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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Filtered Rank Gene green Value Type description Network Comparison Type network_comparison Interaction Map red
Results: HTML CSV LaTeX Showing element 1 to 50 of 77072 in total
Filtered  : 0
Rank
green
Value Type
description
Network Comparison Type
network_comparison
Interaction Map
red
1 0.00001 Measured mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Divided 36400000 High confidence 364
Low confidence
Rooted 1907880 High confidence 19.0788
Low confidence
1.87479 Squared homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 187479 0.00001
7.16592 cab2. [refseq;acc:nm_033419] 716592 High confidence
60.0707 Rooted ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] Subtracted 50.8706 9.20014
Low confidence
6410 Measured 6325 High confidence 85
Low confidence
14977 Ranked mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Divided 2.55362 5865
15915 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] 3.70633 High confidence 4294
21883 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Subtracted 12977 8906
Low confidence
160184 Squared nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 72283 High confidence 232467
Low confidence
2 0.00001 nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] Divided 561325 High confidence 5.61325
Rooted 1240970 12.4097
1.87479 Squared homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 187479 Low confidence 0.00001
7.61577 Rooted mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Subtracted 21.6929 29.3087
9.43398 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Divided 943398 0.00001
60.0707 lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] Subtracted 50.8706 High confidence 9.20014
89 Measured homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Divided 8900000 Low confidence 0.00001
174 cab2. [refseq;acc:nm_033419] 17400000 High confidence
6410 lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] Subtracted 6325 85
14977 Ranked mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Divided 2.55362 5865
15915 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] Subtracted 11621 4294
19621.3 Measured nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 4196.8 Low confidence 23818.1
20617 Ranked neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531] 11010 9607
21883 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Divided 2.45711 8906
345123 Squared histone h4. [swissprot;acc:p02304] Subtracted 71500 High confidence 273623
386144 transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268] 28560 Low confidence 414704
3 0.00001 transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] Divided 561325 High confidence 5.61325
Rooted 1240970 12.4097
1.87479 Squared homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 187479 Low confidence 0.00001
6.85565 Rooted adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] Subtracted 30.0631 High confidence 36.9188
9.43398 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Divided 943398 Low confidence 0.00001
66 anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801] Subtracted 20.3711 45.6289
89 Measured homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Divided 8900000 0.00001
109 pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 10900000 High confidence
7500.75 nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] Subtracted 2393.82 Low confidence 5106.93
10950 Ranked cab2. [refseq;acc:nm_033419] 10916 High confidence 21866
11083.9 nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] Divided 2.47638 4475.84
19621.3 Measured nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Subtracted 4196.8 23818.1
20617 Ranked neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531] Divided 2.14604 Low confidence 9607
neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721] Subtracted 11010
170628 Squared apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] 35348 High confidence 135280
197937 rho gdp-dissociation inhibitor 1 (rho gdi 1) (rho-gdi alpha). [swissprot;acc:p52565] 23051 Low confidence 220988
4 0 Rooted mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 19.0788 19.0788
0.823905 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] Divided 82390.5 0.00001

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/