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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description Rank Gene Filtered Value Type Network Comparison Type Interaction Map red network_comparison green
Results: HTML CSV LaTeX Showing element 101 to 150 of 3730 in total
Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence
description
Rank
Filtered
red
network_comparison
green
40s ribosomal protein s5. [swissprot;acc:p46782] 2343 1 3672.17 1.04413 3516.98
40s ribosomal protein s7 (s8). [swissprot;acc:p23821] 1642 5782.92 1.06977 6186.39
40s ribosomal protein s8. [swissprot;acc:p09058] 1471 5659.45 1.07564 6087.55
40s ribosomal protein s9. [swissprot;acc:p46781] 2628 3933.74 1.0146 3877.14
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] 315 0 1212.82 1.09796 1104.61
2402 1 5078.5 1.03884 5275.76
43 kda receptor-associated protein of the synapse (rapsyn) (acetylcholine receptor-associated 43 kda protein) (43 kda postsynaptic protein). [swissprot;acc:q13702] 1402 6160.06 1.07804 6640.78
44050 protein. [refseq;acc:nm_178832] 376 17385.9 1.16769 14889.2
45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [swissprot;acc:q9brk5] 972 7813.48 1.09684 8570.11
5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] 691 6920.69 1.11949 7747.63
5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] 689
5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] 688 6920.67 7747.6
5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] 687 6920.71 7747.65
5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] 686 6920.69 7747.63
5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] 692
5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] 690
5'-methylthioadenosine phosphorylase (ec 2.4.2.28) (mta phosphorylase) (mtapase). [swissprot;acc:q13126] 1606 5232.99 1.07138 5606.53
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] 57 0 270.264 1.89769 142.417
1229 1 5998.69 1.08519 6509.74
5-aminolevulinic acid synthase, erythroid-specific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-e). [swissprot;acc:p22557] 1910 6858.84 1.06246 7287.27
5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [swissprot;acc:p13196] 287 0 726.245 1.11385 808.929
1915 1 6858.84 1.06246 7287.27
5-formyltetrahydrofolate cyclo-ligase (ec 6.3.3.2) (5,10-methenyl- tetrahydrofolate synthetase) (methenyl-thf synthetase) (mthfs). [swissprot;acc:p49914] 1833 6175.23 1.06439 6572.85
5-methyltetrahydrofolate--homocysteine methyltransferase (ec 2.1.1.13) (methionine synthase, vitamin-b12 dependent) (ms). [swissprot;acc:q99707] 1115 5795.13 1.08957 6314.19
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] 2028 10243.4 1.05746 9686.82
6-phosphofructokinase, liver type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme b) (pfk-b). [swissprot;acc:p17858] 764 4250.18 1.11269 4729.12
6-phosphofructokinase, muscle type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme a) (pfk-a) (phosphofructokinase-m). [swissprot;acc:p08237] 763 4250.54 1.11272 4729.67
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] 759 4254.62 1.11315 4736.03
6-phosphogluconate dehydrogenase, decarboxylating (ec 1.1.1.44). [swissprot;acc:p52209] 1339 5988.06 1.07964 6464.94
6-phosphogluconolactonase (ec 3.1.1.31) (6pgl). [swissprot;acc:o95336] 1627 6038.46 1.07046 6463.9
6-pyruvoyl tetrahydrobiopterin synthase (ec 4.2.3.12) (ptps) (ptp synthase). [swissprot;acc:q03393] 2904 0.00001 1 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] 1313 5457.14 1.08112 5899.85
60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [swissprot;acc:q92993] 1751 6011.57 1.06711 6414.98
60s acidic ribosomal protein p0 (l10e). [swissprot;acc:p05388] 2258 5150.31 1.04616 5388.05
60s acidic ribosomal protein p1. [swissprot;acc:p05386] 313 0 6131.07 1.09921 6739.34
2418 1 4857.03 1.03763 5039.78
60s acidic ribosomal protein p2. [swissprot;acc:p05387] 2743 4824.49 1.0022 4813.92
60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] 269 0 1217.92 1.12309 1367.83
2233 1 3614.08 1.04754 3450.07
60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] 322 0 1621.1 1.09249 1771.04
2255 1 3624.59 1.04655 3463.37
60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7] 2417 3598.55 1.03775 3467.65
60s ribosomal protein l11. [swissprot;acc:p39026] 1834 3593.24 1.06437 3375.93
60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] 330 0 1658.23 1.08882 1805.52
2186 1 3586.3 1.05035 3414.4
60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] 2372 3677.53 1.04278 3526.65
60s ribosomal protein l12. [swissprot;acc:p30050] 328 0 1657.78 1.08884 1805.05
2185 1 3586.32 1.05035 3414.42
60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] 2447 3730.53 1.03309 3611.05
60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] 2449 3730.74 1.03303 3611.45

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/