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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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 [...,...].
Filtered Gene Rank Value Type description Network Comparison Type green network_comparison Interaction Map red
Results: HTML CSV LaTeX Showing element 1 to 50 of 14920 in total
Filtered  : 0
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
Value Type
description
green
network_comparison
red
1 Measured mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 0.00001 36400000 364
Ranked adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] 15915 3.70633 4294
Squared cab2. [refseq;acc:nm_033419] 7.16592 716592 0.00001
Rooted mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 0.00001 1907880 19.0788
2 Measured cab2. [refseq;acc:nm_033419] 174 17400000 0.00001
Ranked mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 14977 2.55362 5865
Squared nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] 0.00001 561325 5.61325
Rooted 1240970 12.4097
3 Measured pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 109 10900000 0.00001
Ranked nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] 11083.9 2.47638 4475.84
Squared transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] 0.00001 561325 5.61325
Rooted 1240970 12.4097
4 Measured homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 89 8900000 0.00001
Ranked mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 21883 2.45711 8906
Squared pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 2.81207 281207 0.00001
Rooted 10.4403 1044030
5 Measured homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 89 8900000
Ranked ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] 11965.7 2.17144 5510.5
Squared homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 1.87479 187479 0.00001
Rooted 9.43398 943398
6 Measured homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 89 8900000
Ranked ubiquitin protein ligase. [refseq;acc:nm_130466] 15339.2 2.03897 7523
Squared homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 1.87479 187479 0.00001
Rooted 9.43398 943398
7 Measured sedlin. [swissprot;acc:o14582] 43 4300000
Ranked cab2. [refseq;acc:nm_033419] 10950 1.99689 21866
Squared homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 1.87479 187479 0.00001
Rooted 9.43398 943398
8 Measured synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] 43 4300000
Ranked nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] 21888 1.89918 11525
Squared ero1-like. [refseq;acc:nm_014584] 0.00001 159148 1.59148
Rooted 905539 9.05539
9 Measured ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 6410 75.4118 85
Ranked transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] 21888 1.89918 11525
Squared similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517] 0.00001 85207.1 0.852071
Rooted 774597 7.74597
10 Measured lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] 6410 75.4118 85
Ranked fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] 14178.1 1.88805 7509.39
Squared guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4] 0.823905 82390.5 0.00001
Rooted 7.68115 768115
11 Measured serpin b12. [swissprot;acc:q96p63] 5.56738 35.8425 199.549
Ranked potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] 6248 1.86092 11627
Squared sedlin. [swissprot;acc:o14582] 0.437633 43763.3 0.00001
Rooted 6.55744 655744
12 Measured hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] 5.71669 34.8539 199.249
Ranked folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] 5208.84 1.81023 9429.18
Squared synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] 0.437633 43763.3 0.00001
Rooted 6.55744 655744
13 Measured adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] 47 29 1363
Ranked heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107] 9264.5 1.77804 5210.5

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/