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 380 to 429 of 3730 in total

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

Rank	description	Filtered	red	green	network_comparison
190	u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621]	1	226.582	198.444	1.14179
191	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]
	sh3 adapter protein spin90 (sh3 protein interacting with nck, 90 kda) (vaca-interacting protein, 54 kda) (vip54) (af3p21) (diaphanous protein interacting protein) (dia interacting protein-1) (dip-1). [swissprot;acc:q9nzq3]	0	18809.5	16764.2	1.122
192	musashi 2 isoform a. [refseq;acc:nm_138962]	1	227.491	199.458	1.14055
	t-complex protein 1, zeta subunit (tcp-1-zeta) (cct-zeta) (cct-zeta-1) (tcp20) (htr3). [swissprot;acc:p40227]	0	12715.9	11333.2	1.122
193	musashi 1. [refseq;acc:nm_002442]	1	227.491	199.458	1.14055
	transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664]	0	10899.5	12217.4	1.12091
194	kappa b-ras 1. [refseq;acc:nm_020345]		12657.7	11299.1	1.12024
	nuclear protein ukp68. [refseq;acc:nm_024824]	1	227.491	199.458	1.14055
195	huntingtin interacting protein c. [refseq;acc:nm_012272]		227.971	200.417	1.13748
	mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650]	0	13942.8	15586.4	1.11788
196	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457]	1	263.215	231.407	1.13745
	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169]	0	11064.2	9897.84	1.11784
197	forkhead box protein p1 (hspc215). [swissprot;acc:q9h334]	1	263.215	231.407	1.13745
	importin 4. [refseq;acc:nm_024658]	0	12337.6	13788.9	1.11763
198	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1]	1	263.191	231.394	1.13741
	ribosomal protein l10-like protein. [refseq;acc:nm_080746]	0	11781.5	10545.3	1.11723
199	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635]		11781.8	10545.7	1.11721
	palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5]	1	242.735	276.059	1.13729
200	egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215]		242.718	276.018	1.1372
	peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570]	0	8786.74	7870.3	1.11644
201	maspin precursor (protease inhibitor 5). [swissprot;acc:p36952]		16853	15123	1.1144
	splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164]	1	240.133	211.382	1.13601
202	serpin b11. [swissprot;acc:q96p15]	0	16853	15123	1.1144
	short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4]	1	201.478	228.784	1.13553
203	cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452]	0	16853	15123	1.1144
	ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6]	1	201.515	228.752	1.13516
204	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]	0	15081.8	16802.1	1.11406
	short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62]	1	201.515	228.752	1.13516
205	60s ribosomal protein l23a. [swissprot;acc:p29316]	0	11844.9	10636.3	1.11363
	luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019]	1	228.1	200.968	1.13501
206	hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934]	0	7479	6716	1.11361
	luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032]	1	228.085	201.006	1.13472
207	dc11 protein. [refseq;acc:nm_020186]	0	7479	6716	1.11361
	presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810]	1	285.684	252.234	1.13261
208	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]	0	11846.3	10638.4	1.11354
	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]	1	285.684	252.234	1.13261
209	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]
	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	0	775	696	1.11351
210	cullin homolog 2 (cul-2). [swissprot;acc:q13617]	1	285.684	252.234	1.13261
	mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362]	0	17144.8	15405.6	1.11289
211	presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768]	1	285.684	252.234	1.13261
	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]	0	10367	9320.25	1.11231
212	cullin homolog 1 (cul-1). [swissprot;acc:q13616]	1	285.684	252.234	1.13261
	metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832]	0	18241.7	16405	1.11196
213	pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388]	1	210.693	186.95	1.127
	protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [swissprot;acc:p07237]	0	9379.47	8436.39	1.11179
214	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]	1	191.644	170.192	1.12605
	probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879]	0	7621.99	8473.85	1.11176
215	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]	1	112	126	1.125

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.