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 775 to 824 of 6456 in total

Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	red	green	network_comparison
388	pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574]	Divided	4533.74	5279.4	1.16447
	swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497]	Subtracted	6252.58	7192.88	940.3
389	probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196]	Divided	4533.74	5279.4	1.16447
	programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340]	Subtracted	6252.58	7192.88	940.3
390	brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732]		6252.27	7192.51	940.24
	rw1 protein (fragment). [swissprot;acc:q92545]	Divided	4533.74	5279.4	1.16447
391	sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626]	Subtracted	6251.99	7192.17	940.18
	tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148]	Divided	3658.76	3144.39	1.16358
392	atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072]		3641.89	4236.95	1.16339
	calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632]	Subtracted	6251.91	7192.08	940.17
393	eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730]	Divided	4490.28	5222.25	1.16301
	grancalcin. [swissprot;acc:p28676]	Subtracted	6251.96	7192.13	940.17
394	bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933]	Divided	4490.28	5222.25	1.16301
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	Subtracted	1834.33	895.134	939.196
395	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798]		1834.36	895.194	939.166
	splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164]	Divided	4532.73	5269.33	1.16251
396	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08]	Subtracted	1834.52	895.507	939.013
	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713]	Divided	6563.65	7627.29	1.16205
397	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670]	Subtracted	1834.59	895.633	938.957
	nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573]	Divided	5367.04	6233.12	1.16137
398	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151]	Subtracted	1834.63	895.697	938.933
	xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7]	Divided	5084.26	5904.1	1.16125
399	neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544]		5201.41	4479.76	1.16109
	u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333]	Subtracted	4633.92	5572.85	938.93
400	adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306]	Divided	5201.41	4479.76	1.16109
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]	Subtracted	1834.73	895.893	938.837
401	adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622]	Divided	5201.41	4479.76	1.16109
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152]	Subtracted	1835.3	896.972	938.328
402	arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069]		6230.94	7168.2	937.26
	leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66]	Divided	5201.41	4479.76	1.16109
403	fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322]
	ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385]	Subtracted	6259.3	7190.91	931.61
404	importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060]		7802.31	8731.82	929.51
	leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71]	Divided	5201.41	4479.76	1.16109
405	guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992]	Subtracted	1836.71	907.546	929.164
	laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047]	Divided	5201.41	4479.76	1.16109
406	guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148]	Subtracted	1836.71	907.564	929.146
	thymic stromal co-transporter. [refseq;acc:nm_033051]	Divided	5201.41	4479.76	1.16109
407	guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086]	Subtracted	1836.76	907.741	929.019
	wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516]	Divided	6603.41	7664.65	1.16071
408	dok-like protein. [refseq;acc:nm_024872]		6102.59	7081.46	1.1604
	guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488]	Subtracted	1836.76	907.763	928.997
409	docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496]	Divided	6102.59	7081.46	1.1604
	guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087]	Subtracted	1836.76	907.774	928.986
410	autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0]		6744.05	5815.13	928.92
	docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704]	Divided	6102.59	7081.46	1.1604
411	guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899]	Subtracted	1836.8	907.903	928.897
	tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685]	Divided	6102.59	7081.46	1.1604
412	guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898]	Subtracted	1836.81	907.978	928.832
	mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390]	Divided	3594.31	4169.95	1.16015

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.