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

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Showing element 868 to 917 of 3228 in total

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

red	green	Rank	description	network_comparison
4368.44	4539.34	2400	malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [swissprot;acc:p40926]	1.03912
4374.32	4126.96	1963	phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439]	1.05994
		1964	pp3111 protein. [refseq;acc:nm_022156]
		1965	syntaxin 18. [swissprot;acc:q9p2w9]
		1966	rd protein. [swissprot;acc:p18615]
		1968	glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417]
		1969	androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108]
		1970	atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539]
		1971	j domain containing protein 1. [swissprot;acc:q9ukb3]
		1972	sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8]
		1973	ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5]
4379.28	4803.59	959	sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633]	1.09689
4383.34	4642.93	1989	m-phase inducer phosphatase 2 (ec 3.1.3.48) (dual specificity phosphatase cdc25b). [swissprot;acc:p30305]	1.05922
4392.63	4776.19	1178	pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790]	1.08732
		1179	solute carrier family 20 (phosphate transporter), member 2; glvr-2; pit-2; gibbon ape leukemia virus receptor 2; murine leukemia virus, amphotropic; receptor. [refseq;acc:nm_006749]
		1180	farnesyl pyrophosphate synthetase (fpp synthetase) (fps) (farnesyl diphosphate synthetase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10)]. [swissprot;acc:p14324]
		1181	protocadherin 15 precursor. [swissprot;acc:q96qu1]
		1182	solute carrier family 20 (phosphate transporter), member 1; glvr-1; pit-1; gibbon ape leukemia virus receptor 1. [refseq;acc:nm_005415]
		1183	lipocalin-interacting membrane receptor. [refseq;acc:nm_018113]
		1184	zinc finger protein gli1 (glioma-associated oncogene) (oncogene gli). [swissprot;acc:p08151]
		1185	suppressor of fused. [refseq;acc:nm_016169]
		1186	zinc finger protein gli3. [swissprot;acc:p10071]
		1187	limb region 1 protein; limb region 1. [refseq;acc:nm_022458]
		1188	gastricsin precursor (ec 3.4.23.3) (pepsinogen c). [swissprot;acc:p20142]
		1189	zinc finger protein gli2 (tax helper protein). [swissprot;acc:p10070]
4405.4	5782.08	141	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330]	1.3125
4413.55	4784.6	1249	trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317]	1.08407
4418.21	4594.87	2388	diphosphomevalonate decarboxylase (ec 4.1.1.33) (mevalonate pyrophosphate decarboxylase) (mevalonate (diphospho)decarboxylase). [swissprot;acc:p53602]	1.03998
4446.72	5553.79	212	transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994]	1.24896
		213	nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983]
4450.17	4721.37	1940	m-phase inducer phosphatase 3 (ec 3.1.3.48) (dual specificity phosphatase cdc25c). [swissprot;acc:p30307]	1.06094
4450.84	4517.54	2606	tyrosyl-trna synthetase (ec 6.1.1.1) (tyrosyl--trna ligase) (tyrrs). [swissprot;acc:p54577]	1.01499
4455.95	5774.03	174	mad protein (max dimerizer). [swissprot;acc:q05195]	1.2958
4456.67	5773.77	175	max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539]	1.29553
4456.93	5773.67	176	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582]	1.29544
4457.06	5773.63	177	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300]	1.29539
4457.6	4642.72	2382	hydroxyacid oxidase 2 (ec 1.1.3.15) (haox2) ((s)-2-hydroxy-acid oxidase, peroxisomal) (long chain alpha-hydroxy acid oxidase) (long- chain l-2-hydroxy acid oxidase). [swissprot;acc:q9nyq3]	1.04153
4483.08	4971.62	815	midasin (midas-containing protein). [swissprot;acc:q9nu22]	1.10897
4483.26	4917.77	957	structure-specific recognition protein 1 (ssrp1) (recombination signal sequence recognition protein) (t160) (chromatin-specific transcription elongation factor 80 kda subunit) (fact 80 kda subunit). [swissprot;acc:q08945]	1.09692
		958	chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192]
4486.83	4499.52	2737	tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888]	1.00283
		2738	tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780]
4489.19	2765.82	60	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	1.6231
		61	glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216]
		62	glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737]
		63	myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]
		64	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]
4489.72	4965.35	832	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]	1.10594
		833	zuotin related factor-1 (m-phase phosphoprotein 11). [swissprot;acc:q99543]
4490.28	5222.25	393	eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730]	1.16301

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.