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 green Filtered Value Type Interaction Map Network Comparison Type red network_comparison
Results: HTML CSV LaTeX Showing element 101 to 150 of 38536 in total
Network Comparison Type  : Divided
Rank
description
green
Filtered
Value Type
Interaction Map
red
network_comparison
7 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 1.87479 0 Squared High confidence 0.00001 187479
9.43398 Rooted 943398
jumonji protein. [swissprot;acc:q92833] 0.140962 Squared Low confidence 14096.2
oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] 240 1 Ranked 318 1.325
oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] 45.9728 Rooted 27.1385 1.69401
1057.25 Squared 128.386 8.23493
2113.5 Measured 736.5 2.86965
sedlin. [swissprot;acc:o14582] 43 0 High confidence 0.00001 4300000
sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906] 18.4255 1 Rooted 33.9632 1.84327
27.2805 Squared 314.926 11.544
339.5 Measured 1153.5 3.39764
tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063] 0.00001 0 Low confidence 2.31962 231962
8 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 6410 85 75.4118
19295.9 Squared 1.73869 11098
db83 protein. [swissprot;acc:p57088] 18.4255 1 Rooted High confidence 33.9632 1.84327
27.2805 Squared 314.926 11.544
339.5 Measured 1153.5 3.39764
ero1-like. [refseq;acc:nm_014584] 0.00001 0 Squared 1.59148 159148
Rooted 9.05539 905539
hbs1-like. [refseq;acc:nm_006620] 322 1 Ranked 215 1.49767
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 13216 0 Low confidence 22286 1.68629
homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099] 0.00001 Rooted 3.60555 360555
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] 21888 Ranked High confidence 11525 1.89918
oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] 240 1 Low confidence 318 1.325
phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326] 5058.5 Measured 3278 1.54317
6056.43 Squared 2543.26 2.38136
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] 43 0 Measured High confidence 0.00001 4300000
thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] 47.6922 1 Rooted Low confidence 31.8641 1.49674
9 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 44 Ranked 58 1.31818
ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 6410 0 Measured High confidence 85 75.4118
gbp protein isoform a. [refseq;acc:nm_017870] 47.7107 1 Rooted Low confidence 31.8923 1.49599
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 13216 0 Ranked 22286 1.68629
homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099] 0.00001 Squared 0.04 4000
jumonji protein. [swissprot;acc:q92833] 3.00407 Rooted 0.00001 300407
n33 protein. [swissprot;acc:q13454] 5058.5 1 Measured 3278 1.54317
6056.43 Squared 2543.26 2.38136
similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517] 0.00001 0 High confidence 0.852071 85207.1
Rooted 7.74597 774597
tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] 35.798 1 19.9625 1.79326
388.696 Squared 37.5863 10.3414
1281.5 Measured 398.5 3.21581
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] 21888 0 Ranked 11525 1.89918
ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607] 10.6048 Measured Low confidence 383.762 36.1876
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 309 1 Ranked High confidence 212 1.45755
10 fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] 14178.1 0 7509.39 1.88805
guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4] 0.823905 Squared 0.00001 82390.5
7.68115 Rooted 768115
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 13216 Ranked Low confidence 22286 1.68629
implantation-associated protein. [refseq;acc:nm_032121] 5058.5 1 Measured 3278 1.54317
6056.43 Squared 2543.26 2.38136

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/