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 1301 to 1350 of 7460 in total
Value Type  : Ranked
Interaction Map  : High confidence
Rank
description
Network Comparison Type
Filtered
red
green
network_comparison
326 40s ribosomal protein s16. [swissprot;acc:p17008] Subtracted 1 241.828 263.62 21.792
60s ribosomal protein l5. [swissprot;acc:p46777] Divided 241.899 265.924 1.09932
dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [refseq;acc:nm_030655] 0 11948.4 11295.6 1.05779
glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [swissprot;acc:q06210] Subtracted 12953.2 12273.2 680
327 3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] Divided 9897.29 10466.5 1.05751
60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] Subtracted 1 241.83 263.615 21.785
dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5] 0 10768.5 11444 675.5
dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] Divided 1 243.817 267.962 1.09903
328 adp-ribosylation factor 3. [swissprot;acc:p16587] Subtracted 0 11627.8 10958.2 669.6
atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] Divided 1 258.437 235.183 1.09888
putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] Subtracted 240.801 262.34 21.539
putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] Divided 0 10897 11520 1.05717
329 clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] Subtracted 10301.4 10957.5 656.1
lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] 1 191.644 170.192 21.452
neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] Divided 312 284 1.09859
signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556] 0 15977.3 15115.5 1.05701
330 chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] 1 312 284 1.09859
crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] Subtracted 224.657 203.235 21.422
dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [refseq;acc:nm_030655] 0 11948.4 11295.6 652.8
pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152] Divided 12320.2 13018.5 1.05668
331 40s ribosomal protein s3a. [swissprot;acc:p49241] 10405.1 10992.4 1.05644
adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741] Subtracted 11634.4 10989.9 644.5
doc-1 related protein (doc-1r). [swissprot;acc:o75956] Divided 1 312 284 1.09859
t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] Subtracted 224.647 203.242 21.405
332 enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] 224.633 203.251 21.382
estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [swissprot;acc:p14061] 0 11634.4 10989.9 644.5
myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] Divided 8125.5 7697.5 1.0556
neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] 1 312 284 1.09859
333 myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] 0 8125.5 7697.5 1.0556
neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] 1 312 284 1.09859
sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961] Subtracted 0 8095.69 8732.68 636.99
transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] 1 265.634 244.304 21.33
334 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] 0 10253.5 9622.45 631.05
myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Divided 8125.5 7697.5 1.0556
neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] 1 312 284 1.09859
ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] Subtracted 232.473 211.207 21.266
335 chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] Divided 312 284 1.09859
multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] Subtracted 223.273 202.423 20.85
myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Divided 0 8125.5 7697.5 1.0556
putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] Subtracted 10897 11520 623
336 camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612] 9270.49 8650.24 620.25
cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] Divided 1 312 284 1.09859
myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] 0 8125.5 7697.5 1.0556
rna polymerase i associated factor 53. [refseq;acc:nm_022490] Subtracted 1 241.045 261.874 20.829
337 60s ribosomal protein l12. [swissprot;acc:p30050] Divided 243.583 267.527 1.0983
glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [swissprot;acc:q06210] 0 12953.2 12273.2 1.05541
microtubule-interacting protein that associates with traf3; interleukin 13 receptor alpha 1-binding protein-1. [refseq;acc:nm_015650] Subtracted 9431 8815 616
source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] 1 200.691 179.88 20.811
338 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] Divided 243.583 267.528 1.0983
f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] Subtracted 0 13801.7 13185.9 615.8

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/