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 description Rank Filtered Value Type Network Comparison Type network_comparison Interaction Map green red
Results: HTML CSV LaTeX Showing element 101 to 150 of 3730 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
description
Rank
Filtered
network_comparison
green
red
40s ribosomal protein s5. [swissprot;acc:p46782] 366 1 1.09602 265.756 242.473
40s ribosomal protein s7 (s8). [swissprot;acc:p23821] 2149 1.00686 219.366 217.871
40s ribosomal protein s8. [swissprot;acc:p09058] 1397 1.02145 214.049 218.64
40s ribosomal protein s9. [swissprot;acc:p46781] 439 1.07866 257.784 238.986
40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865] 298 0 1.07219 12842.5 11977.8
789 1 1.04578 234.511 224.244
43 kda receptor-associated protein of the synapse (rapsyn) (acetylcholine receptor-associated 43 kda protein) (43 kda postsynaptic protein). [swissprot;acc:q13702] 2232 1.00632 214.194 215.547
44050 protein. [refseq;acc:nm_178832] 2506 1.0025 151.009 151.386
45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [swissprot;acc:q9brk5] 2147 1.00688 207.862 206.442
5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] 879 1.03946 203.954 212.002
5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] 877
5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] 876
5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] 875
5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] 874
5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] 880
5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] 878
5'-methylthioadenosine phosphorylase (ec 2.4.2.28) (mta phosphorylase) (mtapase). [swissprot;acc:q13126] 1769 1.01219 225.734 223.016
5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643] 288 0 1.07517 16053 14930.6
1021 1 1.03204 214.409 221.278
5-aminolevulinic acid synthase, erythroid-specific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-e). [swissprot;acc:p22557] 2491 1.00284 195.08 194.527
5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [swissprot;acc:p13196] 412 0 1.03217 8279.69 8546.06
2496 1 1.00284 195.08 194.527
5-formyltetrahydrofolate cyclo-ligase (ec 6.3.3.2) (5,10-methenyl- tetrahydrofolate synthetase) (methenyl-thf synthetase) (mthfs). [swissprot;acc:p49914] 2754 1.00002 210.642 210.638
5-methyltetrahydrofolate--homocysteine methyltransferase (ec 2.1.1.13) (methionine synthase, vitamin-b12 dependent) (ms). [swissprot;acc:q99707] 1921 1.01012 219.386 221.607
54 kda nuclear rna- and dna-binding protein (p54(nrb)) (p54nrb) (55 kda nuclear protein) (nmt55) (non-pou domain-containing octamer- binding protein) (dna-binding p52/p100 complex, 52 kda subunit). [swissprot;acc:q15233] 2532 1.00214 190.812 190.405
6-phosphofructokinase, liver type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme b) (pfk-b). [swissprot;acc:p17858] 1822 1.01151 243.085 240.32
6-phosphofructokinase, muscle type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme a) (pfk-a) (phosphofructokinase-m). [swissprot;acc:p08237] 1830 1.01144 243.069
6-phosphofructokinase, type c (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme c) (pfk-c) (6-phosphofructokinase, platelet type). [swissprot;acc:q01813] 1883 1.01067 242.881 240.317
6-phosphogluconate dehydrogenase, decarboxylating (ec 1.1.1.44). [swissprot;acc:p52209] 2274 1.00542 214.801 213.642
6-phosphogluconolactonase (ec 3.1.1.31) (6pgl). [swissprot;acc:o95336] 1584 1.01633 220.432 216.891
6-pyruvoyl tetrahydrobiopterin synthase (ec 4.2.3.12) (ptps) (ptp synthase). [swissprot;acc:q03393] 2904 1 0.00001 0.00001
60 kda heat shock protein, mitochondrial precursor (hsp60) (60 kda chaperonin) (cpn60) (heat shock protein 60) (hsp-60) (mitochondrial matrix protein p1) (p60 lymphocyte protein) (hucha60). [swissprot;acc:p10809] 2588 1.00151 222.64 222.305
60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [swissprot;acc:q92993] 826 1.04335 213.912 223.186
60s acidic ribosomal protein p0 (l10e). [swissprot;acc:p05388] 1092 1.02941 232.855 226.203
60s acidic ribosomal protein p1. [swissprot;acc:p05386] 233 0 1.1015 10560 9586.97
898 1 1.03874 238.048 229.171
60s acidic ribosomal protein p2. [swissprot;acc:p05387] 720 1.05396 244.435 231.92
60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] 199 0 1.11721 10545.7 11781.8
357 1 1.09683 266.661 243.12
60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] 356 1.09684 266.796 243.24
397 0 1.03414 9676.53 10006.9
60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7] 373 1 1.09442 265.255 242.37
60s ribosomal protein l11. [swissprot;acc:p39026] 283 1.10552 267.346 241.828
60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] 338 1.0983 267.528 243.583
396 0 1.03436 9856.12 10194.8
60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] 369 1 1.09475 265.104 242.159
60s ribosomal protein l12. [swissprot;acc:p30050] 337 1.0983 267.527 243.583
394 0 1.0344 9857.79 10196.9
60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] 390 1 1.09011 263.62 241.828
60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] 392 1.09008 263.615 241.83

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.
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