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 4158 to 4207 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1040 rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] Measured 5421.93 5926.08 1.09298
sterol regulatory element binding protein-1 (srebp-1) (sterol regulatory element-binding transcription factor 1). [swissprot;acc:p36956] Rooted 60.6801 63.8644 1.05248
t-complex protein 1, epsilon subunit (tcp-1-epsilon) (cct-epsilon). [swissprot;acc:p48643] Ranked 163.24 168.359 1.03136
1041 ferritin light chain (ferritin l subunit). [swissprot;acc:p02792] Squared 31994 36719.6 1.1477
heterogeneous nuclear ribonucleoprotein l (hnrnp l). [swissprot;acc:p14866] Ranked 186.774 181.099 1.03134
interleukin-4 induced protein 1 precursor (fig-1 protein). [swissprot;acc:q96rq9] Rooted 61.7511 64.9897 1.05245
myb-related protein a (a-myb). [swissprot;acc:p10243] Measured 5419.18 5922.84 1.09294
1042 cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238] Rooted 60.9639 64.1576 1.05239
disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0] Squared 31994 36719.6 1.1477
estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] Ranked 186.799 181.127 1.03132
similar to lim domain only 7 (fragment). [sptrembl;acc:q8n6m2] Measured 5887.52 6434.32 1.09287
1043 1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7] Ranked 187.834 182.137 1.03128
15 kda selenoprotein precursor. [swissprot;acc:o60613] Measured 6344.41 6933.36 1.09283
ferritin heavy chain (ferritin h subunit). [swissprot;acc:p02794] Squared 31989.3 36713.2 1.14767
signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240] Rooted 59.0741 62.1501 1.05207
1044 apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772] 65.4147 68.8149 1.05198
dna polymerase gamma subunit 1 (ec 2.7.7.7) (mitochondrial dna polymerase catalytic subunit) (polg-alpha). [swissprot;acc:p54098] Squared 23778.9 27287.2 1.14754
mbd2 (methyl-cpg-binding protein)-interacting zinc finger protein. [refseq;acc:nm_015517] Measured 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
fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] Ranked 115.817 119.432 1.03121
immature colon carcinoma transcript 1 (digestion substraction 1) (ds- 1). [swissprot;acc:q14197] Measured 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
shwachman-bodian-diamond syndrome protein (cgi-97). [swissprot;acc:q9y3a5] Squared 17474.6 20047.3 1.14723
skeletal muscle tropomodulin (sk-tmod) (tropomodulin 4). [swissprot;acc:q9nzq9] Measured 4757.46 5198.91 1.09279
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 20357.7 23353.8 1.14717
poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631] Rooted 62.2065 65.4207 1.05167
steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [swissprot;acc:p11474] Ranked 187.022 181.391 1.03104
ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9] Measured 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
40s ribosomal protein s21. [swissprot;acc:p35265] Squared 20357.7 23353.8 1.14717
mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2] Rooted 62.2065 65.4207 1.05167
tropomodulin 1 (erythrocyte tropomodulin) (e-tmod). [swissprot;acc:p28289] Measured 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
cytoplasmic antiproteinase 3 (cap3) (cap-3) (protease inhibitor 9) (serpin b9). [swissprot;acc:p50453] Squared 20357.7 23353.8 1.14717
mct-1 protein. [refseq;acc:nm_014060] Rooted 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
1050 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] Ranked 211.449 217.998 1.03097
maspin precursor (protease inhibitor 5). [swissprot;acc:p36952] Squared 20357.7 23353.8 1.14717
mitochondrial ribosomal protein l22. [refseq;acc:nm_014180] Rooted 57.1984 54.3957 1.05152
neuronal tropomodulin (n-tmod) (tropomodulin 2). [swissprot;acc:q9nzr1] Measured 4757.46 5198.91 1.09279
1051 17 beta-hydroxysteroid dehydrogenase. [sptrembl;acc:q13034] Ranked 211.449 217.998 1.03097
60s ribosomal protein l21. [swissprot;acc:p46778] Rooted 60.1366 63.2237 1.05133
bomapin (protease inhibitor 10) (serpin b10). [swissprot;acc:p48595] Squared 20357.7 23353.8 1.14717
homeobox protein dlx-2. [swissprot;acc:q07687] Measured 4757.46 5198.91 1.09279
1052 homeobox protein dlx-5. [swissprot;acc:p56178]
plasminogen activator inhibitor-2 precursor (pai-2) (placental plasminogen activator inhibitor) (monocyte arg-serpin) (urokinase inhibitor). [swissprot;acc:p05120] Squared 20357.7 23353.8 1.14717
retinol dehydrogenase 8 (all-trans); photoreceptor outer segment all-trans retinol dehydrogenase. [refseq;acc:nm_015725] Ranked 211.449 217.998 1.03097

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/