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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 208 to 257 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	Hugo	description	red	green	network_comparison	
208	SKP1A	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	FBXW7	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	CUL2	cullin homolog 2 (cul-2). [source:swissprot;acc:q13617]	285.684	252.234	1.13261	
211	PSEN1	presenilin 1 (ps-1) (s182 protein). [source:swissprot;acc:p49768]	285.684	252.234	1.13261	
212	CUL1	cullin homolog 1 (cul-1). [source:swissprot;acc:q13616]	285.684	252.234	1.13261	
213	PLDN	pallidin; pallid (mouse) homolog, pallidin. [source:refseq;acc:nm_012388]	210.693	186.95	1.127	
214	LASS2	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	MYH4	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [source:swissprot;acc:q9y623]	112	126	1.125	
217	MYH8	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [source:swissprot;acc:p13535]	112	126	1.125	
218	MYH2	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [source:swissprot;acc:q9ukx2]	112	126	1.125	
219	MYH3	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [source:swissprot;acc:p11055]	112	126	1.125	
220	MYH1	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	MYH7B	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [source:sptrembl;acc:q9h430]	112	126	1.125	
223	MYH13	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [source:swissprot;acc:q9ukx3]	112	126	1.125	
224	SLC15A2	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	SNRPD2	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [source:swissprot;acc:p43330]	226.471	201.769	1.12243	
226	COMP	cartilage oligomeric matrix protein precursor (comp). [source:swissprot;acc:p49747]	239.991	269.238	1.12187	
227	THBS3	thrombospondin 3 precursor. [source:swissprot;acc:p49746]	239.99	269.234	1.12186	
228	SH2D3C	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	BCAR3	breast cancer antiestrogen resistance 3. [source:refseq;acc:nm_003567]	226.401	202.094	1.12028	
230	CSRP1	cysteine-rich protein 1 (crp1) (crp). [source:swissprot;acc:p21291]	239.35	267.915	1.11934	
231	SHCBP1	likely ortholog of mouse shc sh2-domain binding protein 1. [source:refseq;acc:nm_024745]	239.336	267.881	1.11927	
232	CSRP2	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	CSRP3	lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [source:swissprot;acc:p50461]	239.32	267.842	1.11918	
234	CHRAC1	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	PAH	phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [source:swissprot;acc:p00439]	227.357	254.15	1.11785	
236	DUS1L	pp3111 protein. [source:refseq;acc:nm_022156]	227.357	254.15	1.11785	
237	STX18	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	GSTO1	glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [source:swissprot;acc:p78417]	227.357	254.15	1.11785	
240	AIG1	androgen-induced 1; cgi-103 protein; androgen induced protein. [source:refseq;acc:nm_016108]	227.357	254.15	1.11785	
241	ATP5F1	atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [source:swissprot;acc:p24539]	227.357	254.15	1.11785	
242	DNAJC12	j domain containing protein 1. [source:swissprot;acc:q9ukb3]	227.357	254.15	1.11785	
243	SNX13	sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [source:swissprot;acc:q9y5w8]	227.357	254.15	1.11785	
244	GSTO2	ba127l20.1 (novel glutathione-s-transferase). [source:sptrembl;acc:q9h4y5]	227.357	254.15	1.11785	
245	SNRPD3	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [source:swissprot;acc:p43331]	226.109	202.333	1.11751	
246	EIF4G3	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	SYNCRIP	ns1-associated protein 1. [source:refseq;acc:nm_006372]	237.302	212.41	1.11719	
250	HNRNPR	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [source:swissprot;acc:o43390]	237.302	212.41	1.11719	
251	SLC15A1	oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [source:swissprot;acc:p46059]	186.172	166.661	1.11707	
252	EIF4G1	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [source:swissprot;acc:q04637]	237.292	212.457	1.11689	
253	MXD1	mad protein (max dimerizer). [source:swissprot;acc:q05195]	228	204.333	1.11583	
254	STT3B	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [source:refseq;acc:nm_178862]	200.691	179.88	1.11569	
255	STT3A	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [source:swissprot;acc:p46977]	200.691	179.88	1.11569	
256	MXI1	max interacting protein 1 (mxi1 protein). [source:swissprot;acc:p50539]	227.999	204.357	1.11569	
257	DDOST	dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [source:swissprot;acc:p39656]	200.691	179.88	1.11569	

Legend:
- Rank is the rank after comparing the two networks
- Hugo is the HGNC identifier if it exists
- 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/