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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Gene Filtered Rank Value Type description Network Comparison Type Interaction Map green red network_comparison
Results: HTML CSV LaTeX Showing element 101 to 150 of 77072 in total
Filtered  : 0
Rank
Value Type
description
Network Comparison Type
Interaction Map
green
red
network_comparison
7 Ranked cab2. [refseq;acc:nm_033419] Divided High confidence 10950 21866 1.99689
fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] Low confidence 6812 11543 1.69451
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Subtracted 13216 22286 9070
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] High confidence
Squared ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] Low confidence 70431.3 51384.7 19046.6
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Divided High confidence 1.87479 0.00001 187479
jumonji protein. [swissprot;acc:q92833] Low confidence 0.140962 14096.2
small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] Subtracted High confidence 111762 82802.3 28959.7
Rooted carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267] Divided Low confidence 0.00001 6.08276 608276
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] High confidence 9.43398 0.00001 943398
neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721] Subtracted Low confidence 0 16.9115 16.9115
ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] High confidence 49.8523 65.4535 15.6012
8 Measured ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] Divided Low confidence 6410 85 75.4118
nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] Subtracted High confidence 7500.75 5106.93 2393.82
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] Divided 43 0.00001 4300000
zinc finger protein 277. [swissprot;acc:q9nrm2] Subtracted Low confidence 8770.72 7537.89 1232.83
Ranked homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Divided 13216 22286 1.68629
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Subtracted High confidence 9070
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] Divided 21888 11525 1.89918
ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607] Subtracted Low confidence 19873 10889.4 8983.6
Squared ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] Divided 19295.9 1.73869 11098
ero1-like. [refseq;acc:nm_014584] High confidence 0.00001 1.59148 159148
similar to zinc finger protein 277. [sptrembl;acc:q8wwa6] Subtracted Low confidence 61843.5 45424 16419.5
transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268] High confidence 386144 414704 28560
Rooted ero1-like. [refseq;acc:nm_014584] Divided 0.00001 9.05539 905539
homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099] Low confidence 3.60555 360555
nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] Subtracted High confidence 56.7758 72.1137 15.3379
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Low confidence 111.067 126.359 15.292
9 Measured ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] High confidence 14756 12478 2278
Low confidence 11468.3 10255.7 1212.6
ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] Divided High confidence 6410 85 75.4118
ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607] Low confidence 10.6048 383.762 36.1876
Ranked 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] Subtracted 14964 22422 7458
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] High confidence 13216 22286 9070
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Divided Low confidence 1.68629
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] High confidence 21888 11525 1.89918
Squared anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5] Subtracted 170319 195397 25078
homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099] Divided Low confidence 0.00001 0.04 4000
similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517] High confidence 0.852071 85207.1
zinc finger protein 277. [swissprot;acc:q9nrm2] Subtracted Low confidence 61381.6 45108.2 16273.4
Rooted jumonji protein. [swissprot;acc:q92833] Divided 3.00407 0.00001 300407
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Subtracted High confidence 111.067 126.359 15.292
similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517] Divided 0.00001 7.74597 774597
ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607] Subtracted Low confidence 2.21126 17.0721 14.8608
10 Measured dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] 2804 1593 1211
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] Divided High confidence 6410 85 75.4118
myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] Subtracted 6193.07 7830.62 1637.55
serpin b12. [swissprot;acc:q96p63] Divided Low confidence 5.56738 199.549 35.8425
Ranked fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] High confidence 14178.1 7509.39 1.88805
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Low confidence 13216 22286 1.68629

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/