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 200 to 249 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
200	egf-like-domain, multiple 7; neu1 protein. [source:refseq;acc:nm_016215]	242.718	276.018	1.1372	
201	splicing factor 4 isoform b; rna-binding protein. [source:refseq;acc:nm_021164]	240.133	211.382	1.13601	
202	short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [source:swissprot;acc:q9ubn4]	201.478	228.784	1.13553	
203	ebp50-pdz interactor of 64 kda (epi64 protein). [source:swissprot;acc:q9bxi6]	201.515	228.752	1.13516	
204	short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [source:swissprot;acc:q9ul62]	201.515	228.752	1.13516	
205	luc7-like 2; cgi-74 protein; cgi-59 protein. [source:refseq;acc:nm_016019]	228.1	200.968	1.13501	
206	luc7-like; sarcoplasmic reticulum protein luc7b1. [source:refseq;acc:nm_018032]	228.085	201.006	1.13472	
207	presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [source:swissprot;acc:p49810]	285.684	252.234	1.13261	
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]	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]	285.684	252.234	1.13261	
210	cullin homolog 2 (cul-2). [source:swissprot;acc:q13617]	285.684	252.234	1.13261	
211	presenilin 1 (ps-1) (s182 protein). [source:swissprot;acc:p49768]	285.684	252.234	1.13261	
212	cullin homolog 1 (cul-1). [source:swissprot;acc:q13616]	285.684	252.234	1.13261	
213	pallidin; pallid (mouse) homolog, pallidin. [source:refseq;acc:nm_012388]	210.693	186.95	1.127	
214	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [source:refseq;acc:nm_022075]	191.644	170.192	1.12605	
215	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [source:swissprot;acc:p13533]	112	126	1.125	
216	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [source:swissprot;acc:q9y623]	112	126	1.125	
217	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [source:swissprot;acc:p13535]	112	126	1.125	
218	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [source:swissprot;acc:q9ukx2]	112	126	1.125	
219	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [source:swissprot;acc:p11055]	112	126	1.125	
220	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [source:swissprot;acc:p12882]	112	126	1.125	
221	myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [source:swissprot;acc:p12883]	112	126	1.125	
222	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [source:sptrembl;acc:q9h430]	112	126	1.125	
223	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [source:swissprot;acc:q9ukx3]	112	126	1.125	
224	oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [source:swissprot;acc:q16348]	185.969	165.623	1.12285	
225	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [source:swissprot;acc:p43330]	226.471	201.769	1.12243	
226	cartilage oligomeric matrix protein precursor (comp). [source:swissprot;acc:p49747]	239.991	269.238	1.12187	
227	thrombospondin 3 precursor. [source:swissprot;acc:p49746]	239.99	269.234	1.12186	
228	sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [source:refseq;acc:nm_005489]	226.411	202.088	1.12036	
229	breast cancer antiestrogen resistance 3. [source:refseq;acc:nm_003567]	226.401	202.094	1.12028	
230	cysteine-rich protein 1 (crp1) (crp). [source:swissprot;acc:p21291]	239.35	267.915	1.11934	
231	likely ortholog of mouse shc sh2-domain binding protein 1. [source:refseq;acc:nm_024745]	239.336	267.881	1.11927	
232	smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [source:swissprot;acc:q16527]	239.336	267.879	1.11926	
233	lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [source:swissprot;acc:p50461]	239.32	267.842	1.11918	
234	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [source:swissprot;acc:q9nrg0]	287.41	256.835	1.11905	
235	phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [source:swissprot;acc:p00439]	227.357	254.15	1.11785	
236	pp3111 protein. [source:refseq;acc:nm_022156]	227.357	254.15	1.11785	
237	syntaxin 18. [source:swissprot;acc:q9p2w9]	227.357	254.15	1.11785	
238	rd protein. [source:swissprot;acc:p18615]	227.357	254.15	1.11785	
239	glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [source:swissprot;acc:p78417]	227.357	254.15	1.11785	
240	androgen-induced 1; cgi-103 protein; androgen induced protein. [source:refseq;acc:nm_016108]	227.357	254.15	1.11785	
241	atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [source:swissprot;acc:p24539]	227.357	254.15	1.11785	
242	j domain containing protein 1. [source:swissprot;acc:q9ukb3]	227.357	254.15	1.11785	
243	sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [source:swissprot;acc:q9y5w8]	227.357	254.15	1.11785	
244	ba127l20.1 (novel glutathione-s-transferase). [source:sptrembl;acc:q9h4y5]	227.357	254.15	1.11785	
245	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [source:swissprot;acc:p43331]	226.109	202.333	1.11751	
246	eukaryotic translation initiation factor 4 gamma, 3. [source:refseq;acc:nm_003760]	237.312	212.363	1.11748	
247	rna-binding protein. [source:refseq;acc:nm_019027]	237.302	212.41	1.11719	
248	apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [source:refseq;acc:nm_014576]	237.302	212.41	1.11719	
249	ns1-associated protein 1. [source:refseq;acc:nm_006372]	237.302	212.41	1.11719	

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/