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 Rank green network_comparison red Filtered Interaction Map
Results: HTML CSV LaTeX Showing element 1775 to 1824 of 3228 in total
Network Comparison Type  : Divided
Value Type  : Ranked
Filtered  : 1
Interaction Map  : High confidence
description
Rank
green
network_comparison
red
n-acetyltransferase 5 (ec 2.3.1.-). [swissprot;acc:q9y6d2] 2394 220.826 1.00379 221.662
n-deacetylase/n-sulfotransferase (heparan glucosaminyl) 3. [refseq;acc:nm_004784] 1354 223.475 1.02208 228.409
n-deacetylase/n-sulfotransferase 4. [refseq;acc:nm_022569] 1355
n-myc proto-oncogene protein. [swissprot;acc:p04198] 882 219.008 1.03924 227.601
n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] 438 216.674 1.07869 233.723
nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387] 1863 213.147 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] 1762 230.595 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] 3005 0.00001 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] 119 259.004 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] 885 219.017 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] 2795 0.00001 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] 630 202.141 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] 1096 206.339 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] 2386 212.983 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] 118 228.934 1.24382 284.753
nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] 274 267.352 1.10763 241.373
nadph:adrenodoxin oxidoreductase, mitochondrial precursor (ec 1.18.1.2) (adrenodoxin reductase) (ar) (ferredoxin-nadp(+) reductase). [swissprot;acc:p22570] 2228 213.153 1.00634 211.81
nag14 protein. [refseq;acc:nm_022143] 2240 224.337 1.00618 222.959
nanos (fragment). [sptrembl;acc:q8wy41] 2803 0.00001 1 0.00001
nardilysin precursor (ec 3.4.24.61) (n-arginine dibasic convertase) (nrd convertase) (nrd-c). [swissprot;acc:o43847] 2633 225.195 1.00135 224.891
nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] 888 204.05 1.03909 212.027
necdin. [swissprot;acc:q99608] 90 110.265 1.24949 88.2482
nefa-interacting nuclear protein nip30. [refseq;acc:nm_024946] 2608 215.799 1.0014 215.497
neighbor of cox4. [swissprot;acc:o43402] 1818 217.926 1.01164 220.462
nemo-like kinase; likely ortholog of mouse nemo like kinase. [refseq;acc:nm_016231] 1060 211.648 1.03078 218.162
neural cell adhesion molecule l1 precursor (n-cam l1) (cd171 antigen). [swissprot;acc:p32004] 2740 198.321 1.00022 198.278
neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] 559 194.452 1.06612 207.309
neuralized-like. [refseq;acc:nm_004210] 117 266.948 1.24491 332.326
neurocalcin delta. [swissprot;acc:p29554] 1182 230.931 1.02589 225.104
neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] 129 114 1.21277 94
neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [refseq;acc:nm_005863] 785 233.508 1.04685 244.447
neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] 333 284 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
neuromedin u receptor 2. [refseq;acc:nm_020167] 2991 0.00001 1 0.00001
neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] 444 207.549 1.0783 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 230.928 1.02588 225.103
neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822] 1272 167.177 1.02425 171.231
neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] 1276
neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] 1275
neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825] 1268
neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] 465 267.226 1.07686 248.152
neuronal calcium sensor 1 (ncs-1) (frequenin homolog) (frequenin-like protein) (frequenin-like ubiquitous protein). [swissprot;acc:p36610] 1367 228.799 1.02194 223.887
neuronal kinesin heavy chain (nkhc) (kinesin heavy chain isoform 5a) (kinesin heavy chain neuron-specific 1). [swissprot;acc:q12840] 2484 218.72 1.00287 218.093

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/