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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Rank Value Type Gene description Network Comparison Type Filtered Interaction Map red network_comparison green
Results: HTML CSV LaTeX Showing element 101 to 150 of 38536 in total
Network Comparison Type  : Divided
Rank
Value Type
description
Filtered
Interaction Map
red
network_comparison
green
7 Ranked cab2. [refseq;acc:nm_033419] 0 High confidence 21866 1.99689 10950
fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] Low confidence 11543 1.69451 6812
homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 1 High confidence 215 1.49767 322
oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] Low confidence 318 1.325 240
Squared homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 0 High confidence 0.00001 187479 1.87479
jumonji protein. [swissprot;acc:q92833] Low confidence 14096.2 0.140962
oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] 1 128.386 8.23493 1057.25
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] High confidence 314.926 11.544 27.2805
Rooted carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267] 0 Low confidence 6.08276 608276 0.00001
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] High confidence 0.00001 943398 9.43398
oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] 1 Low confidence 27.1385 1.69401 45.9728
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] High confidence 33.9632 1.84327 18.4255
8 Measured ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 0 Low confidence 85 75.4118 6410
db83 protein. [swissprot;acc:p57088] 1 High confidence 1153.5 3.39764 339.5
phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326] Low confidence 3278 1.54317 5058.5
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] 0 High confidence 0.00001 4300000 43
Ranked hbs1-like. [refseq;acc:nm_006620] 1 215 1.49767 322
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 0 Low confidence 22286 1.68629 13216
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] High confidence 11525 1.89918 21888
oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] 1 Low confidence 318 1.325 240
Squared ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 0 1.73869 11098 19295.9
db83 protein. [swissprot;acc:p57088] 1 High confidence 314.926 11.544 27.2805
ero1-like. [refseq;acc:nm_014584] 0 1.59148 159148 0.00001
phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326] 1 Low confidence 2543.26 2.38136 6056.43
Rooted db83 protein. [swissprot;acc:p57088] High confidence 33.9632 1.84327 18.4255
ero1-like. [refseq;acc:nm_014584] 0 9.05539 905539 0.00001
homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099] Low confidence 3.60555 360555
thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] 1 31.8641 1.49674 47.6922
9 Measured ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 0 High confidence 85 75.4118 6410
n33 protein. [swissprot;acc:q13454] 1 Low confidence 3278 1.54317 5058.5
tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] High confidence 398.5 3.21581 1281.5
ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607] 0 Low confidence 383.762 36.1876 10.6048
Ranked 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 1 58 1.31818 44
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 0 22286 1.68629 13216
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] High confidence 11525 1.89918 21888
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 1 212 1.45755 309
Squared homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099] 0 Low confidence 0.04 4000 0.00001
n33 protein. [swissprot;acc:q13454] 1 2543.26 2.38136 6056.43
similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517] 0 High confidence 0.852071 85207.1 0.00001
tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] 1 37.5863 10.3414 388.696
Rooted gbp protein isoform a. [refseq;acc:nm_017870] Low confidence 31.8923 1.49599 47.7107
jumonji protein. [swissprot;acc:q92833] 0 0.00001 300407 3.00407
similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517] High confidence 7.74597 774597 0.00001
tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] 1 19.9625 1.79326 35.798
10 Measured implantation-associated protein. [refseq;acc:nm_032121] Low confidence 3278 1.54317 5058.5
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] 0 High confidence 85 75.4118 6410
serpin b12. [swissprot;acc:q96p63] Low confidence 199.549 35.8425 5.56738
tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] 1 High confidence 398.5 3.21581 1281.5
Ranked fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] 0 7509.39 1.88805 14178.1
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Low confidence 22286 1.68629 13216

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/