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

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/