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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Network Comparison Type Rank Gene Value Type Interaction Map description red network_comparison Filtered green
Results: HTML CSV LaTeX Showing element 1 to 50 of 29840 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
Value Type
description
red
network_comparison
Filtered
green
1 Measured mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 364 36400000 0 0.00001
rad50-interacting protein 1. [refseq;acc:nm_021930] 450.5 5.31521 1 2394.5
Ranked adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] 4294 3.70633 0 15915
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 10 2.4 1 24
Squared cab2. [refseq;acc:nm_033419] 0.00001 716592 0 7.16592
rad50-interacting protein 1. [refseq;acc:nm_021930] 48.0356 28.2513 1 1357.07
Rooted mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 19.0788 1907880 0 0.00001
rad50-interacting protein 1. [refseq;acc:nm_021930] 21.225 2.30547 1 48.9336
2 Measured cab2. [refseq;acc:nm_033419] 0.00001 17400000 0 174
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 450.5 5.31521 1 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] 15 1.86667 28
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 5865 2.55362 0 14977
Squared nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] 5.61325 561325 0.00001
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 48.0356 28.2513 1 1357.07
Rooted nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] 12.4097 1240970 0 0.00001
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 21.225 2.30547 1 48.9336
3 Measured homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 2597.5 3.71868 698.5
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 0.00001 10900000 0 109
Ranked cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 15 1.86667 1 28
nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] 4475.84 2.47638 0 11083.9
Squared homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 1596.92 13.8285 1 115.48
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] 5.61325 561325 0 0.00001
Rooted homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 50.9657 1.92839 1 26.4292
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] 12.4097 1240970 0 0.00001
4 Measured hbs1-like. [refseq;acc:nm_006620] 2597.5 3.71868 1 698.5
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 0.00001 8900000 0 89
Ranked cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 15 1.86667 1 28
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 8906 2.45711 0 21883
Squared hbs1-like. [refseq;acc:nm_006620] 1596.92 13.8285 1 115.48
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 0.00001 281207 0 2.81207
Rooted hbs1-like. [refseq;acc:nm_006620] 50.9657 1.92839 1 26.4292
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 0.00001 1044030 0 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] 1153.5 3.39764 1 339.5
Ranked cytohesin 4. [swissprot;acc:q9uia0] 15 1.86667 28
ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] 5510.5 2.17144 0 11965.7
Squared homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 0.00001 187479 1.87479
junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 314.926 11.544 1 27.2805
Rooted homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 0.00001 943398 0 9.43398
junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 33.9632 1.84327 1 18.4255
6 Measured homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 0.00001 8900000 0 89
junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 1153.5 3.39764 1 339.5
Ranked cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 15 1.86667 28
ubiquitin protein ligase. [refseq;acc:nm_130466] 7523 2.03897 0 15339.2
Squared homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 0.00001 187479 1.87479
junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 314.926 11.544 1 27.2805
Rooted homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 0.00001 943398 0 9.43398
junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 33.9632 1.84327 1 18.4255
7 Measured sedlin. [swissprot;acc:o14582] 0.00001 4300000 0 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] 1153.5 3.39764 1 339.5

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/