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 12364 to 12413 of 29840 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
1044 dna polymerase gamma subunit 1 (ec 2.7.7.7) (mitochondrial dna polymerase catalytic subunit) (polg-alpha). [swissprot;acc:p54098] Squared Divided 23778.9 27287.2 1.14754
heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107] Subtracted 30908.9 34282.7 3373.8
histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106] Measured 3946.32 4475.47 529.15
mbd2 (methyl-cpg-binding protein)-interacting zinc finger protein. [refseq;acc:nm_015517] Divided 4757.46 5198.91 1.09279
t-complex associated-testis-expressed 1-like (protein 91/23). [swissprot;acc:p51808] Ranked 173.475 178.889 1.03121
1045 arginine/serine-rich splicing factor 10 (transformer-2-beta) (htra2- beta) (transformer 2 protein homolog) (silica-induced protein 41) (ra301). [swissprot;acc:q15815] Squared 31783.9 36463.3 1.14723
cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] Ranked Subtracted 205.632 199.266 6.366
epidermal growth factor receptor pathway substrate 8-like protein 1 isoform c; epidermal growth factor receptor pathway substrate 8-related protein 1; eps8-related protein 1. [refseq;acc:nm_139204] Rooted 60.7786 64.0257 3.2471
fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] Ranked Divided 115.817 119.432 1.03121
heat shock cognate 71 kda protein. [swissprot;acc:p11142] Squared Subtracted 30908.9 34282.7 3373.8
histone h2b. [refseq;acc:nm_175055] Measured 3946.32 4475.47 529.15
immature colon carcinoma transcript 1 (digestion substraction 1) (ds- 1). [swissprot;acc:q14197] Divided 5364.32 5862.09 1.09279
mitochondrial gtp binding protein isoform v. [refseq;acc:nm_032620] Rooted 64.2202 67.5585 1.05198
1046 dna polymerase epsilon subunit b (ec 2.7.7.7) (dna polymerase ii subunit b). [swissprot;acc:p56282] 50.1042 52.7052 1.05191
double-strand break repair protein mre11a (mre11 homolog 1). [swissprot;acc:p49959] Ranked 173.475 178.889 1.03121
epidermal growth factor receptor kinase substrate eps8. [swissprot;acc:q12929] Rooted Subtracted 60.7802 64.0247 3.2445
histone h2b.s (h2b/s). [swissprot;acc:p57053] Measured 3946.32 4475.47 529.15
pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] Squared 21156.1 24524.1 3368
shwachman-bodian-diamond syndrome protein (cgi-97). [swissprot;acc:q9y3a5] Divided 17474.6 20047.3 1.14723
skeletal muscle tropomodulin (sk-tmod) (tropomodulin 4). [swissprot;acc:q9nzq9] Measured 4757.46 5198.91 1.09279
transforming protein rhoc (h9). [swissprot;acc:p08134] Ranked Subtracted 205.632 199.266 6.366
1047 40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865] Squared Divided 20357.7 23353.8 1.14717
histone h2b.d (h2b/d). [swissprot;acc:q99877] Measured Subtracted 3946.32 4475.47 529.15
interleukin-4 induced protein 1 precursor (fig-1 protein). [swissprot;acc:q96rq9] Rooted 61.7511 64.9897 3.2386
poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631] Divided 62.2065 65.4207 1.05167
serine/threonine-protein kinase dcamkl1 (ec 2.7.1.-) (doublecortin- like and cam kinase-like 1). [swissprot;acc:o15075] Squared Subtracted 31022.4 34382.7 3360.3
steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [swissprot;acc:p11474] Ranked Divided 187.022 181.391 1.03104
thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] Subtracted 205.632 199.266 6.366
ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9] Measured Divided 4757.46 5198.91 1.09279
1048 1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [swissprot;acc:q9nrz5] Ranked 187.96 182.308 1.031
3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] Subtracted 205.632 199.266 6.366
40s ribosomal protein s21. [swissprot;acc:p35265] Squared Divided 20357.7 23353.8 1.14717
histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695] Measured Subtracted 3946.32 4475.47 529.15
mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2] Rooted Divided 62.2065 65.4207 1.05167
sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] Subtracted 53.6328 56.8668 3.234
splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] Squared 20248.9 23608.3 3359.4
tropomodulin 1 (erythrocyte tropomodulin) (e-tmod). [swissprot;acc:p28289] Measured Divided 4757.46 5198.91 1.09279
1049 adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741] Ranked 211.449 217.998 1.03097
apoptosis antagonizing transcription factor. [refseq;acc:nm_012138] Rooted Subtracted 51.8245 55.0559 3.2314
cytoplasmic antiproteinase 3 (cap3) (cap-3) (protease inhibitor 9) (serpin b9). [swissprot;acc:p50453] Squared Divided 20357.7 23353.8 1.14717
krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887] Subtracted 20248.9 23608.3 3359.4
mct-1 protein. [refseq;acc:nm_014060] Rooted Divided 57.1984 54.3957 1.05152
sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1] Measured 4757.46 5198.91 1.09279
testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610] Subtracted 3946.32 4475.47 529.15
transforming protein rhoa (h12). [swissprot;acc:p06749] Ranked 205.632 199.266 6.366
1050 bystin. [swissprot;acc:q13895] 239.505 233.185 6.32
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] Divided 211.449 217.998 1.03097
histone h2b.e (h2b/e). [swissprot;acc:q99879] Measured Subtracted 3946.32 4475.47 529.15
kinesin protein. [refseq;acc:nm_032559] Rooted 59.2757 62.5044 3.2287
maspin precursor (protease inhibitor 5). [swissprot;acc:p36952] Squared Divided 20357.7 23353.8 1.14717

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/