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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 201 to 250 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
description
Rank
Interaction Map
red
green
network_comparison
45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [swissprot;acc:q9brk5] 2500 Low confidence 198.748 195.198 1.01819
5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] 879 High confidence 212.002 203.954 1.03946
2381 Low confidence 201.395 197.73 1.01854
5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] 877 High confidence 212.002 203.954 1.03946
2351 Low confidence 201.408 197.731 1.0186
5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] 876 High confidence 212.002 203.954 1.03946
1683 Low confidence 200.836 196.78 1.02061
5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] 875 High confidence 212.002 203.954 1.03946
1681 Low confidence 200.826 196.771 1.02061
5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] 874 High confidence 212.002 203.954 1.03946
2295 Low confidence 196.86 193.236 1.01875
5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] 880 High confidence 212.002 203.954 1.03946
2304 Low confidence 196.768 193.154 1.01871
5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] 878 High confidence 212.002 203.954 1.03946
2294 Low confidence 196.869 193.244 1.01876
5'-methylthioadenosine phosphorylase (ec 2.4.2.28) (mta phosphorylase) (mtapase). [swissprot;acc:q13126] 1769 High confidence 223.016 225.734 1.01219
3870 Low confidence 199.433 196.894 1.0129
5'-nucleotidase precursor (ec 3.1.3.5) (ecto-5'-nucleotidase) (5'-nt) (cd73 antigen). [swissprot;acc:p21589] 4657 204.851 203.584 1.00622
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] 841 206.243 201.027 1.02595
1021 High confidence 221.278 214.409 1.03204
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 194.527 195.08 1.00284
2505 Low confidence 198.676 195.131 1.01817
5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [swissprot;acc:p13196] 2496 High confidence 194.527 195.08 1.00284
2520 Low confidence 198.651 195.109 1.01815
5-formyltetrahydrofolate cyclo-ligase (ec 6.3.3.2) (5,10-methenyl- tetrahydrofolate synthetase) (methenyl-thf synthetase) (mthfs). [swissprot;acc:p49914] 2263 196.131 192.502 1.01885
2754 High confidence 210.638 210.642 1.00002
5-methyltetrahydrofolate--homocysteine methyltransferase (ec 2.1.1.13) (methionine synthase, vitamin-b12 dependent) (ms). [swissprot;acc:q99707] 1921 221.607 219.386 1.01012
3629 Low confidence 192.426 189.733 1.01419
5-oxoprolinase (ec 3.5.2.9) (5-oxo-l-prolinase) (pyroglutamase) (5-opase) (fragment). [swissprot;acc:o14841] 3199 195.682 192.595 1.01603
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] 1292 200.544 196.152 1.02239
2532 High confidence 190.405 190.812 1.00214
5t4 oncofetal trophoblast glycoprotein; 5t4-antigen. [refseq;acc:nm_006670] 3485 Low confidence 202.475 199.484 1.01499
6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1 (6pf-2-k/fru- 2,6-p2ase liver isozyme) [includes: 6-phosphofructo-2-kinase (ec 2.7.1.105); fructose-2,6-bisphosphatase (ec 3.1.3.46)]. [swissprot;acc:p16118] 3865 194.792 197.306 1.01291
6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2 (6pf-2-k/fru- 2,6-p2ase heart-type isozyme) (pfk-2/fbpase-2) [includes: 6- phosphofructo-2-kinase (ec 2.7.1.105); fructose-2,6-bisphosphatase (ec 3.1.3.46)]. [swissprot;acc:o60825] 3867
6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (6pf-2-k/fru- 2,6-p2ase brain/placenta-type isozyme) (ipfk-2) [includes: 6- phosphofructo-2-kinase (ec 2.7.1.105); fructose-2,6-bisphosphatase (ec 3.1.3.46)]. [swissprot;acc:q16875] 3864
6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4 (6pf-2-k/fru- 2,6-p2ase testis-type isozyme) [includes: 6-phosphofructo-2-kinase (ec 2.7.1.105); fructose-2,6-bisphosphatase (ec 3.1.3.46)]. [swissprot;acc:q16877] 3868
6-phosphofructokinase, liver type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme b) (pfk-b). [swissprot;acc:p17858] 1822 High confidence 240.32 243.085 1.01151
2739 Low confidence 200.929 197.479 1.01747
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 High confidence 240.32 243.069 1.01144
2769 Low confidence 200.94 197.499 1.01742
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 High confidence 240.317 242.881 1.01067
2706 Low confidence 200.868 197.403 1.01755
6-phosphogluconate dehydrogenase, decarboxylating (ec 1.1.1.44). [swissprot;acc:p52209] 1923 201.484 197.59 1.01971
2274 High confidence 213.642 214.801 1.00542
6-phosphogluconolactonase (ec 3.1.1.31) (6pgl). [swissprot;acc:o95336] 1584 216.891 220.432 1.01633
2807 Low confidence 200.157 196.756 1.01729
6-pyruvoyl tetrahydrobiopterin synthase (ec 4.2.3.12) (ptps) (ptp synthase). [swissprot;acc:q03393] 2904 High confidence 0.00001 0.00001 1
4128 Low confidence 198.355 196.271 1.01062
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 High confidence 222.305 222.64 1.00151
2591 Low confidence 199.427 195.908 1.01796

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/