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

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Showing element 1 to 50 of 502 in total

Hugo  : no value
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 0

Rank	description	red	green	network_comparison
3	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	4475.84	11083.9	2.47638
4	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	8906	21883	2.45711
5	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	5510.5	11965.7	2.17144
8	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	11525	21888	1.89918
13	heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107]	5210.5	9264.5	1.77804
14	dystrophin. [swissprot;acc:p11532]	10232.5	18054.8	1.76446
15	succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521]	19403	11267	1.72211
17	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	11543	6812	1.69451
18	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	22286	13216	1.68629
19	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]
20	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]
24	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	13730.5	8257	1.66289
25	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]
27	ptd016 protein. [refseq;acc:nm_016125]	18050	11234	1.60673
30	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	7395	11625	1.57201
32	importin 9. [refseq;acc:nm_018085]	13292.2	8691.76	1.52929
33	nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733]
35	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	3208.8	4871.6	1.5182
37	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]	3859	2582	1.49458
39	ero1-like. [refseq;acc:nm_014584]	13853	20536	1.48242
40	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]	3845	5699	1.48218
41	60s ribosomal protein l21. [swissprot;acc:p46778]	9994.33	6758.83	1.47871
45	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	14592	21113.7	1.44694
46	60s ribosomal protein l37a. [swissprot;acc:p12751]	12941.7	18499.2	1.42943
49	brain protein 16. [refseq;acc:nm_016458]	6890.54	4854.99	1.41927
53	ubiquitin-conjugating enzyme e2-18 kda ubch7 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (ubcm4) (e2-f1) (l-ubc). [swissprot;acc:p51966]	3284	4554.5	1.38688
56	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	22440	16388	1.36929
67	presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341]	10793.5	14291.5	1.32408
68	purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491]	8932.56	11823.3	1.32362
69	collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400]	7704.7	10174.1	1.32051
70	protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981]	13975.7	10593.2	1.31931
73	phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [swissprot;acc:p18669]	4119	5397	1.31027
74	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973]	6742.5	8759.5	1.29915
75	nanos (fragment). [sptrembl;acc:q8wy41]	8782	11350	1.29242
76	spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813]	3474	2695	1.28905
78	repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273]	7584.72	9706.12	1.27969
82	dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6]	7706.5	6058	1.27212
86	high mobility group protein 1 (hmg-1). [swissprot;acc:p09429]	5677.96	4546.87	1.24876
92	dok-like protein. [refseq;acc:nm_024872]	17571	21783	1.23971
97	microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378]	8335.82	10228.3	1.22703
100	creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532]	9183.49	11217.7	1.22151
101	dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7]	14548.5	11915.2	1.221
102	60s ribosomal protein l18a. [swissprot;acc:q02543]	12738.7	10437.1	1.22052
105	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]	17410.5	14360	1.21243
111	protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031]	9940.69	11929	1.20002
112	40s ribosomal protein s26. [swissprot;acc:p02383]	14269.7	17098	1.1982
114	bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132]	8871.11	10603.2	1.19525
115	spir-2 protein (fragment). [sptrembl;acc:q8wwl2]	18662.8	15627	1.19427
117	basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811]	11545	13771.5	1.19285
119	mesoderm induction early response 1. [refseq;acc:nm_020948]	3609	4302.5	1.19216

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
- Hugo is the HGNC identifier if it exists
- 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.