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 [...,...].
Gene Rank green Value Type Network Comparison Type network_comparison description Interaction Map red Filtered
Results: HTML CSV LaTeX Showing element 51 to 100 of 29840 in total
Interaction Map  : High confidence
Rank
green
Value Type
Network Comparison Type
network_comparison
description
red
Filtered
4 10.4403 Rooted Divided 1044030 pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 0.00001 0
26.4292 1.92839 hbs1-like. [refseq;acc:nm_006620] 50.9657 1
Subtracted 24.5365
28 Ranked Divided 1.86667 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 15
89 Measured 8900000 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 0.00001 0
115.48 Squared 13.8285 hbs1-like. [refseq;acc:nm_006620] 1596.92 1
232 Ranked Subtracted 105 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 337
698.5 Measured Divided 3.71868 hbs1-like. [refseq;acc:nm_006620] 2597.5
21730 Subtracted 3026 small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] 18704 0
21883 Ranked Divided 2.45711 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 8906
21888 Subtracted 10363 nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] 11525
33356.5 Measured 8126 cytohesin 4. [swissprot;acc:q9uia0] 41482.5 1
105900 Squared 30453.3 similar to zinc finger protein 277. [sptrembl;acc:q8wwa6] 75446.7 0
263351 143938 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 407289 1
5 0 Rooted 19.0788 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 19.0788 0
1.87479 Squared Divided 187479 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 0.00001
9.43398 Rooted 943398
18.4255 1.84327 junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 33.9632 1
27.2805 Squared 11.544 314.926
28 Ranked 1.86667 cytohesin 4. [swissprot;acc:q9uia0] 15
89 Measured 8900000 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 0.00001 0
168.796 Rooted Subtracted 23.245 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 145.551 1
309 Ranked 97 xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 212
339.5 Measured Divided 3.39764 junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 1153.5
11965.7 Ranked 2.17144 ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] 5510.5 0
21888 Subtracted 10363 transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] 11525
24446.3 Measured 2673.2 histone h4. [swissprot;acc:p02304] 21773.1
33356.5 8126 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 41482.5 1
105900 Squared 30453.3 zinc finger protein 277. [swissprot;acc:q9nrm2] 75446.7 0
263351 143938 cytohesin 4. [swissprot;acc:q9uia0] 407289 1
6 1.87479 Divided 187479 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 0.00001 0
9.43398 Rooted 943398
18.4255 1.84327 junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 33.9632 1
27.2805 Squared 11.544 314.926
27.8029 Rooted Subtracted 15.6374 potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] 12.1655 0
28 Ranked Divided 1.86667 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 15 1
89 Measured 8900000 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 0.00001 0
168.796 Rooted Subtracted 23.245 pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] 145.551 1
309 Ranked 97 protein x 0004. [refseq;acc:nm_016301] 212
339.5 Measured Divided 3.39764 junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 1153.5
14977 Ranked Subtracted 9112 mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 5865 0
15339.2 Divided 2.03897 ubiquitin protein ligase. [refseq;acc:nm_130466] 7523
15605.1 Measured Subtracted 2430.4 similar to zinc finger protein 277. [sptrembl;acc:q8wwa6] 13174.7
36927.5 7563 putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 44490.5 1
102814 Squared 29733.2 ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] 73080.8 0
263351 143938 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 407289 1
7 1.87479 Divided 187479 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 0.00001 0
9.43398 Rooted 943398
18.4255 1.84327 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] 33.9632 1
27.2805 Squared 11.544 314.926

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/