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 Interaction Map Network Comparison Type Filtered network_comparison red green
Results: HTML CSV LaTeX Showing element 1 to 50 of 14920 in total
Interaction Map  : High confidence
Network Comparison Type  : Divided
Rank
Value Type
description
Filtered
network_comparison
red
green
1 Measured mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 0 36400000 364 0.00001
rad50-interacting protein 1. [refseq;acc:nm_021930] 1 5.31521 450.5 2394.5
Ranked adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] 0 3.70633 4294 15915
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 1 2.4 10 24
Squared cab2. [refseq;acc:nm_033419] 0 716592 0.00001 7.16592
rad50-interacting protein 1. [refseq;acc:nm_021930] 1 28.2513 48.0356 1357.07
Rooted mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 0 1907880 19.0788 0.00001
rad50-interacting protein 1. [refseq;acc:nm_021930] 1 2.30547 21.225 48.9336
2 Measured cab2. [refseq;acc:nm_033419] 0 17400000 0.00001 174
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 1 5.31521 450.5 2394.5
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] 1.86667 15 28
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 0 2.55362 5865 14977
Squared nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] 561325 5.61325 0.00001
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 1 28.2513 48.0356 1357.07
Rooted nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] 0 1240970 12.4097 0.00001
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 1 2.30547 21.225 48.9336
3 Measured homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 3.71868 2597.5 698.5
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 0 10900000 0.00001 109
Ranked cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 1 1.86667 15 28
nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] 0 2.47638 4475.84 11083.9
Squared homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 1 13.8285 1596.92 115.48
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] 0 561325 5.61325 0.00001
Rooted homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 1 1.92839 50.9657 26.4292
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] 0 1240970 12.4097 0.00001
4 Measured hbs1-like. [refseq;acc:nm_006620] 1 3.71868 2597.5 698.5
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 0 8900000 0.00001 89
Ranked cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 1 1.86667 15 28
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 0 2.45711 8906 21883
Squared hbs1-like. [refseq;acc:nm_006620] 1 13.8285 1596.92 115.48
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 0 281207 0.00001 2.81207
Rooted hbs1-like. [refseq;acc:nm_006620] 1 1.92839 50.9657 26.4292
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 0 1044030 0.00001 10.4403
5 Measured homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 8900000 89
junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 1 3.39764 1153.5 339.5
Ranked cytohesin 4. [swissprot;acc:q9uia0] 1.86667 15 28
ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] 0 2.17144 5510.5 11965.7
Squared homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 187479 0.00001 1.87479
junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 1 11.544 314.926 27.2805
Rooted homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 0 943398 0.00001 9.43398
junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 1 1.84327 33.9632 18.4255
6 Measured homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 0 8900000 0.00001 89
junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 1 3.39764 1153.5 339.5
Ranked cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 1.86667 15 28
ubiquitin protein ligase. [refseq;acc:nm_130466] 0 2.03897 7523 15339.2
Squared homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 187479 0.00001 1.87479
junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 1 11.544 314.926 27.2805
Rooted homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 0 943398 0.00001 9.43398
junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 1 1.84327 33.9632 18.4255
7 Measured sedlin. [swissprot;acc:o14582] 0 4300000 0.00001 43
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 3.39764 1153.5 339.5

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/