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	Network Comparison Type	Interaction Map	Value Type	green	red	network_comparison	Filtered

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Showing element 401 to 450 of 3730 in total

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

Rank	description	green	red	network_comparison	Filtered
201	maspin precursor (protease inhibitor 5). [swissprot;acc:p36952]	15123	16853	1.1144	0
	splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164]	211.382	240.133	1.13601	1
202	serpin b11. [swissprot;acc:q96p15]	15123	16853	1.1144	0
	short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4]	228.784	201.478	1.13553	1
203	cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452]	15123	16853	1.1144	0
	ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6]	228.752	201.515	1.13516	1
204	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]	16802.1	15081.8	1.11406	0
	short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62]	228.752	201.515	1.13516	1
205	60s ribosomal protein l23a. [swissprot;acc:p29316]	10636.3	11844.9	1.11363	0
	luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019]	200.968	228.1	1.13501	1
206	hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934]	6716	7479	1.11361	0
	luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032]	201.006	228.085	1.13472	1
207	dc11 protein. [refseq;acc:nm_020186]	6716	7479	1.11361	0
	presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810]	252.234	285.684	1.13261	1
208	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]	10638.4	11846.3	1.11354	0
	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]	252.234	285.684	1.13261	1
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]	696	775	1.11351	0
210	cullin homolog 2 (cul-2). [swissprot;acc:q13617]	252.234	285.684	1.13261	1
	mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362]	15405.6	17144.8	1.11289	0
211	presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768]	252.234	285.684	1.13261	1
	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]	9320.25	10367	1.11231	0
212	cullin homolog 1 (cul-1). [swissprot;acc:q13616]	252.234	285.684	1.13261	1
	metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832]	16405	18241.7	1.11196	0
213	pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388]	186.95	210.693	1.127	1
	protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [swissprot;acc:p07237]	8436.39	9379.47	1.11179	0
214	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]	170.192	191.644	1.12605	1
	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]	8473.85	7621.99	1.11176	0
215	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]	126	112	1.125	1
	myosin vi. [swissprot;acc:q9um54]	11250.5	10121.5	1.11154	0
216	maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708]	11732	10559.7	1.11102
	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623]	126	112	1.125	1
217	baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [swissprot;acc:o15392]	6406.18	7101.79	1.10858	0
	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535]	126	112	1.125	1
218	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]	17469.2	19355	1.10795	0
	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2]	126	112	1.125	1
219	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055]
	succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040]	11009.7	12196.2	1.10777	0
220	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882]	126	112	1.125	1
	neurocalcin delta. [swissprot;acc:p29554]	15473.5	13973.6	1.10734	0
221	estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454]	13497.2	12190.3	1.10721
	myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883]	126	112	1.125	1
222	40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	11013.2	12183	1.10622	0
	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430]	126	112	1.125	1
223	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]
	pnas-18. [sptrembl;acc:q9bzu3]	13939.6	12602.7	1.10608	0
224	atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031]	8889.93	9815.6	1.10413
	oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348]	165.623	185.969	1.12285	1
225	40s ribosomal protein s29. [swissprot;acc:p30054]	9997.71	11035.3	1.10378	0
	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330]	201.769	226.471	1.12243	1

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.