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.


Navigation/Query Panel:
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 description Gene Value Type Filtered Network Comparison Type green Interaction Map red network_comparison
Results: HTML CSV LaTeX Showing element 1 to 50 of 9634 in total
Value Type  : Measured
Network Comparison Type  : Divided
Rank
description
Filtered
green
Interaction Map
red
network_comparison
1 lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] 1 543.5 Low confidence 2399.5 4.4149
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 0 0.00001 High confidence 364 36400000
Low confidence
rad50-interacting protein 1. [refseq;acc:nm_021930] 1 2394.5 High confidence 450.5 5.31521
2 cab2. [refseq;acc:nm_033419] 0 174 0.00001 17400000
cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] 1 543.5 Low confidence 2399.5 4.4149
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 0 89 0.00001 8900000
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 1 2394.5 High confidence 450.5 5.31521
3 cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] 543.5 Low confidence 2399.5 4.4149
homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 698.5 High confidence 2597.5 3.71868
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 0 89 Low confidence 0.00001 8900000
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 109 High confidence 10900000
4 hbs1-like. [refseq;acc:nm_006620] 1 698.5 2597.5 3.71868
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 0 89 Low confidence 0.00001 8900000
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] High confidence
lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] 1 543.5 Low confidence 2399.5 4.4149
5 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 0 89 High confidence 0.00001 8900000
jumonji protein. [swissprot;acc:q92833] 17.5166 Low confidence 1751660
junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 1 339.5 High confidence 1153.5 3.39764
oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] 2113.5 Low confidence 736.5 2.86965
6 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 0 89 High confidence 0.00001 8900000
homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099] 0.00001 Low confidence 13 1300000
junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 1 339.5 High confidence 1153.5 3.39764
oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] 2113.5 Low confidence 736.5 2.86965
7 oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2]
sedlin. [swissprot;acc:o14582] 0 43 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] 1 339.5 1153.5 3.39764
tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063] 0 0.00001 Low confidence 2.31962 231962
8 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 6410 85 75.4118
db83 protein. [swissprot;acc:p57088] 1 339.5 High confidence 1153.5 3.39764
phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326] 5058.5 Low confidence 3278 1.54317
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] 0 43 High confidence 0.00001 4300000
9 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 6410 85 75.4118
n33 protein. [swissprot;acc:q13454] 1 5058.5 Low confidence 3278 1.54317
tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] 1281.5 High confidence 398.5 3.21581
ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607] 0 10.6048 Low confidence 383.762 36.1876
10 implantation-associated protein. [refseq;acc:nm_032121] 1 5058.5 3278 1.54317
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] 0 6410 High confidence 85 75.4118
serpin b12. [swissprot;acc:q96p63] 5.56738 Low confidence 199.549 35.8425
tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] 1 1281.5 High confidence 398.5 3.21581
11 dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]
hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] 0 5.71669 Low confidence 199.249 34.8539
serpin b12. [swissprot;acc:q96p63] 5.56738 High confidence 199.549 35.8425
thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] 1 2950.5 Low confidence 1917.64 1.53861
12 cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] 1281.5 High confidence 398.5 3.21581
gbp protein isoform a. [refseq;acc:nm_017870] 2954.24 Low confidence 1921.96 1.5371
hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] 0 5.71669 High confidence 199.249 34.8539
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 58 Low confidence 859 14.8103
13 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] 47 High confidence 1363 29
cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] 1 1281.5 398.5 3.21581

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/