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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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1675 to 1724 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
838 chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192] Subtracted 237.62 228.762 8.858
rw1 protein (fragment). [swissprot;acc:q92545] Divided 231.734 222.222 1.0428
839 dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325] Subtracted 230.764 239.62 8.856
stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975] Divided 177.776 170.499 1.04268
840 deformed epidermal autoregulatory factor 1 homolog (nuclear deaf-1 related transcriptional regulator) (nudr) (suppressin) (zinc finger mynd domain containing protein 5). [swissprot;acc:o75398] Subtracted 236.741 245.547 8.806
mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388] Divided 198.781 190.66 1.04259
841 peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855]
rio kinase 1 isoform 1; ad034 protein. [refseq;acc:nm_031480] Subtracted 236.741 245.547 8.806
842 jm1 protein. [refseq;acc:nm_014008] Divided 219.762 210.806 1.04248
map/microtubule affinity-regulating kinase 1. [refseq;acc:nm_018650] Subtracted 236.741 245.547 8.806
843 map/microtubule affinity-regulating kinase 2 isoform b; elkl motif kinase 1; elkl motif kinase. [refseq;acc:nm_004954]
trifunctional purine biosynthetic protein adenosine-3 [includes: phosphoribosylamine--glycine ligase (ec 6.3.4.13) (gars) (glycinamide ribonucleotide synthetase) (phosphoribosylglycinamide synthetase); phosphoribosylformylglycinamidine cyclo-ligase (ec 6.3.3.1) (airs) (phosphoribosyl-aminoimidazole synthetase) (air synthase); phosphoribosylglycinamide formyltransferase (ec 2.1.2.2) (gart) (gar transformylase) (5'-phosphoribosylglycinamide transformylase)]. [swissprot;acc:p22102] Divided 218.521 227.796 1.04244
844 c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] 178.033 170.82 1.04223
meiotic recombination protein spo11. [swissprot;acc:q9y5k1] Subtracted 236.741 245.547 8.806
845 hydroxyacid oxidase 2 (ec 1.1.3.15) (haox2) ((s)-2-hydroxy-acid oxidase, peroxisomal) (long chain alpha-hydroxy acid oxidase) (long- chain l-2-hydroxy acid oxidase). [swissprot;acc:q9nyq3] 232.512 241.288 8.776
u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] Divided 228.599 219.399 1.04193
846 methyltransferase like 2. [refseq;acc:nm_018396] 147.211 153.371 1.04184
parafibromin. [refseq;acc:nm_024529] Subtracted 239.704 230.991 8.713
847 cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] Divided 147.211 153.371 1.04184
l-myc-1 proto-oncogene protein. [swissprot;acc:p12524] Subtracted 227.604 219.001 8.603
848 fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] Divided 147.211 153.371 1.04184
wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516] Subtracted 206.214 197.614 8.6
849 proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824] Divided 147.211 153.371 1.04184
transcription factor iib. [refseq;acc:nm_013242] Subtracted 206.068 197.471 8.597
850 cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693] Divided 107.842 112.329 1.04161
splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872] Subtracted 206.068 197.471 8.597
851 n-myc proto-oncogene protein. [swissprot;acc:p04198] 227.601 219.008 8.593
trs85 homolog. [swissprot;acc:q9y2l5] Divided 107.842 112.329 1.04161
852 ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] Subtracted 227.596 219.017 8.579
hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] Divided 193.114 185.412 1.04154
853 ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [swissprot;acc:q06545] Subtracted 227.596 219.017 8.579
wd-repeat protein wdc146. [swissprot;acc:q9c0j8] Divided 108.289 112.772 1.0414
854 cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]
nadh-ubiquinone oxidoreductase 23 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-23kd) (ci-23kd) (tyky subunit). [swissprot;acc:o00217] Subtracted 227.596 219.017 8.579
855 elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60] 219.018 8.578
tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] Divided 178.514 171.42 1.04138
856 myc proto-oncogene protein (c-myc). [swissprot;acc:p01106] Subtracted 227.585 219.037 8.548
xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736] Divided 215.028 206.623 1.04068
857 midasin (midas-containing protein). [swissprot;acc:q9nu22] Subtracted 237.218 228.698 8.52
putatative 28 kda protein. [refseq;acc:nm_020143] Divided 227.241 236.467 1.0406
858 signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9] Subtracted 221.306 212.806 8.5
syntaxin 12. [refseq;acc:nm_177424] Divided 217.446 208.997 1.04043
859 60s ribosomal protein l39. [swissprot;acc:p02404] 234.025 224.958 1.04031
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Subtracted 50.7983 42.3003 8.498
860 60s ribosomal protein l18a. [swissprot;acc:q02543] Divided 234.025 224.958 1.04031
nucleolar rna-associated protein alpha isoform. [refseq;acc:nm_022917] Subtracted 242.024 233.544 8.48
861 40s ribosomal protein s19. [swissprot;acc:p39019] Divided 234.025 224.958 1.04031
syntaxin 12. [refseq;acc:nm_177424] Subtracted 217.446 208.997 8.449
862 60s ribosomal protein l31. [swissprot;acc:p12947] Divided 234.025 224.958 1.04031
pyruvate kinase, m1 isozyme (ec 2.7.1.40) (pyruvate kinase muscle isozyme) (cytosolic thyroid hormone-binding protein) (cthbp) (thbp1). [swissprot;acc:p14618] Subtracted 231.357 239.778 8.421

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/