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 301 to 350 of 3228 in total

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

Rank	description	red	green	network_comparison
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
325	septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599]	16177.9	19235.4	1.18899
326	atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7]	3432.96	4081.21	1.18883
327	septin 10 isoform 1. [refseq;acc:nm_144710]	16067.4	19094.4	1.18839
328	brain protein 44. [swissprot;acc:o95563]	15999.1	19007.1	1.18801
329	septin 7 (cdc10 protein homolog). [swissprot;acc:q16181]
330	septin 6. [swissprot;acc:q14141]	15959.9	18957.1	1.1878
331	pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913]	20287.2	17083.8	1.18751
332	pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669]	5051.16	5975.51	1.183
333	nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502]	5039.63	5961.83	1.18299
334	septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236]	14924.4	17655.2	1.18298
335	probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93]	3494.31	4129.6	1.18181
336	dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33]	3751.3	4431.34	1.18128
337	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	20446.1	24136.4	1.18049
338	homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483]
339	homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444]
340	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]
341	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016]
342	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067]
343	homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719]
344	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]
345	retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246]
346	septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6]	14229.2	16780.7	1.17931
347	enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073]	4991.02	5885.09	1.17914
348	splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435]
349	putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143]	4714.85	5554.38	1.17806
350	sedlin. [swissprot;acc:o14582]	17396.9	20483.9	1.17745

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.