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 2101 to 2150 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	Hugo	description	red	green	network_comparison	
2101	ACRC	acrc protein; putative nuclear protein. [source:refseq;acc:nm_052957]	211.71	213.27	1.00737	
2102	EIF5AP1	eukaryotic translation initiation factor 5a (eif-5a) (eif-4d) (rev- binding factor). [source:swissprot;acc:p10159]	208.727	210.263	1.00736	
2103	TKT	transketolase (ec 2.2.1.1) (tk). [source:swissprot;acc:p29401]	214.666	216.236	1.00731	
2104	DTYMK	thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [source:swissprot;acc:p23919]	209.328	207.813	1.00729	
2105	EIF5A2	eif-5a2 protein. [source:refseq;acc:nm_020390]	208.591	210.111	1.00729	
2106	ISL1	insulin gene enhancer protein isl-1 (islet-1). [source:swissprot;acc:p20663]	197.489	196.061	1.00728	
2107	LMO7	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]	216.23	217.801	1.00727	
2108	ASL	argininosuccinate lyase (ec 4.3.2.1) (arginosuccinase) (asal). [source:swissprot;acc:p04424]	216.36	217.93	1.00726	
2109	RANBP2	ran-binding protein 2 (ranbp2) (nuclear pore complex protein nup358) (nucleoporin nup358) (358 kda nucleoporin) (p270). [source:swissprot;acc:p49792]	219.032	217.47	1.00718	
2110	COG6	conserved oligomeric golgi complex component 6. [source:swissprot;acc:q9y2v7]	211.099	209.607	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]	219.047	217.511	1.00706	
2112	POLR3K	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]	223.415	224.989	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]	219.055	217.533	1.007	
2114	LIPF	triacylglycerol lipase, gastric precursor (ec 3.1.1.3) (gastric lipase) (gl). [source:swissprot;acc:p07098]	214.632	213.14	1.007	
2115	LIPM	ba304i5.1 (novel lipase) (fragment). [source:sptrembl;acc:q96lg2]	214.632	213.14	1.007	
2116	LIPA	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]	214.632	213.14	1.007	
2117	SARS2	seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [source:swissprot;acc:q9np81]	214.632	213.14	1.007	
2118	SARS	seryl-trna synthetase (ec 6.1.1.11) (serine--trna ligase) (serrs). [source:swissprot;acc:p49591]	214.632	213.14	1.007	
2119	KCMF1	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]	221.248	222.788	1.00696	
2120	SLC23A1	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]	221.248	222.788	1.00696	
2121	HNRPA3	heterogeneous nuclear ribonucleoprotein a3 (hnrnp a3) (d10s102). [source:swissprot;acc:p51991]	221.248	222.788	1.00696	
2122	LGALS9	galectin-9 (hom-hd-21) (ecalectin). [source:swissprot;acc:o00182]	206.473	207.911	1.00696	
2123	ARF4	adp-ribosylation factor 4. [source:swissprot;acc:p18085]	221.248	222.788	1.00696	
2124	AKTIP	fused toes homolog; likely ortholog of mouse fused toes. [source:refseq;acc:nm_022476]	221.248	222.788	1.00696	
2125	SHC1	shc transforming protein. [source:swissprot;acc:p29353]	221.248	222.788	1.00696	
2126	ZNF289	zinc finger protein 289, id1 regulated; likely ortholog of mouse zfp289. [source:refseq;acc:nm_032389]	221.248	222.788	1.00696	
2127	SHC3	neuronal shc. [source:refseq;acc:nm_016848]	221.248	222.788	1.00696	
2128	ARF1	adp-ribosylation factor 1. [source:swissprot;acc:p32889]	221.248	222.788	1.00696	
2129	HNRNPA1	heterogeneous nuclear ribonucleoprotein a1 (helix-destabilizing protein) (single-strand binding protein) (hnrnp core protein a1). [source:swissprot;acc:p09651]	221.248	222.788	1.00696	
2130	ARF3	adp-ribosylation factor 3. [source:swissprot;acc:p16587]	221.248	222.788	1.00696	
2131	GCH1	gtp cyclohydrolase i (ec 3.5.4.16) (gtp-ch-i). [source:swissprot;acc:p30793]	226.277	227.851	1.00696	
2132	SHC2	protein sck (fragment). [source:swissprot;acc:p98077]	221.248	222.788	1.00696	
2133	NR4A1	orphan nuclear receptor hmr (early response protein nak1) (tr3 orphan receptor). [source:swissprot;acc:p22736]	207.74	206.305	1.00696	
2134	HNRNPA2B1	heterogeneous nuclear ribonucleoproteins a2/b1 (hnrnp a2 / hnrnp b1). [source:swissprot;acc:p22626]	221.248	222.788	1.00696	
2135	NR4A3	nuclear hormone receptor nor-1 (neuron-derived orphan receptor 1) (mitogen induced nuclear orphan receptor). [source:swissprot;acc:q92570]	207.743	206.308	1.00696	
2136	OCIAD1	ovarian carcinoma immunoreactive antigen. [source:refseq;acc:nm_017830]	221.248	222.788	1.00696	
2137	ARFGAP3	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [source:swissprot;acc:q9np61]	221.248	222.788	1.00696	
2138	SLC23A2	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]	221.248	222.788	1.00696	
2139	MAP2K7	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]	221.248	222.788	1.00696	
2140	CSTF2	cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [source:swissprot;acc:p33240]	161.547	162.665	1.00692	
2141	NR4A2	orphan nuclear receptor nurr1 (immediate-early response protein not) (transcriptionally inducible nuclear receptor). [source:swissprot;acc:p43354]	207.765	206.343	1.00689	
2142	EPB41	protein 4.1 (band 4.1) (p4.1) (epb4.1) (4.1r). [source:swissprot;acc:p11171]	206.443	207.864	1.00688	
2143	SPTBN5	spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [source:swissprot;acc:q9nrc6]	206.442	207.862	1.00688	
2144	EPB41L1	band 4.1-like protein 1 (neuronal protein 4.1) (4.1n). [source:swissprot;acc:q9h4g0]	206.443	207.864	1.00688	
2145	EPB41L3	band 4.1-like protein 3 (4.1b) (differentially expressed in adenocarcinoma of the lung protein 1) (dal-1). [source:swissprot;acc:q9y2j2]	206.442	207.862	1.00688	
2146	EPB41L2	band 4.1-like protein 2 (generally expressed protein 4.1) (4.1g). [source:swissprot;acc:o43491]	206.443	207.864	1.00688	
2147	SDF4	45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [source:swissprot;acc:q9brk5]	206.442	207.862	1.00688	
2148		ba271b5.1 (similar to ribosomal protein s7). [source:sptrembl;acc:q9h1s9]	217.871	219.366	1.00686	
2149	RPS7	40s ribosomal protein s7 (s8). [source:swissprot;acc:p23821]	217.871	219.366	1.00686	
2150	PSMD14	26s proteasome-associated pad1 homolog. [source:refseq;acc:nm_005805]	217.871	219.366	1.00686	

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/