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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2551 to 2600 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
Filtered
red
green
network_comparison
319 scratch; scratch 1. [refseq;acc:nm_031309] Squared 0 5976.46 5135.5 1.16375
sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1] Ranked 8918.54 9465.32 1.06131
320 40s ribosomal protein s29. [swissprot;acc:p30054] Rooted 1 50.2784 45.294 1.11005
adp-ribosylation factor 3. [swissprot;acc:p16587] Ranked 0 11627.8 10958.2 1.0611
dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6] Squared 5127.13 5964.46 1.16331
epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] Ranked 1 241.892 265.96 1.0995
epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [swissprot;acc:p07099] Squared 87971.9 69563.1 1.26463
mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426] Rooted 0 28.7027 26.9929 1.06334
ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] Measured 1 20911 24908.5 1.19117
syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623] 0 142.802 156.3 1.09452
321 adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741] Ranked 11634.4 10989.9 1.05864
arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143] Squared 5671.94 6590.82 1.162
c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] Ranked 1 241.892 265.959 1.09949
dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [swissprot;acc:p31513] Measured 0 628.072 686.693 1.09333
putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] Squared 1 33526 42390.2 1.2644
ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Measured 20911 24908.5 1.19117
sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538] Rooted 0 42.9302 40.4104 1.06236
u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] 1 55.9231 62.0565 1.10968
322 60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] Measured 0 1621.1 1771.04 1.09249
anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] 1 20911 24908.5 1.19117
casein kinase i alpha s-like. [refseq;acc:nm_145203] Squared 0 7795.92 9052.52 1.16119
deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Ranked 1 86.7483 78.8995 1.09948
estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [swissprot;acc:p14061] 0 11634.4 10989.9 1.05864
nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [swissprot;acc:p15531] Squared 1 33522.8 42384.8 1.26436
repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] Rooted 0 46.9819 44.2892 1.0608
rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] 1 60.594 67.2244 1.10942
323 60s ribosomal protein l23a. [swissprot;acc:p29316] Ranked 241.884 265.945 1.09947
cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] Rooted 50.3803 45.4193 1.10923
dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] Squared 0 5936.62 5112.71 1.16115
ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447] Rooted 27.5028 29.1579 1.06018
histone deacetylase 2 (hd2). [swissprot;acc:q92769] Measured 2056.14 2244.06 1.09139
nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [swissprot;acc:p22392] Squared 1 33514.4 42370.8 1.26426
ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154] Ranked 0 17387.1 16427.3 1.05843
u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] Measured 1 4620.76 5501.94 1.1907
324 40s ribosomal protein s23. [swissprot;acc:p39028] Ranked 243.944 268.195 1.09941
ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376] Squared 0 1742.44 1500.84 1.16098
deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Measured 1 28136.5 33457.6 1.18912
fad synthetase. [refseq;acc:nm_025207] Rooted 50.3803 45.4193 1.10923
histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590] Squared 34527.9 43507.9 1.26008
myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829] Rooted 0 27.5028 29.1579 1.06018
ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658] Ranked 17387.1 16427.3 1.05843
testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8] Measured 3036.29 2784.08 1.09059
325 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] Ranked 1 243.944 268.195 1.09941
bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] Rooted 50.3803 45.4193 1.10923
histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081] Squared 34506.3 43476 1.25994
mstp028 protein. [refseq;acc:nm_031954] Ranked 0 7965.66 7528.21 1.05811
septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Measured 1 16177.9 19235.4 1.18899
swi/snf-related matrix-associated actin-dependent regulator of chromatin c2 isoform a; mammalian chromatin remodeling complex brg1-associated factor 170; chromatin remodeling complex baf170 subunit; swi3-like protein; swi/snf complex 170 kda subunit. [refseq;acc:nm_003075] Rooted 0 16.5182 17.4854 1.05855
testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7] Measured 3036.85 2784.59 1.09059
ubiquitin-conjugating enzyme e2-18 kda ubch7 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (ubcm4) (e2-f1) (l-ubc). [swissprot;acc:p51966] Squared 1742.44 1500.84 1.16098

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/