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

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Showing element 875 to 924 of 3228 in total

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

red	Rank	green	description	network_comparison
4374.32	1970	4126.96	atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539]	1.05994
	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	959	4803.59	sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633]	1.09689
4383.34	1989	4642.93	m-phase inducer phosphatase 2 (ec 3.1.3.48) (dual specificity phosphatase cdc25b). [swissprot;acc:p30305]	1.05922
4392.63	1178	4776.19	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	141	5782.08	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330]	1.3125
4413.55	1249	4784.6	trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317]	1.08407
4418.21	2388	4594.87	diphosphomevalonate decarboxylase (ec 4.1.1.33) (mevalonate pyrophosphate decarboxylase) (mevalonate (diphospho)decarboxylase). [swissprot;acc:p53602]	1.03998
4446.72	212	5553.79	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	1940	4721.37	m-phase inducer phosphatase 3 (ec 3.1.3.48) (dual specificity phosphatase cdc25c). [swissprot;acc:p30307]	1.06094
4450.84	2606	4517.54	tyrosyl-trna synthetase (ec 6.1.1.1) (tyrosyl--trna ligase) (tyrrs). [swissprot;acc:p54577]	1.01499
4455.95	174	5774.03	mad protein (max dimerizer). [swissprot;acc:q05195]	1.2958
4456.67	175	5773.77	max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539]	1.29553
4456.93	176	5773.67	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582]	1.29544
4457.06	177	5773.63	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300]	1.29539
4457.6	2382	4642.72	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	815	4971.62	midasin (midas-containing protein). [swissprot;acc:q9nu22]	1.10897
4483.26	957	4917.77	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	2737	4499.52	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	60	2765.82	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	832	4965.35	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	393	5222.25	eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730]	1.16301
	394		bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933]
4508.81	2631	4446.41	highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101]	1.01403
4509.54	416	5223.95	n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227]	1.15842
4510.61	608	5098.74	nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208]	1.13039
4512.19	204	5655.52	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	1.25339
	205		small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356]
4521	1896	4805.16	m-phase inducer phosphatase 1 (ec 3.1.3.48) (dual specificity phosphatase cdc25a). [swissprot;acc:p30304]	1.06285

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.