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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 3858 to 3907 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
242	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]	Ranked	Subtracted	1	241.892	265.959	24.067
	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]	Rooted	Divided	0	23.9664	21.5733	1.11093
	ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8]	Squared			21584.2	16770.2	1.28706
	huntingtin interacting protein c. [refseq;acc:nm_012272]	Rooted	Subtracted		22.1446	19.7536	2.391
	j domain containing protein 1. [swissprot;acc:q9ukb3]	Ranked	Divided	1	227.357	254.15	1.11785
	keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060]		Subtracted	0	10551.6	11573.6	1022
	kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719]	Squared		1	35991.8	46002.9	10011.1
	likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745]	Measured		0	1293.73	1161.64	132.09
	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300]	Rooted		1	55.65	65.1448	9.4948
	max protein. [swissprot;acc:p25912]	Measured	Divided		4640.26	5704.87	1.22943
	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]	Rooted			137.446	120.823	1.13758
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	Squared	Subtracted	0	174.646	0.796213	173.85
	neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297]		Divided	1	42411.6	55802.1	1.31573
	neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681]	Measured	Subtracted		9649.61	11053.5	1403.89
	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]		Divided	0	729.216	642.343	1.13524
243	60s ribosomal protein l23a. [swissprot;acc:p29316]	Ranked	Subtracted	1	241.884	265.945	24.061
	adp-ribosylation factor 3. [swissprot;acc:p16587]	Rooted		0	14.8377	17.2252	2.3875
	alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298]		Divided		28.4971	25.6518	1.11092
	dead-box protein. [refseq;acc:nm_018665]	Measured	Subtracted		313.667	183	130.667
	dr1-associated protein 1; negative cofactor 2 alpha; dr1-associated corepressor. [refseq;acc:nm_006442]	Squared		1	51805.2	41916.4	9888.8
	homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839]	Measured	Divided		4246.95	5208.98	1.22652
	keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059]	Ranked	Subtracted	0	10551.6	11573.5	1021.9
	keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4]	Measured	Divided		1225.09	1079.36	1.13502
	neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297]		Subtracted	1	9649.61	11053.5	1403.89
	pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388]	Rooted			63.1192	72.584	9.4648
	phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6]	Squared	Divided	0	8335.79	6506.81	1.28109
	polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361]	Ranked			1251	1373	1.09752
	sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538]	Squared	Subtracted		803.941	631.169	172.772
	sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8]	Ranked	Divided	1	227.357	254.15	1.11785
	sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0]	Squared			42411.6	55802.1	1.31573
	trophinin. [swissprot;acc:q12816]	Rooted			137.446	120.823	1.13758
244	60s ribosomal protein l23a. [swissprot;acc:p29316]			0	22.6514	25.1571	1.11062
	60s ribosomal protein l5. [swissprot;acc:p46777]	Ranked	Subtracted	1	241.899	265.924	24.025
	ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5]		Divided		227.357	254.15	1.11785
	brain protein 16. [refseq;acc:nm_016458]	Squared	Subtracted	0	2538.95	2371.77	167.18
	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]		Divided	1	14728.8	19330.8	1.31245
	keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184]	Measured		0	1225.09	1079.36	1.13502
	keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8]	Ranked	Subtracted		10551.6	11573.5	1021.9
	keratin associated protein 9.2. [refseq;acc:nm_031961]		Divided		10551.1	11579.9	1.09751
	mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362]	Squared			80.1214	102.556	1.28001
	myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]	Rooted		1	146.94	167.046	1.13683
	neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]		Subtracted		27.9136	37.2872	9.3736
	scratch; scratch 1. [refseq;acc:nm_031309]	Squared			40388.9	49827.5	9438.6
	sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0]	Measured			9649.61	11053.5	1403.89
	sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772]			0	1334.19	1205.1	129.09
	succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040]	Rooted			53.8642	56.248	2.3838
	ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807]	Measured	Divided	1	4250.14	5211.25	1.22614
245	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	Squared			8875.01	6768.05	1.31131
	60s ribosomal protein l19. [swissprot;acc:p14118]	Ranked	Subtracted		240.73	264.729	23.999
	basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811]	Measured		0	292	421	129

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.