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

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Showing element 268 to 317 of 3228 in total

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

Rank	network_comparison	red	description	green
268	1.21593	24473.9	cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0]	20127.8
269	1.21466	4590.18	u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777]	5575.52
270	1.21358	23640.2	fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917]	19479.8
271	1.21092	2554.89	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0]	3093.78
272	1.21012	3858.52	histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929]	4669.27
273	1.20985	3199.4	eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010]	3870.8
274	1.20953	3119.98	chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286]	2579.49
275			regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795]
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	1.20935	5221.28	polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195]	6314.35
284			paxillin. [swissprot;acc:p49023]
285	1.20885	23326.5	poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003]	19296.4
286	1.20878	23316	exocyst complex component sec5. [swissprot;acc:q96kp1]	19288.8
287	1.2087	23303.1	poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3]	19279.5
288	1.20857	23422.4	cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6]	19380.3
289	1.20571	4682.88	u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8]	5646.19
290	1.20487	4991.48	tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9]	6014.08
291	1.20481	44490.5	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	36927.5
292	1.20419	4641.09	nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384]	5588.75
293			nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2]
294	1.20387	22515.5	cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326]	18702.6
295	1.20368	13261.9	ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6]	11017.8
296	1.20306	4911.81	splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428]	5909.18
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	1.20262	4633.92	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
299	1.20203	4914.27	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]	5907.12
300			u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661]
301	1.20078	13768.2	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]	11466
302	1.19999	5894.75	pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388]	7073.65
303	1.1998	22268.8	serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873]	18560.4
304	1.19958	4855.46	pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629]	5824.52
305	1.19912	3856.29	odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260]	4624.15
306	1.19903	13680.5	pnas-18. [sptrembl;acc:q9bzu3]	11409.6
307	1.19892	12365.2	t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368]	14824.9
308	1.19878	4977.09	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640]	5966.44
309	1.19855	4977.8	segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641]	5966.14
310	1.19736	4909.79	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]	5878.79
311	1.19734	4981.52	segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997]	5964.58
312	1.19622	4598.21	u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45]	5500.48
313	1.1959	21644.2	protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]	18098.7
314	1.19583	21632.5	type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210]	18090
315	1.19413	21370.8	ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050]	17896.5
316			serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129]
317	1.19329	3153.1	adiponectin receptor 2. [refseq;acc:nm_024551]	3762.56

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.