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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Gene Rank Value Type description Network Comparison Type Filtered Interaction Map red green network_comparison
Results: HTML CSV LaTeX Showing element 1 to 50 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
Value Type
description
Filtered
red
green
network_comparison
1 Measured mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 0 364 0.00001 36400000
rad50-interacting protein 1. [refseq;acc:nm_021930] 1 450.5 2394.5 5.31521
Ranked adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] 0 4294 15915 3.70633
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 1 10 24 2.4
Squared cab2. [refseq;acc:nm_033419] 0 0.00001 7.16592 716592
rad50-interacting protein 1. [refseq;acc:nm_021930] 1 48.0356 1357.07 28.2513
Rooted mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 0 19.0788 0.00001 1907880
rad50-interacting protein 1. [refseq;acc:nm_021930] 1 21.225 48.9336 2.30547
2 Measured cab2. [refseq;acc:nm_033419] 0 0.00001 174 17400000
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 1 450.5 2394.5 5.31521
Ranked mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] 15 28 1.86667
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 0 5865 14977 2.55362
Squared nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] 5.61325 0.00001 561325
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 1 48.0356 1357.07 28.2513
Rooted nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] 0 12.4097 0.00001 1240970
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 1 21.225 48.9336 2.30547
3 Measured homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 2597.5 698.5 3.71868
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 0 0.00001 109 10900000
Ranked cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 1 15 28 1.86667
nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] 0 4475.84 11083.9 2.47638
Squared homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 1 1596.92 115.48 13.8285
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] 0 5.61325 0.00001 561325
Rooted homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 1 50.9657 26.4292 1.92839
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] 0 12.4097 0.00001 1240970
4 Measured hbs1-like. [refseq;acc:nm_006620] 1 2597.5 698.5 3.71868
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 0 0.00001 89 8900000
Ranked cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 1 15 28 1.86667
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 0 8906 21883 2.45711
Squared hbs1-like. [refseq;acc:nm_006620] 1 1596.92 115.48 13.8285
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 0 0.00001 2.81207 281207
Rooted hbs1-like. [refseq;acc:nm_006620] 1 50.9657 26.4292 1.92839
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 0 0.00001 10.4403 1044030
5 Measured homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 89 8900000
junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 1 1153.5 339.5 3.39764
Ranked cytohesin 4. [swissprot;acc:q9uia0] 15 28 1.86667
ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] 0 5510.5 11965.7 2.17144
Squared homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 0.00001 1.87479 187479
junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 1 314.926 27.2805 11.544
Rooted homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 0 0.00001 9.43398 943398
junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 1 33.9632 18.4255 1.84327
6 Measured homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 0 0.00001 89 8900000
junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 1 1153.5 339.5 3.39764
Ranked cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 15 28 1.86667
ubiquitin protein ligase. [refseq;acc:nm_130466] 0 7523 15339.2 2.03897
Squared homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 0.00001 1.87479 187479
junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 1 314.926 27.2805 11.544
Rooted homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 0 0.00001 9.43398 943398
junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 1 33.9632 18.4255 1.84327
7 Measured sedlin. [swissprot;acc:o14582] 0 0.00001 43 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 1153.5 339.5 3.39764

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/