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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Network Comparison Type Value Type Gene description Rank Filtered Interaction Map network_comparison red green
Results: HTML CSV LaTeX Showing element 1768 to 1817 of 3228 in total
Network Comparison Type  : Divided
Value Type  : Ranked
Filtered  : 1
Interaction Map  : High confidence
description
Rank
network_comparison
red
green
myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] 21 1.32082 185.678 245.247
myotubularin-related protein 1 (ec 3.1.3.-). [swissprot;acc:q13613] 3190 1 0.00001 0.00001
myotubularin-related protein 2 (ec 3.1.3.-). [swissprot;acc:q13614] 3166
n-acetylgalactosamine kinase (ec 2.7.1.-) (galnac kinase) (galactokinase 2). [swissprot;acc:q01415] 1336 1.02257 215.162 210.412
n-acetylglucosamine kinase (ec 2.7.1.59) (glcnac kinase). [swissprot;acc:q9uj70] 3022 1 0.00001 0.00001
n-acetylglutamate synthase. [refseq;acc:nm_153006] 1616 1.01538 223.179 226.611
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] 728 1.05187 208.874 219.708
n-acetyltransferase 5 (ec 2.3.1.-). [swissprot;acc:q9y6d2] 2394 1.00379 221.662 220.826
n-deacetylase/n-sulfotransferase (heparan glucosaminyl) 3. [refseq;acc:nm_004784] 1354 1.02208 228.409 223.475
n-deacetylase/n-sulfotransferase 4. [refseq;acc:nm_022569] 1355
n-myc proto-oncogene protein. [swissprot;acc:p04198] 882 1.03924 227.601 219.008
n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] 438 1.07869 233.723 216.674
nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387] 1863 1.01087 210.856 213.147
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] 1762 1.01238 233.45 230.595
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] 3005 1 0.00001 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] 119 1.23157 318.982 259.004
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] 885 1.03917 227.596 219.017
nadh-ubiquinone oxidoreductase 24 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3). [swissprot;acc:p19404] 2795 1 0.00001 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] 630 1.05993 214.256 202.141
nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9] 1096 1.02911 212.345 206.339
nadh-ubiquinone oxidoreductase pdsw subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-pdsw) (ci-pdsw). [swissprot;acc:o96000] 2386 1.00393 213.82 212.983
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] 118 1.24382 284.753 228.934
nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] 274 1.10763 241.373 267.352
nadph:adrenodoxin oxidoreductase, mitochondrial precursor (ec 1.18.1.2) (adrenodoxin reductase) (ar) (ferredoxin-nadp(+) reductase). [swissprot;acc:p22570] 2228 1.00634 211.81 213.153
nag14 protein. [refseq;acc:nm_022143] 2240 1.00618 222.959 224.337
nanos (fragment). [sptrembl;acc:q8wy41] 2803 1 0.00001 0.00001
nardilysin precursor (ec 3.4.24.61) (n-arginine dibasic convertase) (nrd convertase) (nrd-c). [swissprot;acc:o43847] 2633 1.00135 224.891 225.195
nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] 888 1.03909 212.027 204.05
necdin. [swissprot;acc:q99608] 90 1.24949 88.2482 110.265
nefa-interacting nuclear protein nip30. [refseq;acc:nm_024946] 2608 1.0014 215.497 215.799
neighbor of cox4. [swissprot;acc:o43402] 1818 1.01164 220.462 217.926
nemo-like kinase; likely ortholog of mouse nemo like kinase. [refseq;acc:nm_016231] 1060 1.03078 218.162 211.648
neural cell adhesion molecule l1 precursor (n-cam l1) (cd171 antigen). [swissprot;acc:p32004] 2740 1.00022 198.278 198.321
neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] 559 1.06612 207.309 194.452
neuralized-like. [refseq;acc:nm_004210] 117 1.24491 332.326 266.948
neurocalcin delta. [swissprot;acc:p29554] 1182 1.02589 225.104 230.931
neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] 129 1.21277 94 114
neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [refseq;acc:nm_005863] 785 1.04685 244.447 233.508
neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] 333 1.09859 312 284
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
neuromedin u receptor 2. [refseq;acc:nm_020167] 2991 1 0.00001 0.00001
neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] 444 1.0783 223.801 207.549
neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [refseq;acc:nm_145117] 443 223.79 207.539
neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] 445 223.801 207.549
neuron specific calcium-binding protein hippocalcin (p23k) (calcium- binding protein bdr-2). [swissprot;acc:p32076] 1183 1.02588 225.103 230.928

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/