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 443 to 492 of 6456 in total 
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
222	60s ribosomal protein l14 (cag-isl 7). [source:swissprot;acc:p50914]	Subtracted	242.153	266.673	24.52	
222	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [source:sptrembl;acc:q9h430]	Divided	112	126	1.125	
223	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [source:swissprot;acc:q9ukx3]	Divided	112	126	1.125	
223	serine racemase (ec 5.1.1.-). [source:swissprot;acc:q9gzt4]	Subtracted	242.153	266.673	24.52	
224	60s ribosomal protein l34. [source:swissprot;acc:p49207]	Subtracted	242.153	266.673	24.52	
224	oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [source:swissprot;acc:q16348]	Divided	185.969	165.623	1.12285	
225	protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [source:swissprot;acc:q9y2r3]	Subtracted	242.153	266.673	24.52	
225	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [source:swissprot;acc:p43330]	Divided	226.471	201.769	1.12243	
226	cartilage oligomeric matrix protein precursor (comp). [source:swissprot;acc:p49747]	Divided	239.991	269.238	1.12187	
226	protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [source:swissprot;acc:p38378]	Subtracted	242.153	266.673	24.52	
227	methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [source:swissprot;acc:p53582]	Subtracted	244.126	268.604	24.478	
227	thrombospondin 3 precursor. [source:swissprot;acc:p49746]	Divided	239.99	269.234	1.12186	
228	methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [source:swissprot;acc:p50579]	Subtracted	244.126	268.604	24.478	
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]	Divided	226.411	202.088	1.12036	
229	60s ribosomal protein l3-like. [source:swissprot;acc:q92901]	Subtracted	242.195	266.663	24.468	
229	breast cancer antiestrogen resistance 3. [source:refseq;acc:nm_003567]	Divided	226.401	202.094	1.12028	
230	cysteine-rich protein 1 (crp1) (crp). [source:swissprot;acc:p21291]	Divided	239.35	267.915	1.11934	
230	protein translation factor sui1 homolog (sui1iso1). [source:swissprot;acc:p41567]	Subtracted	242.694	267.017	24.323	
231	likely ortholog of mouse shc sh2-domain binding protein 1. [source:refseq;acc:nm_024745]	Divided	239.336	267.881	1.11927	
231	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]	Subtracted	226.411	202.088	24.323	
232	breast cancer antiestrogen resistance 3. [source:refseq;acc:nm_003567]	Subtracted	226.401	202.094	24.307	
232	smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [source:swissprot;acc:q16527]	Divided	239.336	267.879	1.11926	
233	60s ribosomal protein l7. [source:swissprot;acc:p18124]	Subtracted	235.727	259.984	24.257	
233	lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [source:swissprot;acc:p50461]	Divided	239.32	267.842	1.11918	
234	40s ribosomal protein s23. [source:swissprot;acc:p39028]	Subtracted	243.944	268.195	24.251	
234	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [source:swissprot;acc:q9nrg0]	Divided	287.41	256.835	1.11905	
235	28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [source:swissprot;acc:o15235]	Subtracted	243.944	268.195	24.251	
235	phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [source:swissprot;acc:p00439]	Divided	227.357	254.15	1.11785	
236	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [source:swissprot;acc:q16576]	Subtracted	252.644	228.42	24.224	
236	pp3111 protein. [source:refseq;acc:nm_022156]	Divided	227.357	254.15	1.11785	
237	mitochondrial 60s ribosomal protein l3 (l3mt). [source:swissprot;acc:p09001]	Subtracted	242.011	266.18	24.169	
237	syntaxin 18. [source:swissprot;acc:q9p2w9]	Divided	227.357	254.15	1.11785	
238	metastasis-associated protein mta1. [source:swissprot;acc:q13330]	Subtracted	252.512	228.356	24.156	
238	rd protein. [source:swissprot;acc:p18615]	Divided	227.357	254.15	1.11785	
239	dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [source:swissprot;acc:p24928]	Subtracted	243.817	267.962	24.145	
239	glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [source:swissprot;acc:p78417]	Divided	227.357	254.15	1.11785	
240	androgen-induced 1; cgi-103 protein; androgen induced protein. [source:refseq;acc:nm_016108]	Divided	227.357	254.15	1.11785	
240	chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [source:swissprot;acc:q09028]	Subtracted	252.39	228.297	24.093	
241	atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [source:swissprot;acc:p24539]	Divided	227.357	254.15	1.11785	
241	epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [source:swissprot;acc:p12830]	Subtracted	241.892	265.96	24.068	
242	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [source:sptrembl;acc:q9br02]	Subtracted	241.892	265.959	24.067	
242	j domain containing protein 1. [source:swissprot;acc:q9ukb3]	Divided	227.357	254.15	1.11785	
243	60s ribosomal protein l23a. [source:swissprot;acc:p29316]	Subtracted	241.884	265.945	24.061	
243	sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [source:swissprot;acc:q9y5w8]	Divided	227.357	254.15	1.11785	
244	60s ribosomal protein l5. [source:swissprot;acc:p46777]	Subtracted	241.899	265.924	24.025	
244	ba127l20.1 (novel glutathione-s-transferase). [source:sptrembl;acc:q9h4y5]	Divided	227.357	254.15	1.11785	
245	60s ribosomal protein l19. [source:swissprot;acc:p14118]	Subtracted	240.73	264.729	23.999	
245	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [source:swissprot;acc:p43331]	Divided	226.109	202.333	1.11751	
246	60s ribosomal protein l12 like protein. [source:sptrembl;acc:o60886]	Subtracted	243.583	267.528	23.945	
246	eukaryotic translation initiation factor 4 gamma, 3. [source:refseq;acc:nm_003760]	Divided	237.312	212.363	1.11748	

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/