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

Results: HTML CSV LaTeX

Showing element 275 to 324 of 3228 in total

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

Rank	description	red	green	network_comparison
275	regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795]	3119.98	2579.49	1.20953
276	putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37]
277	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]
278	transcription factor lbx1. [swissprot;acc:p52954]
279	mosaic protein lgn. [swissprot;acc:p81274]
280	regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6]
281	guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471]
282	rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736]
283	polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195]	5221.28	6314.35	1.20935
284	paxillin. [swissprot;acc:p49023]
285	poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003]	23326.5	19296.4	1.20885
286	exocyst complex component sec5. [swissprot;acc:q96kp1]	23316	19288.8	1.20878
287	poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3]	23303.1	19279.5	1.2087
288	cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6]	23422.4	19380.3	1.20857
289	u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8]	4682.88	5646.19	1.20571
290	tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9]	4991.48	6014.08	1.20487
291	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	44490.5	36927.5	1.20481
292	nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384]	4641.09	5588.75	1.20419
293	nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2]
294	cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326]	22515.5	18702.6	1.20387
295	ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6]	13261.9	11017.8	1.20368
296	splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428]	4911.81	5909.18	1.20306
297	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]
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]	4633.92	5572.85	1.20262
299	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]	4914.27	5907.12	1.20203
300	u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661]
301	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]	13768.2	11466	1.20078
302	pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388]	5894.75	7073.65	1.19999
303	serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873]	22268.8	18560.4	1.1998
304	pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629]	4855.46	5824.52	1.19958
305	odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260]	3856.29	4624.15	1.19912
306	pnas-18. [sptrembl;acc:q9bzu3]	13680.5	11409.6	1.19903
307	t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368]	12365.2	14824.9	1.19892
308	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640]	4977.09	5966.44	1.19878
309	segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641]	4977.8	5966.14	1.19855
310	squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146]	4909.79	5878.79	1.19736
311	segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997]	4981.52	5964.58	1.19734
312	u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45]	4598.21	5500.48	1.19622
313	protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]	21644.2	18098.7	1.1959
314	type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210]	21632.5	18090	1.19583
315	ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050]	21370.8	17896.5	1.19413
316	serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129]
317	adiponectin receptor 2. [refseq;acc:nm_024551]	3153.1	3762.56	1.19329
318	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	34190.9	40795.8	1.19318
319	ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570]	20911	24908.5	1.19117
320	ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157]
321	ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]
322	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685]
323	u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0]	4620.76	5501.94	1.1907
324	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	28136.5	33457.6	1.18912

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.