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 Network Comparison Type Value Type Interaction Map red Filtered network_comparison green

Results: HTML CSV LaTeX

Showing element 2113 to 2162 of 3228 in total

Network Comparison Type	Divided
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	red	network_comparison	green	
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	1.007	217.533	
2114	triacylglycerol lipase, gastric precursor (ec 3.1.1.3) (gastric lipase) (gl). [source:swissprot;acc:p07098]	214.632	1.007	213.14	
2115	ba304i5.1 (novel lipase) (fragment). [source:sptrembl;acc:q96lg2]	214.632	1.007	213.14	
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]	214.632	1.007	213.14	
2117	seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [source:swissprot;acc:q9np81]	214.632	1.007	213.14	
2118	seryl-trna synthetase (ec 6.1.1.11) (serine--trna ligase) (serrs). [source:swissprot;acc:p49591]	214.632	1.007	213.14	
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]	221.248	1.00696	222.788	
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]	221.248	1.00696	222.788	
2121	heterogeneous nuclear ribonucleoprotein a3 (hnrnp a3) (d10s102). [source:swissprot;acc:p51991]	221.248	1.00696	222.788	
2122	galectin-9 (hom-hd-21) (ecalectin). [source:swissprot;acc:o00182]	206.473	1.00696	207.911	
2123	adp-ribosylation factor 4. [source:swissprot;acc:p18085]	221.248	1.00696	222.788	
2124	fused toes homolog; likely ortholog of mouse fused toes. [source:refseq;acc:nm_022476]	221.248	1.00696	222.788	
2125	shc transforming protein. [source:swissprot;acc:p29353]	221.248	1.00696	222.788	
2126	zinc finger protein 289, id1 regulated; likely ortholog of mouse zfp289. [source:refseq;acc:nm_032389]	221.248	1.00696	222.788	
2127	neuronal shc. [source:refseq;acc:nm_016848]	221.248	1.00696	222.788	
2128	adp-ribosylation factor 1. [source:swissprot;acc:p32889]	221.248	1.00696	222.788	
2129	heterogeneous nuclear ribonucleoprotein a1 (helix-destabilizing protein) (single-strand binding protein) (hnrnp core protein a1). [source:swissprot;acc:p09651]	221.248	1.00696	222.788	
2130	adp-ribosylation factor 3. [source:swissprot;acc:p16587]	221.248	1.00696	222.788	
2131	gtp cyclohydrolase i (ec 3.5.4.16) (gtp-ch-i). [source:swissprot;acc:p30793]	226.277	1.00696	227.851	
2132	protein sck (fragment). [source:swissprot;acc:p98077]	221.248	1.00696	222.788	
2133	orphan nuclear receptor hmr (early response protein nak1) (tr3 orphan receptor). [source:swissprot;acc:p22736]	207.74	1.00696	206.305	
2134	heterogeneous nuclear ribonucleoproteins a2/b1 (hnrnp a2 / hnrnp b1). [source:swissprot;acc:p22626]	221.248	1.00696	222.788	
2135	nuclear hormone receptor nor-1 (neuron-derived orphan receptor 1) (mitogen induced nuclear orphan receptor). [source:swissprot;acc:q92570]	207.743	1.00696	206.308	
2136	ovarian carcinoma immunoreactive antigen. [source:refseq;acc:nm_017830]	221.248	1.00696	222.788	
2137	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [source:swissprot;acc:q9np61]	221.248	1.00696	222.788	
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]	221.248	1.00696	222.788	
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]	221.248	1.00696	222.788	
2140	cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [source:swissprot;acc:p33240]	161.547	1.00692	162.665	
2141	orphan nuclear receptor nurr1 (immediate-early response protein not) (transcriptionally inducible nuclear receptor). [source:swissprot;acc:p43354]	207.765	1.00689	206.343	
2142	protein 4.1 (band 4.1) (p4.1) (epb4.1) (4.1r). [source:swissprot;acc:p11171]	206.443	1.00688	207.864	
2143	spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [source:swissprot;acc:q9nrc6]	206.442	1.00688	207.862	
2144	band 4.1-like protein 1 (neuronal protein 4.1) (4.1n). [source:swissprot;acc:q9h4g0]	206.443	1.00688	207.864	
2145	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	1.00688	207.862	
2146	band 4.1-like protein 2 (generally expressed protein 4.1) (4.1g). [source:swissprot;acc:o43491]	206.443	1.00688	207.864	
2147	45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [source:swissprot;acc:q9brk5]	206.442	1.00688	207.862	
2148	ba271b5.1 (similar to ribosomal protein s7). [source:sptrembl;acc:q9h1s9]	217.871	1.00686	219.366	
2149	40s ribosomal protein s7 (s8). [source:swissprot;acc:p23821]	217.871	1.00686	219.366	
2150	26s proteasome-associated pad1 homolog. [source:refseq;acc:nm_005805]	217.871	1.00686	219.366	
2151	apolipoprotein b-100 precursor (apo b-100) [contains: apolipoprotein b-48 (apo b-48)]. [source:swissprot;acc:p04114]	217.871	1.00686	219.366	
2152	vesicle-associated membrane protein 2 (vamp-2) (synaptobrevin 2). [source:swissprot;acc:p19065]	200.063	1.00681	198.71	
2153	vesicle-associated membrane protein 1 (vamp-1) (synaptobrevin 1). [source:swissprot;acc:p23763]	200.063	1.00681	198.71	
2154	vesicule-associated membrane protein 4 (vamp-4). [source:swissprot;acc:o75379]	200.063	1.00681	198.71	
2155	cdp-diacylglycerol--inositol 3-phosphatidyltransferase (ec 2.7.8.11) (phosphatidylinositol synthase) (ptdins synthase) (pi synthase). [source:swissprot;acc:o14735]	200.063	1.00681	198.71	
2156	adp-ribosylation factor gtpase activating protein 1 (adp-ribosylation factor 1 gtpase activating protein) (arf1 gap) (arf1-directed gtpase- activating protein) (gap protein). [source:swissprot;acc:q8n6t3]	200.063	1.00681	198.71	
2157	vesicle-associated membrane protein 3 (vamp-3) (synaptobrevin 3) (cellubrevin) (ceb). [source:swissprot;acc:q15836]	200.063	1.00681	198.71	
2158	galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [source:swissprot;acc:p56470]	206.401	1.00676	207.796	
2159	mitogen-activated protein kinase 3 (ec 2.7.1.37) (extracellular signal-regulated kinase 1) (erk-1) (insulin-stimulated map2 kinase) (map kinase 1) (mapk 1) (p44-erk1) (ert2) (p44-mapk) (microtubule- associated protein-2 kinase). [source:swissprot;acc:p27361]	215.921	1.00675	214.474	
2160	ribosomal protein s6 kinase alpha 3 (ec 2.7.1.37) (s6k-alpha 3) (90 kda ribosomal protein s6 kinase 3) (p90-rsk 3) (ribosomal s6 kinase 2) (rsk-2) (pp90rsk2) (insulin-stimulated protein kinase 1) (ispk-1). [source:swissprot;acc:p51812]	215.925	1.00673	214.481	
2161	calcium/calmodulin-dependent protein kinase type ii gamma chain (ec 2.7.1.123) (cam-kinase ii gamma chain) (cam kinase ii gamma subunit) (camk-ii gamma subunit) (fragment). [source:swissprot;acc:q13555]	215.925	1.00673	214.481	
2162	calcium/calmodulin-dependent protein kinase type ii delta chain (ec 2.7.1.123) (cam-kinase ii delta chain) (cam kinase ii delta subunit) (camk-ii delta subunit). [source:swissprot;acc:q13557]	215.925	1.00673	214.481	

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/