Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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
Results: HTML CSV LaTeX 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). [source: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). [source:swissprot;acc:p21333]	1	226.582	198.444	1.14179	
191	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). [source:swissprot;acc:q9nzq3]	0	18809.5	16764.2	1.122	
192	musashi 2 isoform a. [source:refseq;acc:nm_138962]	1	227.491	199.458	1.14055	
192	t-complex protein 1, zeta subunit (tcp-1-zeta) (cct-zeta) (cct-zeta-1) (tcp20) (htr3). [source:swissprot;acc:p40227]	0	12715.9	11333.2	1.122	
193	musashi 1. [source:refseq;acc:nm_002442]	1	227.491	199.458	1.14055	
193	transcription factor iiia (factor a) (tfiiia). [source:swissprot;acc:q92664]	0	10899.5	12217.4	1.12091	
194	kappa b-ras 1. [source:refseq;acc:nm_020345]	0	12657.7	11299.1	1.12024	
194	nuclear protein ukp68. [source:refseq;acc:nm_024824]	1	227.491	199.458	1.14055	
195	huntingtin interacting protein c. [source:refseq;acc:nm_012272]	1	227.971	200.417	1.13748	
195	mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [source:swissprot;acc:p82650]	0	13942.8	15586.4	1.11788	
196	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [source:refseq;acc:nm_138457]	1	263.215	231.407	1.13745	
196	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [source:refseq;acc:nm_003169]	0	11064.2	9897.84	1.11784	
197	forkhead box protein p1 (hspc215). [source:swissprot;acc:q9h334]	1	263.215	231.407	1.13745	
197	importin 4. [source:refseq;acc:nm_024658]	0	12337.6	13788.9	1.11763	
198	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [source:swissprot;acc:q9bzs1]	1	263.191	231.394	1.13741	
198	ribosomal protein l10-like protein. [source:refseq;acc:nm_080746]	0	11781.5	10545.3	1.11723	
199	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [source:swissprot;acc:p27635]	0	11781.8	10545.7	1.11721	
199	palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [source:swissprot;acc:q9umr5]	1	242.735	276.059	1.13729	
200	egf-like-domain, multiple 7; neu1 protein. [source:refseq;acc:nm_016215]	1	242.718	276.018	1.1372	
200	peptide chain release factor 1, mitochondrial precursor (mrf-1). [source:swissprot;acc:o75570]	0	8786.74	7870.3	1.11644	
201	maspin precursor (protease inhibitor 5). [source:swissprot;acc:p36952]	0	16853	15123	1.1144	
201	splicing factor 4 isoform b; rna-binding protein. [source:refseq;acc:nm_021164]	1	240.133	211.382	1.13601	
202	serpin b11. [source:swissprot;acc:q96p15]	0	16853	15123	1.1144	
202	short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [source:swissprot;acc:q9ubn4]	1	201.478	228.784	1.13553	
203	cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [source:swissprot;acc:p50452]	0	16853	15123	1.1144	
203	ebp50-pdz interactor of 64 kda (epi64 protein). [source:swissprot;acc:q9bxi6]	1	201.515	228.752	1.13516	
204	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [source:refseq;acc:nm_017743]	0	15081.8	16802.1	1.11406	
204	short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [source:swissprot;acc:q9ul62]	1	201.515	228.752	1.13516	
205	60s ribosomal protein l23a. [source:swissprot;acc:p29316]	0	11844.9	10636.3	1.11363	
205	luc7-like 2; cgi-74 protein; cgi-59 protein. [source:refseq;acc:nm_016019]	1	228.1	200.968	1.13501	
206	hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [source:refseq;acc:nm_023934]	0	7479	6716	1.11361	
206	luc7-like; sarcoplasmic reticulum protein luc7b1. [source:refseq;acc:nm_018032]	1	228.085	201.006	1.13472	
207	dc11 protein. [source:refseq;acc:nm_020186]	0	7479	6716	1.11361	
207	presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [source: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). [source:sptrembl;acc:q9br02]	0	11846.3	10638.4	1.11354	
208	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). [source: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. [source:refseq;acc:nm_018315]	1	285.684	252.234	1.13261	
209	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [source:swissprot;acc:p08578]	0	775	696	1.11351	
210	cullin homolog 2 (cul-2). [source:swissprot;acc:q13617]	1	285.684	252.234	1.13261	
210	mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [source:refseq;acc:nm_022362]	0	17144.8	15405.6	1.11289	
211	presenilin 1 (ps-1) (s182 protein). [source:swissprot;acc:p49768]	1	285.684	252.234	1.13261	
211	ribosomal protein s6 kinase-like 1. [source:refseq;acc:nm_031464]	0	10367	9320.25	1.11231	
212	cullin homolog 1 (cul-1). [source:swissprot;acc:q13616]	1	285.684	252.234	1.13261	
212	metabotropic glutamate receptor 3 precursor (mglur3). [source:swissprot;acc:q14832]	0	18241.7	16405	1.11196	
213	pallidin; pallid (mouse) homolog, pallidin. [source:refseq;acc:nm_012388]	1	210.693	186.95	1.127	
213	protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [source:swissprot;acc:p07237]	0	9379.47	8436.39	1.11179	
214	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [source:refseq;acc:nm_022075]	1	191.644	170.192	1.12605	
214	probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [source:swissprot;acc:o75879]	0	7621.99	8473.85	1.11176	
215	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [source:swissprot;acc:p13533]	1	112	126	1.125	

Legend:
- Rank is the rank after comparing the two networks
- 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.
- http://analysis.yellowcouch.org/