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 594 to 643 of 3730 in total

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

Rank	description	Filtered	red	green	network_comparison
297	daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959]	0	8123.75	8719	1.07327
298	40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865]		11977.8	12842.5	1.07219
	calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655]	1	268.632	243.588	1.10281
299	3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8]	0	12338.7	11512.3	1.07178
	calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384]	1	268.635	243.592	1.10281
300	camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612]	0	9270.49	8650.24	1.0717
	metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889]	1	150.959	166.351	1.10196
301	beta-1,4 mannosyltransferase. [refseq;acc:nm_019109]		150.982	166.372	1.10193
	sh2-b homolog; likely ortholog of mouse sh2 domain-containing putative adapter sh2-b; sh2-b gamma signaling protein; sh2-b alpha signaling protein. [refseq;acc:nm_015503]	0	12783	13698	1.07158
302	60s ribosomal protein l26. [swissprot;acc:q02877]	1	242.326	267.008	1.10185
	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]	0	7386.71	6895.44	1.07125
303	60s ribosomal protein l35. [swissprot;acc:p42766]	1	242.333	266.999	1.10179
	intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3]	0	11431.4	12244.1	1.07109
304	40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	1	242.339	266.986	1.1017
	sprouty homolog 4 (spry-4). [swissprot;acc:q9c004]	0	8021.78	7496.8	1.07003
305	microtubule-interacting protein that associates with traf3; interleukin 13 receptor alpha 1-binding protein-1. [refseq;acc:nm_015650]		9431	8815	1.06988
	mitochondrial ribosomal protein l2. [refseq;acc:nm_015950]	1	242.339	266.986	1.1017
306	60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]		242.153	266.673	1.10126
	williams-beuren syndrome chromosome region 14 protein (ws basic-helix- loop-helix leucine zipper protein) (ws-bhlh) (mlx interactor). [swissprot;acc:q9np71]	0	5540	5921	1.06877
307	ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9]		1091	1021	1.06856
	serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4]	1	242.153	266.673	1.10126
308	60s ribosomal protein l34. [swissprot;acc:p49207]
	intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811]	0	11414.1	12191.8	1.06814
309	lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428]		13651	14572	1.06747
	protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3]	1	242.153	266.673	1.10126
310	glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434]	0	9328.78	8741.55	1.06718
	protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378]	1	242.153	266.673	1.10126
311	60s ribosomal protein l23 (l17). [swissprot;acc:p23131]	0	10253.5	9622.45	1.06558
	protein translation factor sui1 homolog gc20. [swissprot;acc:o60739]	1	242.627	267.151	1.10108
312	60s ribosomal protein l3-like. [swissprot;acc:q92901]		242.195	266.663	1.10103
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]	0	11959.8	12731.1	1.06449
313	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]		11935.6	12698.9	1.06395
	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713]	1	232.473	211.207	1.10069
314	clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675]	0	10301.4	10957.5	1.06369
	methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582]	1	244.126	268.604	1.10027
315	methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [swissprot;acc:p50579]
	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921]	0	12121.6	12887.6	1.06319
316	dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5]		10768.5	11444	1.06273
	protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567]	1	242.694	267.017	1.10022
317	protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]	0	19939	18778	1.06183
	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]	1	224.445	204.044	1.09998
318	mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001]		242.011	266.18	1.09987
	ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9]	0	8918.54	9465.32	1.06131
319	60s ribosomal protein l19. [swissprot;acc:p14118]	1	240.73	264.729	1.09969
	sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1]	0	8918.54	9465.32	1.06131
320	adp-ribosylation factor 3. [swissprot;acc:p16587]		11627.8	10958.2	1.0611
	epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830]	1	241.892	265.96	1.0995
321	adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741]	0	11634.4	10989.9	1.05864
	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]	1	241.892	265.959	1.09949
322	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]		86.7483	78.8995	1.09948

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.