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 11864 to 11913 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
1483 ww domain binding protein 2 (wbp-2). [swissprot;acc:q969t9] Squared Subtracted 25925.4 28590.5 2665.1
1484 2-oxoisovalerate dehydrogenase alpha subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component alpha chain) (bckdh e1-alpha). [swissprot;acc:p12694] Ranked Divided 198.927 202.726 1.0191
abl-interactor 2; abl-interacting protein 1 (sh3-containing protein); abl binding protein 3; arg protein tyrosine kinase-binding protein; abl-interactor protein 2b; similar to spectrin sh3 domain binding protein 1. [refseq;acc:nm_005759] Squared Subtracted 26621.3 29286.1 2664.8
cytochrome c. [swissprot;acc:p00001] Ranked 228.419 232.376 3.957
dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409] Squared Divided 22974.7 25619.9 1.11514
evolutionarily conserved signaling intermediate in toll pathway; ecsit. [refseq;acc:nm_016581] Rooted 64.2463 66.6861 1.03798
pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152] Subtracted 60.4911 58.1154 2.3757
ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916] Measured Divided 5372.25 5775.21 1.07501
vacuolar protein sorting 11 (hvps11) (pp3476). [swissprot;acc:q9h270] Subtracted 6048.57 6487.65 439.08
1485 chromosome 11 open reading frame2; chromosome 11 open reading frame2. [refseq;acc:nm_013265] Squared Divided 26696.5 29768.6 1.11508
heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174] Ranked Subtracted 228.419 232.376 3.957
intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3] Rooted 60.4911 58.1154 2.3757
j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] Ranked Divided 207.877 203.989 1.01906
lamin b2. [swissprot;acc:q03252] Squared Subtracted 27353.9 30016.1 2662.2
methionyl-trna formyltransferase, mitochondrial precursor (ec 2.1.2.9) (mtfmt). [swissprot;acc:q96dp5] Rooted Divided 59.2072 61.4511 1.0379
tryptophanyl-trna synthetase, mitochondrial precursor (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) ((mt)trprs). [swissprot;acc:q9ugm6] Measured 5372.25 5775.21 1.07501
vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1] Subtracted 6048.57 6487.65 439.08
1486 40s ribosomal protein s3a. [swissprot;acc:p49241] Squared 19516.8 22178 2661.2
ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] Rooted Divided 79.3006 82.3013 1.03784
heparan sulfate 6-o-sulfotransferase; heparan-sulfate 6-sulfotransferase. [refseq;acc:nm_004807] Ranked Subtracted 228.419 232.376 3.957
hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [refseq;acc:nm_006076] Rooted 60.4911 58.1154 2.3757
human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503] Ranked Divided 207.877 203.989 1.01906
kinesin-like protein kif13a (kinesin-like protein rbkin). [swissprot;acc:q9h1h9] Squared 26696.5 29768.6 1.11508
p300/cbp-associated factor (ec 2.3.1.-) (p/caf) (histone acetylase pcaf). [swissprot;acc:q92831] Measured Subtracted 7210.87 7649.23 438.36
thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445] Divided 5372.25 5775.21 1.07501
1487 cgthba protein (-14 gene protein). [swissprot;acc:q12980] Rooted Subtracted 60.4911 58.1154 2.3757
conserved oligomeric golgi complex component 2 (low density lipoprotein receptor defect c-complementing protein). [swissprot;acc:q14746] Squared Divided 26696.5 29768.6 1.11508
dual specificity mitogen-activated protein kinase kinase 1 (ec 2.7.1.-) (map kinase kinase 1) (mapkk 1) (erk activator kinase 1) (mapk/erk kinase 1) (mek1). [swissprot;acc:q02750] Rooted 62.3212 64.678 1.03782
fatty acid hydroxylase domain containing 1. [refseq;acc:nm_024306] Ranked Subtracted 228.419 232.376 3.957
folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] Squared 19620.8 22280.7 2659.9
glucose-6-phosphate 1-dehydrogenase (ec 1.1.1.49) (g6pd). [swissprot;acc:p11413] Measured 6025.86 6464.16 438.3
nicotinamide nucleotide adenylyltransferase 3; pyridine nucleotide adenylyltransferase 3. [refseq;acc:nm_178177] Divided 5573.64 5991.58 1.07499
zinc finger protein 40 (human immunodeficiency virus type i enhancer- binding protein 1) (hiv-ep1) (major histocompatibility complex binding protein 1) (mbp-1) (positive regulatory domain ii binding factor 1) (prdii-bf1). [swissprot;acc:p15822] Ranked 207.877 203.989 1.01906
1488 delta 1-pyrroline-5-carboxylate synthetase (p5cs) [includes: glutamate 5-kinase (ec 2.7.2.11) (gamma-glutamyl kinase) (gk); gamma-glutamyl phosphate reductase (gpr) (ec 1.2.1.41) (glutamate-5-semialdehyde dehydrogenase) (glutamyl-gamma-semialdehyde dehydrogenase)]. [swissprot;acc:p54886] Measured 5573.64 5991.58 1.07499
dna-repair protein xrcc3 (x-ray repair cross-complementing protein 3). [swissprot;acc:o43542] Subtracted 6025.86 6464.16 438.3
hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500] Rooted 60.4911 58.1154 2.3757
human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629] Ranked Divided 207.877 203.989 1.01906
ischemia/reperfusion inducible protein. [refseq;acc:nm_024640] Squared Subtracted 28024.6 30683.7 2659.1
kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8] Divided 26696.5 29768.6 1.11508
similar to kinase suppressor of ras (fragment). [sptrembl;acc:q8ivt5] Rooted 62.3212 64.678 1.03782
ww domain binding protein 11; npw38-binding protein npwbp; sh3 domain-binding protein snp70. [refseq;acc:nm_016312] Ranked Subtracted 228.419 232.376 3.957
1489 26s protease regulatory subunit 6b (mip224) (mb67 interacting protein) (tat-binding protein-7) (tbp-7). [swissprot;acc:p43686] Squared Divided 26277.3 29299.3 1.115
dual specificity mitogen-activated protein kinase kinase 2 (ec 2.7.1.-) (map kinase kinase 2) (mapkk 2) (erk activator kinase 2) (mapk/erk kinase 2) (mek2). [swissprot;acc:p36507] Rooted 62.3212 64.678 1.03782
elac homolog 2; putative prostate cancer susceptibility protein; elac (e. coli) homolog 2. [refseq;acc:nm_018127] Ranked Subtracted 228.419 232.376 3.957
f-actin capping protein alpha-3 subunit (capz alpha-3) (germ cell- specific protein 3). [swissprot;acc:q96kx2] Squared 30593.4 33250.7 2657.3
general control of amino acid synthesis protein 5-like 2 (ec 2.3.1.-) (histone acetyltransferase gcn5) (hsgcn5). [swissprot;acc:q92830] Measured 7210.64 7648.94 438.3
megf11 protein. [refseq;acc:nm_032445] Rooted 60.599 62.9716 2.3726
mitogen-activated protein kinase kinase kinase 7 (ec 2.7.1.-) (transforming growth factor-beta-activated kinase 1) (tgf-beta- activated kinase 1). [swissprot;acc:o43318] Ranked Divided 213.251 209.264 1.01905
vesicle-fusing atpase (ec 3.6.4.6) (vesicular-fusion protein nsf) (n- ethylmaleimide sensitive fusion protein) (nem-sensitive fusion protein). [swissprot;acc:p46459] Measured 6192.38 6656.34 1.07492
1490 atp-dependent dna helicase q5 (recq protein-like 5) (recq5). [swissprot;acc:o94762] Subtracted 6025.86 6464.16 438.3

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/