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 green red network_comparison
Results: HTML CSV LaTeX Showing element 2601 to 2650 of 3730 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	green	red	network_comparison	
2099	ubiquitin-like protein smt3a. [source:swissprot;acc:p55854]	213.27	211.71	1.00737	
2100	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [source:swissprot;acc:p55855]	213.27	211.71	1.00737	
2101	acrc protein; putative nuclear protein. [source:refseq;acc:nm_052957]	213.27	211.71	1.00737	
2102	eukaryotic translation initiation factor 5a (eif-5a) (eif-4d) (rev- binding factor). [source:swissprot;acc:p10159]	210.263	208.727	1.00736	
2103	transketolase (ec 2.2.1.1) (tk). [source:swissprot;acc:p29401]	216.236	214.666	1.00731	
2104	thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [source:swissprot;acc:p23919]	207.813	209.328	1.00729	
2105	eif-5a2 protein. [source:refseq;acc:nm_020390]	210.111	208.591	1.00729	
2106	insulin gene enhancer protein isl-1 (islet-1). [source:swissprot;acc:p20663]	196.061	197.489	1.00728	
2107	lim domain only 7; zinc-finger domain-containing protein; lomp protein; f-box only protein 20; f-box protein fbx20. [source:refseq;acc:nm_005358]	217.801	216.23	1.00727	
2108	argininosuccinate lyase (ec 4.3.2.1) (arginosuccinase) (asal). [source:swissprot;acc:p04424]	217.93	216.36	1.00726	
2109	ran-binding protein 2 (ranbp2) (nuclear pore complex protein nup358) (nucleoporin nup358) (358 kda nucleoporin) (p270). [source:swissprot;acc:p49792]	217.47	219.032	1.00718	
2110	conserved oligomeric golgi complex component 6. [source:swissprot;acc:q9y2v7]	209.607	211.099	1.00712	
2111	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [source:refseq;acc:nm_032260]	217.511	219.047	1.00706	
2112	dna-directed rna polymerases iii 12.5 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c11 subunit) (hsc11p) (hrpc11) (my010 protein). [source:swissprot;acc:q9y2y1]	224.989	223.415	1.00705	
2113	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [source:refseq;acc:nm_032260]	217.533	219.055	1.007	
2114	triacylglycerol lipase, gastric precursor (ec 3.1.1.3) (gastric lipase) (gl). [source:swissprot;acc:p07098]	213.14	214.632	1.007	
2115	ba304i5.1 (novel lipase) (fragment). [source:sptrembl;acc:q96lg2]	213.14	214.632	1.007	
2116	lysosomal acid lipase/cholesteryl ester hydrolase precursor (ec 3.1.1.13) (lal) (acid cholesteryl ester hydrolase) (sterol esterase) (lipase a) (cholesteryl esterase). [source:swissprot;acc:p38571]	213.14	214.632	1.007	
2117	seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [source:swissprot;acc:q9np81]	213.14	214.632	1.007	
2118	seryl-trna synthetase (ec 6.1.1.11) (serine--trna ligase) (serrs). [source:swissprot;acc:p49591]	213.14	214.632	1.007	
2119	potassium channel modulatory factor 1; potassium channel modulatory factor; differentially expressed in branching tubulogenesis 91; zinc finger, zz domain containing 1. [source:refseq;acc:nm_020122]	222.788	221.248	1.00696	
2120	solute carrier family 23, member 1 (sodium-dependent vitamin c transporter 1) (hsvct1) (na(+)/l-ascorbic acid transporter 1) (yolk sac permease-like molecule 3). [source:swissprot;acc:q9uhi7]	222.788	221.248	1.00696	
2121	heterogeneous nuclear ribonucleoprotein a3 (hnrnp a3) (d10s102). [source:swissprot;acc:p51991]	222.788	221.248	1.00696	
2122	galectin-9 (hom-hd-21) (ecalectin). [source:swissprot;acc:o00182]	207.911	206.473	1.00696	
2123	adp-ribosylation factor 4. [source:swissprot;acc:p18085]	222.788	221.248	1.00696	
2124	fused toes homolog; likely ortholog of mouse fused toes. [source:refseq;acc:nm_022476]	222.788	221.248	1.00696	
2125	shc transforming protein. [source:swissprot;acc:p29353]	222.788	221.248	1.00696	
2126	zinc finger protein 289, id1 regulated; likely ortholog of mouse zfp289. [source:refseq;acc:nm_032389]	222.788	221.248	1.00696	
2127	neuronal shc. [source:refseq;acc:nm_016848]	222.788	221.248	1.00696	
2128	adp-ribosylation factor 1. [source:swissprot;acc:p32889]	222.788	221.248	1.00696	
2129	heterogeneous nuclear ribonucleoprotein a1 (helix-destabilizing protein) (single-strand binding protein) (hnrnp core protein a1). [source:swissprot;acc:p09651]	222.788	221.248	1.00696	
2130	adp-ribosylation factor 3. [source:swissprot;acc:p16587]	222.788	221.248	1.00696	
2131	gtp cyclohydrolase i (ec 3.5.4.16) (gtp-ch-i). [source:swissprot;acc:p30793]	227.851	226.277	1.00696	
2132	protein sck (fragment). [source:swissprot;acc:p98077]	222.788	221.248	1.00696	
2133	orphan nuclear receptor hmr (early response protein nak1) (tr3 orphan receptor). [source:swissprot;acc:p22736]	206.305	207.74	1.00696	
2134	heterogeneous nuclear ribonucleoproteins a2/b1 (hnrnp a2 / hnrnp b1). [source:swissprot;acc:p22626]	222.788	221.248	1.00696	
2135	nuclear hormone receptor nor-1 (neuron-derived orphan receptor 1) (mitogen induced nuclear orphan receptor). [source:swissprot;acc:q92570]	206.308	207.743	1.00696	
2136	ovarian carcinoma immunoreactive antigen. [source:refseq;acc:nm_017830]	222.788	221.248	1.00696	
2137	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [source:swissprot;acc:q9np61]	222.788	221.248	1.00696	
2138	solute carrier family 23, member 2 (sodium-dependent vitamin c transporter 2) (hsvct2) (na(+)/l-ascorbic acid transporter 2) (yolk sac permease-like molecule 2) (nucleobase transporter-like 1 protein). [source:swissprot;acc:q9ugh3]	222.788	221.248	1.00696	
2139	dual specificity mitogen-activated protein kinase kinase 7 (ec 2.7.1.-) (map kinase kinase 7) (mapkk 7) (mapk/erk kinase 7) (jnk activating kinase 2) (c-jun n-terminal kinase kinase 2) (jnk kinase 2) (jnkk 2). [source:swissprot;acc:o14733]	222.788	221.248	1.00696	
2140	cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [source:swissprot;acc:p33240]	162.665	161.547	1.00692	
2141	orphan nuclear receptor nurr1 (immediate-early response protein not) (transcriptionally inducible nuclear receptor). [source:swissprot;acc:p43354]	206.343	207.765	1.00689	
2142	protein 4.1 (band 4.1) (p4.1) (epb4.1) (4.1r). [source:swissprot;acc:p11171]	207.864	206.443	1.00688	
2143	spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [source:swissprot;acc:q9nrc6]	207.862	206.442	1.00688	
2144	band 4.1-like protein 1 (neuronal protein 4.1) (4.1n). [source:swissprot;acc:q9h4g0]	207.864	206.443	1.00688	
2145	band 4.1-like protein 3 (4.1b) (differentially expressed in adenocarcinoma of the lung protein 1) (dal-1). [source:swissprot;acc:q9y2j2]	207.862	206.442	1.00688	
2146	band 4.1-like protein 2 (generally expressed protein 4.1) (4.1g). [source:swissprot;acc:o43491]	207.864	206.443	1.00688	
2147	45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [source:swissprot;acc:q9brk5]	207.862	206.442	1.00688	
2148	ba271b5.1 (similar to ribosomal protein s7). [source:sptrembl;acc:q9h1s9]	219.366	217.871	1.00686	

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/