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

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Showing element 551 to 600 of 14920 in total

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

Rank	description	Filtered	green	red	network_comparison
276	apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]	0	12125.1	10817.1	1.12092
	putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37]	1	2579.49	3119.98	1.20953
277	disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6]	0	975.647	870.93	1.12024
	regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [swissprot;acc:o76081]	1	2579.49	3119.98	1.20953
278	rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513]	0	1932	2162.33	1.11922
	transcription factor lbx1. [swissprot;acc:p52954]	1	2579.49	3119.98	1.20953
279	cell adhesion molecule with homology to l1cam precursor; neural cell adhesion molecule; cell adhesion molecule l1-like; l1 cell adhesion molecule 2. [refseq;acc:nm_006614]	0	610.424	545.902	1.11819
	mosaic protein lgn. [swissprot;acc:p81274]	1	2579.49	3119.98	1.20953
280	neural cell adhesion molecule l1 precursor (n-cam l1) (cd171 antigen). [swissprot;acc:p32004]	0	610.424	545.902	1.11819
	regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6]	1	2579.49	3119.98	1.20953
281	guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471]
	transcription initiation factor tfiid 31 kda subunit (tafii-31) (tafii-32) (tafii32). [swissprot;acc:q16594]	0	610.424	545.902	1.11819
282	pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790]		199.751	178.955	1.11621
	rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736]	1	2579.49	3119.98	1.20953
283	lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [swissprot;acc:p36776]	0	753.849	841.301	1.11601
	polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195]	1	6314.35	5221.28	1.20935
284	60s ribosomal protein l23 (l17). [swissprot;acc:p23131]	0	1956.36	1753.85	1.11547
	paxillin. [swissprot;acc:p49023]	1	6314.35	5221.28	1.20935
285	dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9]	0	3010.22	2698.62	1.11547
	poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003]	1	19296.4	23326.5	1.20885
286	clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675]	0	6127.24	5497.01	1.11465
	exocyst complex component sec5. [swissprot;acc:q96kp1]	1	19288.8	23316	1.20878
287	5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [swissprot;acc:p13196]	0	808.929	726.245	1.11385
	poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3]	1	19279.5	23303.1	1.2087
288	cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6]		19380.3	23422.4	1.20857
	likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745]	0	1161.64	1293.73	1.11371
289	tubby protein homolog. [swissprot;acc:p50607]		4228.27	3797.57	1.11341
	u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8]	1	5646.19	4682.88	1.20571
290	dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880]	0	1525.56	1370.82	1.11288
	tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9]	1	6014.08	4991.48	1.20487
291	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]		36927.5	44490.5	1.20481
	similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9]	0	2179.77	1961.09	1.11151
292	ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9]		12473	11223	1.11138
	nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384]	1	5588.75	4641.09	1.20419
293	block 23. [sptrembl;acc:q8nhw5]	0	2159.55	1943.32	1.11127
	nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2]	1	5588.75	4641.09	1.20419
294	cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326]		18702.6	22515.5	1.20387
	mesoderm induction early response 1. [refseq;acc:nm_020948]	0	1723.5	1914.5	1.11082
295	adaptor-related protein complex 1, mu 2 subunit (mu-adaptin 2) (adaptor protein complex ap-1 mu-2 subunit) (golgi adaptor ha1/ap1 adaptin mu-2 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 2) (ap-mu chain family member mu1b). [swissprot;acc:q9y6q5]		384.843	426.8	1.10902
	ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6]	1	11017.8	13261.9	1.20368
296	pnas-18. [sptrembl;acc:q9bzu3]	0	2035.28	2256.05	1.10847
	splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428]	1	5909.18	4911.81	1.20306
297	40s ribosomal protein s29. [swissprot;acc:p30054]	0	1895.38	1711.6	1.10737
	krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887]	1	5909.18	4911.81	1.20306
298	u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333]		5572.85	4633.92	1.20262
	williams-beuren syndrome chromosome region 14 protein (ws basic-helix- loop-helix leucine zipper protein) (ws-bhlh) (mlx interactor). [swissprot;acc:q9np71]	0	848	939	1.10731
299	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]	1	5907.12	4914.27	1.20203
	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]	0	2015.09	2231.05	1.10717
300	sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772]		1205.1	1334.19	1.10712
	u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661]	1	5907.12	4914.27	1.20203

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.