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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Filtered Rank description Value Type Interaction Map Gene Network Comparison Type red green network_comparison
Results: HTML CSV LaTeX Showing element 501 to 550 of 9634 in total
Filtered  : 0
Value Type  : Ranked
Network Comparison Type  : Divided
Rank
description
Interaction Map
red
green
network_comparison
251 keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060] High confidence 10551.6 11573.6 1.09686
zinc finger protein 93 (zinc finger protein htf34) (fragment). [swissprot;acc:p35789] Low confidence 4257.49 4854.46 1.14022
252 keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059] High confidence 10551.6 11573.5 1.09685
zinc finger protein zfp. [refseq;acc:nm_018651] Low confidence 4257.65 4854.63 1.14021
253 keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8] High confidence 10551.6 11573.5 1.09685
krab zinc finger protein. [sptrembl;acc:q96jc4] Low confidence 4257.65 4854.63 1.14021
254 keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854] High confidence 10551.6 11573.5 1.09685
zinc finger protein loc163140 (fragment). [sptrembl;acc:q86wm6] Low confidence 4257.81 4854.79 1.14021
255 star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095] High confidence 10551.6 11573.5 1.09685
zinc finger protein 431. [swissprot;acc:q8tf32] Low confidence 4258.04 4855.04 1.14021
256 espin. [refseq;acc:nm_031475] High confidence 10551.6 11573.4 1.09684
zinc finger protein 267 (zinc finger protein hzf2). [swissprot;acc:q14586] Low confidence 4258.04 4855.04 1.14021
257 keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191] High confidence 10552.2 11566.4 1.09611
zinc finger protein 180 (hhz168). [swissprot;acc:q9ujw8] Low confidence 4258.04 4855.04 1.14021
258 40s ribosomal protein s28. [swissprot;acc:p25112] High confidence 12967.1 14193.6 1.09459
zinc finger protein 28 homolog (zfp-28) (kruppel-like zinc finger factor x6). [swissprot;acc:q8nhy6] Low confidence 4257.81 4854.79 1.14021
259 adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123] High confidence 10438.3 9549.77 1.09304
zinc finger protein 79 (znfpt7) (fragment). [swissprot;acc:q15937] Low confidence 4258.04 4855.04 1.14021
260 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] High confidence 12447.6 11392.6 1.0926
zinc finger protein 463; c2h2-like zinc finger protein. [refseq;acc:nm_018555] Low confidence 4258.35 4855.37 1.1402
261 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] High confidence 12448.9 11393.9 1.09259
zinc finger protein 126 (hzf-2) (fragment). [swissprot;acc:p35275] Low confidence 4259.13 4856.2 1.14019
262 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] High confidence 3464 3778 1.09065
zinc finger protein 345 (zinc finger protein hzf10). [swissprot;acc:q14585] Low confidence 4259.67 4856.77 1.14018
263 dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] High confidence 13573.3 14801.2 1.09046
zinc finger protein 253 (bone marrow zinc finger 1) (bmzf-1). [swissprot;acc:o75346] Low confidence 4259.28 4856.36 1.14018
264 arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [swissprot;acc:o43681] High confidence 10037.1 10935.1 1.08947
zinc finger protein 135. [swissprot;acc:p52742] Low confidence 4260.59 4857.75 1.14016
265 glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488] High confidence 13653.8 14874 1.08937
zinc finger protein 271 (zinc finger protein hzf7) (zinc finger protein znfphex133). [swissprot;acc:q14591] Low confidence 4261.28 4858.48 1.14015
266 transcription factor btf3 homolog 3. [swissprot;acc:q13892] High confidence 13483.3 14685.4 1.08915
zinc finger protein 426; hypothetical protein mgc2663. [refseq;acc:nm_024106] Low confidence 4267.19 4864.77 1.14004
267 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] 9151.76 10432.9 1.13999
transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268] High confidence 8054.34 8772.02 1.0891
268 arf gtpase-activating protein. [refseq;acc:nm_133446] Low confidence 14890 16969 1.13962
maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168] High confidence 14257.4 13134.5 1.08549
269 ischemia/reperfusion inducible protein. [refseq;acc:nm_024640] 12463.5 11482.6 1.08542
up-regulated in liver cancer 1; similar to development- and differentiation-enhancing factor 2. [refseq;acc:nm_017707] Low confidence 14890 16969 1.13962
270 acidic leucine-rich nuclear phosphoprotein 32 family member c (tumorigenic protein pp32r1). [swissprot;acc:o43423] 17542 15399 1.13916
ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447] High confidence 10735.1 9891.37 1.0853
271 acidic leucine-rich nuclear phosphoprotein 32 family member d (tumorigenic protein pp32r2). [swissprot;acc:o95626] Low confidence 17542 15399 1.13916
myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829] High confidence 10735.1 9891.37 1.0853
272 maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168] Low confidence 13821.1 15716.7 1.13715
sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] High confidence 7163.55 7759.61 1.08321
273 pp3111 protein. [refseq;acc:nm_022156] Low confidence 14235.1 16177.4 1.13644
wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6] High confidence 12748.1 11770.9 1.08302
274 disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] 10432.4 11298.4 1.08301
piwi-like 2; miwi like. [refseq;acc:nm_018068] Low confidence 13206.7 15008.1 1.1364
275 cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] High confidence 10783 11674.1 1.08264
jumonji protein. [swissprot;acc:q92833] Low confidence 22296.2 19621 1.13634

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/