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

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Showing element 194 to 243 of 3228 in total

Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

Rank	description	network_comparison	green	red
194	nuclear protein ukp68. [refseq;acc:nm_024824]	1.14055	199.458	227.491
195	huntingtin interacting protein c. [refseq;acc:nm_012272]	1.13748	200.417	227.971
196	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457]	1.13745	231.407	263.215
197	forkhead box protein p1 (hspc215). [swissprot;acc:q9h334]
198	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1]	1.13741	231.394	263.191
199	palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5]	1.13729	276.059	242.735
200	egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215]	1.1372	276.018	242.718
201	splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164]	1.13601	211.382	240.133
202	short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4]	1.13553	228.784	201.478
203	ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6]	1.13516	228.752	201.515
204	short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62]
205	luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019]	1.13501	200.968	228.1
206	luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032]	1.13472	201.006	228.085
207	presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810]	1.13261	252.234	285.684
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). [swissprot;acc:p34991]
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]
210	cullin homolog 2 (cul-2). [swissprot;acc:q13617]
211	presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768]
212	cullin homolog 1 (cul-1). [swissprot;acc:q13616]
213	pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388]	1.127	186.95	210.693
214	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]	1.12605	170.192	191.644
215	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]	1.125	126	112
216	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623]
217	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535]
218	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2]
219	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055]
220	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882]
221	myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883]
222	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430]
223	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]
224	oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348]	1.12285	165.623	185.969
225	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330]	1.12243	201.769	226.471
226	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]	1.12187	269.238	239.991
227	thrombospondin 3 precursor. [swissprot;acc:p49746]	1.12186	269.234	239.99
228	sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489]	1.12036	202.088	226.411
229	breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567]	1.12028	202.094	226.401
230	cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291]	1.11934	267.915	239.35
231	likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745]	1.11927	267.881	239.336
232	smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527]	1.11926	267.879
233	lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461]	1.11918	267.842	239.32
234	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0]	1.11905	256.835	287.41
235	phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439]	1.11785	254.15	227.357
236	pp3111 protein. [refseq;acc:nm_022156]
237	syntaxin 18. [swissprot;acc:q9p2w9]
238	rd protein. [swissprot;acc:p18615]
239	glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417]
240	androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108]
241	atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539]
242	j domain containing protein 1. [swissprot;acc:q9ukb3]
243	sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8]

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.