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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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 1963 to 2012 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
123 ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858] Measured Divided 0 2285.62 1681.3 1.35944
secreted modular calcium-binding protein 1. [refseq;acc:nm_022137] Squared 31.8185 16.8625 1.88694
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Ranked Subtracted 1 227.032 193.056 33.976
transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724] Squared 0 20492.7 19487.2 1005.5
voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] Rooted 28.1043 32.1981 4.0938
zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58] Ranked Divided 11522.8 13684.9 1.18764
124 aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087] Squared Subtracted 1 71389.9 96037.6 24647.7
brain protein 16. [refseq;acc:nm_016458] Measured 0 2155.75 2418.14 262.39
ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] Rooted 1 46.7419 60.9337 14.1918
cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] Ranked 0 12328.5 10501 1827.5
f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] Rooted Divided 10.6611 13.034 1.22258
fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Measured Subtracted 1 4944.3 7038.04 2093.74
glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [swissprot;acc:q06210] Squared 0 4766.78 3763.9 1002.88
high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] Ranked Divided 1 208.52 171.595 1.21519
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Measured 24255.7 18168.9 1.33501
nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Rooted 54.6625 67.9477 1.24304
presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Ranked Subtracted 285.684 252.234 33.45
regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754] Measured Divided 0 3248.95 2399.76 1.35386
sh2-b homolog; likely ortholog of mouse sh2 domain-containing putative adapter sh2-b; sh2-b gamma signaling protein; sh2-b alpha signaling protein. [refseq;acc:nm_015503] Squared 2.70982 1.44 1.88182
swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5] Rooted Subtracted 56.49 52.4119 4.0781
type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] Squared Divided 1 192779 126095 1.52884
zinc finger imprinted 2. [swissprot;acc:q9nzv7] Ranked 0 11520.7 13680.4 1.18746
125 aquaporin 5. [swissprot;acc:p55064] Squared Subtracted 1 71388.5 96035.2 24646.7
cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] Ranked 0 12314.9 10489.3 1825.6
dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7] Rooted 13.7413 17.8164 4.0751
glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448] Measured 3691.15 3952.59 261.44
high-mobility group 20a. [refseq;acc:nm_018200] Ranked Divided 1 208.588 171.778 1.21429
hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Measured Subtracted 12471.7 14561.7 2090
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Divided 24255.7 18168.9 1.33501
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Squared Subtracted 0 1495.1 509.542 985.558
pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790] Divided 10.3503 19.2071 1.8557
phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750] Ranked 22038 18578 1.18624
pp3111 protein. [refseq;acc:nm_022156] Rooted 28.0891 23.0217 1.22011
probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] Measured 1095.42 812.166 1.34876
ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] Squared 1 189976 124480 1.52616
s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] Ranked Subtracted 285.684 252.234 33.45
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Rooted Divided 54.8203 67.934 1.23921
son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583] Subtracted 35.6294 49.8119 14.1825
126 aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181] Squared 71387.4 96033.4 24646
associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Ranked Divided 94 114 1.21277
calcyphosine. [swissprot;acc:q13938] Measured 0 472.524 635.875 1.3457
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 1 24250 18164.9 1.33499
cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329] Ranked Subtracted 0 12314.9 10489.3 1825.6
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] Squared Divided 118.204 219.216 1.85456
dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658] Subtracted 3339.18 2360.97 978.21
dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] Rooted Divided 21.3244 25.9172 1.21538
f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] Ranked Subtracted 1 285.684 252.234 33.45
high-mobility group 20a. [refseq;acc:nm_018200] Rooted 60.9353 75.094 14.1587
high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] Divided 60.9342 75.1387 1.23311
importin 7; ran-binding protein 7. [refseq;acc:nm_006391] Subtracted 0 11.0328 6.96286 4.06994

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/