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 14822 to 14871 of 29840 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
1351 prohibitin. [swissprot;acc:p35232] Ranked Divided 211.513 206.941 1.02209
proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] Squared 14753.6 16612.9 1.12602
synaptotagmin xii (sytxii). [swissprot;acc:q8iv01] Rooted 61.6779 64.2009 1.04091
1352 cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] Measured Subtracted 5655.85 6120.64 464.79
dual specificity mitogen-activated protein kinase kinase 3 (ec 2.7.1.-) (map kinase kinase 3) (mapkk 3) (mapk/erk kinase 3). [swissprot;acc:p46734] Divided 6104.11 6586.48 1.07902
ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [swissprot;acc:q06545] Squared Subtracted 20823.1 23668.4 2845.3
megf6 (fragment). [sptrembl;acc:o75095] Rooted Divided 61.7068 64.2305 1.0409
prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [refseq;acc:nm_024831] Squared 26925.7 30311.3 1.12574
prohibitin. [swissprot;acc:p35232] Ranked Subtracted 211.513 206.941 4.572
repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] Divided 1.02209
t-box transcription factor tbx6 (t-box protein 6). [swissprot;acc:o95947] Rooted Subtracted 61.2224 58.6404 2.582
1353 casein kinase i, delta isoform (ec 2.7.1.-) (cki-delta) (ckid). [swissprot;acc:p48730] 58.0327 60.6143 2.5816
cyclin c. [swissprot;acc:p24863] Measured Divided 6200.93 6690.57 1.07896
cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329] Subtracted 5655.85 6120.64 464.79
heparin sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.-) (n- hsst) (n-heparin sulfate sulfotransferase) (glucosaminyl n- deacetylase/n-sulfotransferase). [swissprot;acc:p52849] Ranked Divided 228.409 223.475 1.02208
nadh-ubiquinone oxidoreductase 23 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-23kd) (ci-23kd) (tyky subunit). [swissprot;acc:o00217] Squared Subtracted 20823.1 23668.4 2845.3
orphan nuclear receptor hmr (early response protein nak1) (tr3 orphan receptor). [swissprot;acc:p22736] Rooted Divided 65.1528 67.8168 1.04089
pdz/coiled-coil domain binding partner for the rho-family gtpase tc10; fused in glioblastoma; golgi associated pdz and coiled-coil motif containing protein; cftr-associated ligand. [refseq;acc:nm_020399] Squared 26925.7 30311.3 1.12574
repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] Ranked Subtracted 211.513 206.941 4.572
1354 actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571] Measured Divided 6036.22 6512.64 1.07893
chaperone-activity of bc1 complex-like, mitochondrial precursor (chaperone-abc1-like). [swissprot;acc:q8ni60] Rooted Subtracted 62.7228 65.296 2.5732
cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] Measured 5655.85 6120.64 464.79
elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60] Squared 20823.5 23668.7 2845.2
eyes absent homolog 2. [swissprot;acc:o00167] Ranked 218.417 213.848 4.569
n-deacetylase/n-sulfotransferase (heparan glucosaminyl) 3. [refseq;acc:nm_004784] Divided 228.409 223.475 1.02208
nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [swissprot;acc:p52594] Rooted 60.4911 58.1154 1.04088
rad54-like protein; rad54 homolog. [refseq;acc:nm_003579] Squared 25950.5 29212.5 1.1257
1355 aarf domain containing kinase 2; putative ubiquinone biosynthesis protein aarf. [refseq;acc:nm_052853] Rooted Subtracted 62.7228 65.296 2.5732
dj18d14.4 (cytochrome p450, subfamily iva, polypeptide 11). [sptrembl;acc:q9ntl5] Measured 5655.85 6120.64 464.79
glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [swissprot;acc:p23378] Squared Divided 25294.8 28473 1.12565
heat shock protein hsp 90-alpha (hsp 86). [swissprot;acc:p07900] Subtracted 26940.8 29785.9 2845.1
intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811] Rooted Divided 60.4911 58.1154 1.04088
lipoic acid synthetase, mitochondrial (lip-syn) (lipoate synthase) (hussy-01) (fragment). [swissprot;acc:o43766] Ranked Subtracted 204.961 209.517 4.556
n-deacetylase/n-sulfotransferase 4. [refseq;acc:nm_022569] Divided 228.409 223.475 1.02208
ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [swissprot;acc:p00480] Measured 5783.9 6240.19 1.07889
1356 aarf domain containing kinase 4. [refseq;acc:nm_024876] Rooted Subtracted 62.7228 65.296 2.5732
calcipressin 1 (down syndrome critical region protein 1) (myocyte- enriched calcineurin interacting protein 1) (mcip1) (adapt78). [swissprot;acc:p53805] Measured Divided 5657.71 6103.57 1.07881
cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [swissprot;acc:p17544] Ranked Subtracted 218.667 214.118 4.549
cytochrome p450 4b1 (ec 1.14.14.1) (cypivb1) (p450-hp). [swissprot;acc:p13584] Measured 5655.85 6120.64 464.79
heparan sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.8) (n-hsst) (hsnst) ([heparan sulfate]-glucosamine n-sulfotransferase) (n-heparan sulfate sulfotransferase) (glucosaminyl n-deacetylase/n- sulfotransferase). [swissprot;acc:p52848] Ranked Divided 228.409 223.475 1.02208
hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597] Squared 23066.6 25964.6 1.12564
pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152] Rooted 60.4911 58.1154 1.04088
uv excision repair protein rad23 homolog a (hhr23a). [swissprot;acc:p54725] Squared Subtracted 23913 26757.8 2844.8
1357 26s proteasome non-atpase regulatory subunit 4 (26s proteasome regulatory subunit s5a) (rpn10) (multiubiquitin chain binding protein) (antisecretory factor-1) (af) (asf). [swissprot;acc:p55036]
aarf domain containing kinase 1. [refseq;acc:nm_020421] Rooted 62.7228 65.296 2.5732
cyclic-amp-dependent transcription factor atf-2 (activating transcription factor 2) (camp response element binding protein cre- bp1) (hb16). [swissprot;acc:p15336] Ranked 218.657 214.11 4.547
dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2] Measured Divided 5657.71 6103.54 1.0788
flotillin-1. [swissprot;acc:o75955] Subtracted 5655.85 6120.64 464.79
importin 7; ran-binding protein 7. [refseq;acc:nm_006391] Squared Divided 24948.9 28072.6 1.1252
nuclear hormone receptor nor-1 (neuron-derived orphan receptor 1) (mitogen induced nuclear orphan receptor). [swissprot;acc:q92570] Rooted 65.1521 67.8158 1.04088

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/