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

Results: HTML CSV LaTeX

Showing element 151 to 200 of 3730 in total

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

Rank	description	Filtered	red	network_comparison	green
76	dead-box protein. [refseq;acc:nm_018665]	0	313.667	1.71403	183
	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154]	1	4599.26	1.50373	3058.57
77	inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268]	0	712.071	1.70956	416.524
	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153]	1	4612.39	1.49095	3093.6
78	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]		4800.81	1.48573	7132.71
	low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734]	0	161	1.69474	95
79	polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393]		323.79	1.68316	544.991
	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	1	3074.57	1.48558	4567.51
80	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483]		4133.47	1.43834	5945.32
	prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765]	0	293	1.68259	493
81	nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085]	1	4136.36	1.43691	5943.56
	transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084]	0	30	1.66667	50
82	importin 7; ran-binding protein 7. [refseq;acc:nm_006391]		191.333	1.65896	115.333
	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641]	1	4172.91	1.42694	5954.48
83	elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720]	0	166.114	1.64654	100.887
	proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100]	1	4932.27	1.42597	7033.29
84	jun dimerization protein. [refseq;acc:nm_130469]
	peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570]	0	973.698	1.64478	1601.52
85	fos-related antigen 2. [swissprot;acc:p15408]	1	4941.95	1.42395	7037.11
	rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [swissprot;acc:p31150]	0	679.449	1.62908	1106.88
86	alpha crystallin a chain. [swissprot;acc:p02489]		55.3059	1.61366	89.2447
	protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539]	1	4942.49	1.42384	7037.32
87	fos-related antigen 1 (fra-1). [swissprot;acc:p15407]		4944.3	1.42347	7038.04
	ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916]	0	304.664	1.58801	483.809
88	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	1	2411.93	1.42259	1695.45
	thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445]	0	304.664	1.58801	483.809
89	cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929]	1	2414.22	1.4217	1698.12
	suppressor of actin 1. [refseq;acc:nm_014016]	0	23.6076	1.58781	37.4843
90	metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832]		34.6667	1.57692	54.6667
	potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980]	1	2414.77	1.4215	1698.75
91	potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979]		2416.53	1.42082	1700.8
	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931]	0	39.7924	1.56338	62.2106
92	adp-ribosylation factor 3. [swissprot;acc:p16587]		300.697	1.56086	469.346
	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	1	4117.67	1.40882	5801.04
93	dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6]	0	528.5	1.54494	816.5
	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	1	4245.52	1.39977	5942.75
94	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]		4247.86	1.39879	5941.88
	myosin vi. [swissprot;acc:q9um54]	0	345.865	1.54338	224.096
95	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]		154	15400000	0.00001
	son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583]	1	2397.19	1.39481	3343.62
96	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]		4110.14	1.3856	5694.99
	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	0	154	15400000	0.00001
97	60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268]		728.65	1.52879	476.619
	amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410]	1	2820.51	1.3817	3897.1
98	pp3111 protein. [refseq;acc:nm_022156]	0	789	1.48868	530
	presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810]	1	2353.63	1.3705	3225.65
99	s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991]
	transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3]	0	817.81	1.48306	551.434
100	atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [swissprot;acc:p12956]		594	1.47761	402
	f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315]	1	2353.63	1.3705	3225.65

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.