4
	122	1.18575	Low confidence	10506.7	12458.3
hexokinase, type i (ec 2.7.1.1) (hk i) (brain form hexokinase). [swissprot;acc:p19367]	339	1.10269		13838.9	12550.1
high mobility group protein 1 (hmg-1). [swissprot;acc:p09429]	86	1.24876	High confidence	4546.87	5677.96
	476	1.06357	Low confidence	12697.5	11938.6
high mobility group protein 1-like 10 (hmg-1l10). [swissprot;acc:q9ugv6]	88	1.24852	High confidence	4547.66	5677.86
	475	1.06362	Low confidence	12658.3	11901.1
high mobility group protein 4-like (hmg-4l). [swissprot;acc:q9uj13]	90	1.24755	High confidence	4550.87	5677.45
	478	1.06291	Low confidence	12367.2	11635.2
high-glucose-regulated protein 8 (ny-ren-2 antigen). [swissprot;acc:q9y5a9]	190	1.122	High confidence	16764.2	18809.5
	624	1.03017	Low confidence	11780.9	12136.3
histone deacetylase 2 (hd2). [swissprot;acc:q92769]	431	1.02495	High confidence	9799.17	10043.7
	812	1.00373	Low confidence	11786.9	11743.1
histone h1.4 (histone h1b). [swissprot;acc:p10412]	682	1.01989		11087.2	10871
histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001]	468	1.01391	High confidence	20914	21205
	783	1.00757	Low confidence	12027.5	12118.5
histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]	467	1.01391	High confidence	20914	21205
	782	1.00757	Low confidence	12027.5	12118.5
histone h2a; h2a histone family, member r. [refseq;acc:nm_170745]	469	1.01391	High confidence	20914	21205
	784	1.00757	Low confidence	12027.5	12118.5
histone h2b. [refseq;acc:nm_175055]	439	1.0228	High confidence	8574.79	8770.3
	768	1.00869	Low confidence	11646.6	11546.3
histone h2b.c (h2b/c). [swissprot;acc:q99880]	441	1.02276	High confidence	8574.98	8770.14
	772	1.00857	Low confidence	11645.3	11546.4
histone h2b.d (h2b/d). [swissprot;acc:q99877]	436	1.02293	High confidence	8574.19	8770.82
	774	1.00857	Low confidence	11646.2	11547.2
histone h2b.e (h2b/e). [swissprot;acc:q99879]	440	1.0228	High confidence	8574.81	8770.28
	769	1.00869	Low confidence	11646.6	11546.3
histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778]	435	1.02296	High confidence	8574.04	8770.94
	773	1.00857	Low confidence	11646.4	11547.4
histone h2b.s (h2b/s). [swissprot;acc:p57053]	437	1.02283	High confidence	8574.66	8770.41
	770	1.00867	Low confidence	11646.6	11546.5
histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106]	438	1.0228	High confidence	7586.42	7759.36
	588	1.03989	Low confidence	11799.6	12270.3
histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351]	445	1.02237	High confidence	7790.78	7965.06
	589	1.03961	Low confidence	11787.5	12254.4
histone h4. [swissprot;acc:p02304]	410	1.03248	High confidence	9308.99	9611.37
	809	1.00403	Low confidence	11720.2	11673.1
histone-lysine n-methyltransferase, h3 lysine-79 specific (ec 2.1.1.43) (histone h3-k79 methyltransferase) (h3-k79-hmtase) (dot1-like protein). [swissprot;acc:q8tek3]	78	1.23114		13236	10751
homeobox protein cdx-2 (caudal-type homeobox protein 2) (cdx-3). [swissprot;acc:q99626]	494	1.05985		11549.1	12240.3
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	10	1.68629		13216	22286
	20		High confidence

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.