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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Gene Network Comparison Type Value Type description green Rank network_comparison red Filtered Interaction Map

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Showing element 1763 to 1812 of 3228 in total

Network Comparison Type

: Divided
Value Type

: Ranked
Filtered

: 1
Interaction Map

: High confidence

description	green	Rank	network_comparison	red
myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	46	152	1.19565	55
myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]		150
myosin vc (myosin 5c). [swissprot;acc:q9nqx4]		151
myosin vi. [swissprot;acc:q9um54]	225.468	1435	1.02028	220.987
myosin viia. [swissprot;acc:q13402]	220.386	2639	1.00123	220.658
myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]	245.247	21	1.32082	185.678
myotubularin-related protein 1 (ec 3.1.3.-). [swissprot;acc:q13613]	0.00001	3190	1	0.00001
myotubularin-related protein 2 (ec 3.1.3.-). [swissprot;acc:q13614]	0.00001	3166	1	0.00001
n-acetylgalactosamine kinase (ec 2.7.1.-) (galnac kinase) (galactokinase 2). [swissprot;acc:q01415]	210.412	1336	1.02257	215.162
n-acetylglucosamine kinase (ec 2.7.1.59) (glcnac kinase). [swissprot;acc:q9uj70]	0.00001	3022	1	0.00001
n-acetylglutamate synthase. [refseq;acc:nm_153006]	226.611	1616	1.01538	223.179
n-acetyllactosaminide beta-1,3-n-acetylglucosaminyltransferase (ec 2.4.1.149) (poly-n-acetyllactosamine extension enzyme) (i-beta- 1,3-n-acetylglucosaminyltransferase) (ignt) (udp-glcnac:betagal beta- 1,3-n-acetylglucosaminyltransferase 6). [swissprot;acc:o43505]	219.708	728	1.05187	208.874
n-acetyltransferase 5 (ec 2.3.1.-). [swissprot;acc:q9y6d2]	220.826	2394	1.00379	221.662
n-deacetylase/n-sulfotransferase (heparan glucosaminyl) 3. [refseq;acc:nm_004784]	223.475	1354	1.02208	228.409
n-deacetylase/n-sulfotransferase 4. [refseq;acc:nm_022569]	223.475	1355	1.02208	228.409
n-myc proto-oncogene protein. [swissprot;acc:p04198]	219.008	882	1.03924	227.601
n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227]	216.674	438	1.07869	233.723
nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387]	213.147	1863	1.01087	210.856
nadh-ubiquinone oxidoreductase 13 kda-a subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-a) (ci-13kd-a). [swissprot;acc:o75380]	230.595	1762	1.01238	233.45
nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718]	0.00001	3005	1	0.00001
nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181]	259.004	119	1.23157	318.982
nadh-ubiquinone oxidoreductase 23 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-23kd) (ci-23kd) (tyky subunit). [swissprot;acc:o00217]	219.017	885	1.03917	227.596
nadh-ubiquinone oxidoreductase 24 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3). [swissprot;acc:p19404]	0.00001	2795	1	0.00001
nadh-ubiquinone oxidoreductase 30 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-30kd) (ci-30kd). [swissprot;acc:o75489]		3081
nadh-ubiquinone oxidoreductase 39 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-39kd) (ci-39kd). [swissprot;acc:q16795]		2954
nadh-ubiquinone oxidoreductase 49 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-49kd) (ci-49kd). [swissprot;acc:o75306]		2878
nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556]	202.141	630	1.05993	214.256
nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9]	206.339	1096	1.02911	212.345
nadh-ubiquinone oxidoreductase pdsw subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-pdsw) (ci-pdsw). [swissprot;acc:o96000]	212.983	2386	1.00393	213.82
nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09]	228.934	118	1.24382	284.753
nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435]	267.352	274	1.10763	241.373
nadph:adrenodoxin oxidoreductase, mitochondrial precursor (ec 1.18.1.2) (adrenodoxin reductase) (ar) (ferredoxin-nadp(+) reductase). [swissprot;acc:p22570]	213.153	2228	1.00634	211.81
nag14 protein. [refseq;acc:nm_022143]	224.337	2240	1.00618	222.959
nanos (fragment). [sptrembl;acc:q8wy41]	0.00001	2803	1	0.00001
nardilysin precursor (ec 3.4.24.61) (n-arginine dibasic convertase) (nrd convertase) (nrd-c). [swissprot;acc:o43847]	225.195	2633	1.00135	224.891
nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594]	204.05	888	1.03909	212.027
necdin. [swissprot;acc:q99608]	110.265	90	1.24949	88.2482
nefa-interacting nuclear protein nip30. [refseq;acc:nm_024946]	215.799	2608	1.0014	215.497
neighbor of cox4. [swissprot;acc:o43402]	217.926	1818	1.01164	220.462
nemo-like kinase; likely ortholog of mouse nemo like kinase. [refseq;acc:nm_016231]	211.648	1060	1.03078	218.162
neural cell adhesion molecule l1 precursor (n-cam l1) (cd171 antigen). [swissprot;acc:p32004]	198.321	2740	1.00022	198.278
neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401]	194.452	559	1.06612	207.309
neuralized-like. [refseq;acc:nm_004210]	266.948	117	1.24491	332.326
neurocalcin delta. [swissprot;acc:p29554]	230.931	1182	1.02589	225.104
neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079]	114	129	1.21277	94
neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [refseq;acc:nm_005863]	233.508	785	1.04685	244.447
neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562]	284	333	1.09859	312
neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]		329
neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90]		334
neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8]		332

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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/