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 38536 in total
Filtered  : 0
Network Comparison Type  : Divided
Rank
green
Value Type
description
network_comparison
Interaction Map
red
1 0.00001 Measured mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 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
14977 Ranked mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 2.55362 Low confidence 5865
15915 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] 3.70633 High confidence 4294
2 0.00001 Squared nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] 561325 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
9.43398 Rooted homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 943398
89 Measured 8900000
174 cab2. [refseq;acc:nm_033419] 17400000 High confidence
14977 Ranked mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 2.55362 5865
21883 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 2.45711 Low confidence 8906
3 0.00001 Squared transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] 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
9.43398 Rooted homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 943398
89 Measured 8900000
109 pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 10900000 High confidence
11083.9 Ranked nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] 2.47638 4475.84
20617 neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531] 2.14604 Low confidence 9607
4 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] 82390.5 0.00001
2.81207 pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 281207 High confidence
9.43398 Rooted homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 943398 Low confidence
10.4403 pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 1044030 High confidence
89 Measured homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 8900000 Low confidence
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] High confidence
20617 Ranked neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721] 2.14604 Low confidence 9607
21883 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 2.45711 High confidence 8906
5 0.00001 Squared carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615] 32402.4 Low confidence 0.324024
1.87479 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 187479 High confidence 0.00001
7.68115 Rooted 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] 768115 Low confidence
9.43398 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 943398 High confidence
17.5166 Measured jumonji protein. [swissprot;acc:q92833] 1751660 Low confidence
89 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 8900000 High confidence
11965.7 Ranked ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] 2.17144 5510.5
19873 ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607] 1.82499 Low confidence 10889.4
6 0.00001 Measured homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099] 1300000 13
Squared carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267] 32402.4 0.324024
Rooted carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615] 608276 6.08276
1.87479 Squared homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 187479 High confidence 0.00001
9.43398 Rooted 943398
89 Measured homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 8900000
9583.37 Ranked trinucleotide repeat containing 15. [refseq;acc:nm_015575] 1.71877 Low confidence 5575.71
15339.2 ubiquitin protein ligase. [refseq;acc:nm_130466] 2.03897 High confidence 7523
7 0.00001 Measured tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063] 231962 Low confidence 2.31962
Rooted carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267] 608276 6.08276

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/