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	red	green	network_comparison

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Showing element 318 to 367 of 3730 in total

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

Rank	description	Filtered	red	green	network_comparison
159	necdin. [swissprot;acc:q99608]	1	23693.7	18263	1.29736
160	huntingtin interacting protein c. [refseq;acc:nm_012272]	0	1653.74	1296.38	1.27566
	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]	1	23693.7	18263	1.29736
161	glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434]	0	903.767	1152.06	1.27473
	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	1	23693.7	18263	1.29736
162	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	0	5734.28	7252.02	1.26468
	melanoma antigen, family b, 6. [refseq;acc:nm_173523]	1	23693.7	18263	1.29736
163	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]
	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	0	7830.62	6193.07	1.26442
164	aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181]		1711.55	1354.26	1.26383
	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	1	23693.7	18263	1.29736
165	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]
	mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2]	0	1002.2	793.818	1.26251
166	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]		5629.62	7099.51	1.2611
	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]	1	23693.7	18263	1.29736
167	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]
	transcription factor mafk (erythroid transcription factor nf-e2 p18 subunit). [swissprot;acc:o60675]	0	331.61	417.983	1.26047
168	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]	1	23693.7	18263	1.29736
	transcription factor mafg (v-maf musculoaponeurotic fibrosarcoma oncogene homolog g) (hmaf). [swissprot;acc:o15525]	0	334.012	420.355	1.2585
169	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]		244	194	1.25773
	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]	1	23693.7	18263	1.29736
170	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]
	williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645]	0	112.666	141.702	1.25772
171	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]	1	23693.7	18263	1.29736
	williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [refseq;acc:nm_018044]	0	112.666	141.702	1.25772
172	trophinin. [swissprot;acc:q12816]	1	23693.7	18263	1.29736
	williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158]	0	112.666	141.702	1.25772
173	breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567]	1	4579.34	5940.64	1.29727
	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]	0	3265.25	4102.97	1.25656
174	dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2]		488.43	612.604	1.25423
	mad protein (max dimerizer). [swissprot;acc:q05195]	1	4455.95	5774.03	1.2958
175	cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247]	0	1382.5	1107	1.24887
	max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539]	1	4456.67	5773.77	1.29553
176	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582]		4456.93	5773.67	1.29544
	small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072]	0	3023.85	2436.4	1.24111
177	acrc protein; putative nuclear protein. [refseq;acc:nm_052957]		4131.06	3340.03	1.23683
	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300]	1	4457.06	5773.63	1.29539
178	dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7]	0	498.07	615.233	1.23523
	myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]	1	21591.5	27904.5	1.29238
179	hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934]	0	556	681	1.22482
	myosin vc (myosin 5c). [swissprot;acc:q9nqx4]	1	21591.5	27904.5	1.29238
180	dc11 protein. [refseq;acc:nm_020186]	0	556	681	1.22482
	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	1	21591.5	27904.5	1.29238
181	enigma protein; lim domain protein. [refseq;acc:nm_005451]	0	187.25	153	1.22386
	eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760]	1	4068.56	5252.6	1.29102
182	rna-binding protein. [refseq;acc:nm_019027]		4069.83	5252.17	1.29051
	transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664]	0	971.889	794.63	1.22307
183	apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576]	1	4069.83	5252.17	1.29051
	blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161]	0	375.07	306.727	1.22281
184	blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577]

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.