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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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 5458 to 5507 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
683 aflatoxin b1 aldehyde reductase 2 (ec 1.-.-.-) (afb1-ar 2). [swissprot;acc:o95154] Squared Subtracted 23526.4 27879.3 4352.9
dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] Measured 3751.3 4431.34 680.04
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Ranked Divided 132.413 125.389 1.05602
osteoclast stimulating factor 1. [swissprot;acc:q92882] Subtracted 231.809 243.289 11.48
sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961] Measured Divided 7139.5 7994.06 1.11969
tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [refseq;acc:nm_024885] Rooted 72.8809 78.3254 1.0747
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [swissprot;acc:q15118] Squared 22328.1 26222.3 1.17441
684 alpha/beta hydrolase domain containing protein 3; lung alpha/beta hydrolase 3. [refseq;acc:nm_138340] Subtracted 23526.4 27879.3 4352.9
dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] Rooted 49.9856 45.4432 4.5424
eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884] Measured Divided 4359.82 4880.99 1.11954
homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Ranked 132.413 125.389 1.05602
phosphoribosylformylglycinamidine synthase (ec 6.3.5.3) (fgam synthase) (fgams) (formylglycinamide ribotide amidotransferase) (fgarat) (formylglycinamide ribotide synthetase). [swissprot;acc:o15067] Subtracted 223.58 235.027 11.447
transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545] Rooted Divided 72.9862 78.4342 1.07464
u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] Measured Subtracted 5575.18 6254.85 679.67
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [swissprot;acc:q15119] Squared Divided 22328.2 26222.4 1.17441
685 bifunctional purine biosynthesis protein purh [includes: phosphoribosylaminoimidazolecarboxamide formyltransferase (ec 2.1.2.3) (aicar transformylase); imp cyclohydrolase (ec 3.5.4.10) (inosinicase) (imp synthetase) (atic)]. [swissprot;acc:p31939] Ranked Subtracted 223.58 235.027 11.447
epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] Rooted 50.4663 45.9313 4.535
golgi membrane protein sb140; smooth muscle cell associated protein 5. [refseq;acc:nm_030799] Squared 23526.4 27879.3 4352.9
hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] Rooted Divided 57.4644 61.7491 1.07456
homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Ranked 132.413 125.389 1.05602
metaxin 1. [swissprot;acc:q13505] Measured 9327.58 10442.2 1.1195
step ii splicing factor slu7. [refseq;acc:nm_006425] Subtracted 5575.18 6254.85 679.67
translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [swissprot;acc:p13693] Squared Divided 42363.8 36083.8 1.17404
686 5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] Measured 6920.69 7747.63 1.11949
alpha/beta hydrolase domain containing protein 1 isoform 2; lung alpha/beta hydrolase protein 1. [refseq;acc:nm_152870] Squared Subtracted 23526.4 27879.3 4352.9
c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] Rooted Divided 86.4264 92.8635 1.07448
c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] Subtracted 50.4666 45.9317 4.5349
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Ranked Divided 132.413 125.389 1.05602
multifunctional protein ade2 [includes: phosphoribosylaminoimidazole- succinocarboxamide synthase (ec 6.3.2.6) (saicar synthetase); phosphoribosylaminoimidazole carboxylase (ec 4.1.1.21) (air carboxylase) (airc)]. [swissprot;acc:p22234] Subtracted 223.58 235.027 11.447
peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521] Squared Divided 28982.3 34012.8 1.17357
uba/ubx 33.3 kda protein. [swissprot;acc:q04323] Measured Subtracted 6562.98 7242.37 679.39
687 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] Divided 6920.71 7747.65 1.11949
60s ribosomal protein l5. [swissprot;acc:p46777] Rooted Subtracted 50.4641 45.9293 4.5348
dendritic cell protein. [refseq;acc:nm_006360] Ranked 223.121 211.685 11.436
ero1-like. [refseq;acc:nm_014584] Measured 6562.98 7242.37 679.39
meiotic recombination protein dmc1/lim15 homolog. [swissprot;acc:q14565] Squared Divided 24633.6 28893.6 1.17293
methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial precursor (ec 1.2.1.27) (mmsdh). [swissprot;acc:q02252] Subtracted 23526.5 27879.4 4352.9
putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] Rooted Divided 57.6308 61.9165 1.07436
retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Ranked 132.413 125.389 1.05602
688 10 kda heat shock protein, mitochondrial (hsp10) (10 kda chaperonin) (cpn10). [swissprot;acc:q04984] Squared Subtracted 23526.4 27879.3 4352.9
5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] Measured Divided 6920.67 7747.6 1.11949
60s ribosomal protein l23a. [swissprot;acc:p29316] Rooted Subtracted 50.4703 45.9373 4.533
adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [swissprot;acc:p23526] Squared Divided 22245.5 26087.5 1.17271
dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] Rooted 60.7997 65.3199 1.07435
dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [swissprot;acc:o15514] Ranked 237.554 250.823 1.05586
potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436] Subtracted 223.121 211.685 11.436
retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749] Measured 6311.83 6989.6 677.77
689 5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] Divided 6920.69 7747.63 1.11949
carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [swissprot;acc:p15169] Ranked Subtracted 223.121 211.685 11.436
dendritic cell protein. [refseq;acc:nm_006360] Squared Divided 33104 38818.5 1.17262

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/