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 red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 3680 to 3729 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1840 cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] Divided 3591.95 3375.34 1.06417
1841 fad synthetase. [refseq;acc:nm_025207]
ring finger protein 20. [refseq;acc:nm_019592] Subtracted 5419.54 5793.94 374.4
1842 bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] Divided 3591.95 3375.34 1.06417
ring finger protein 40; 95 kda retinoblastoma protein binding protein; likely ortholog of rat staring. [refseq;acc:nm_014771] Subtracted 5419.54 5793.94 374.4
1843 ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] Divided 3591.95 3375.34 1.06417
spectrin beta chain, brain 2 (spectrin, non-erythroid beta chain 2) (beta-iii spectrin). [swissprot;acc:o15020] Subtracted 5232.14 5605.8 373.66
1844 bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o43252] Divided 3591.95 3375.34 1.06417
spectrin beta chain, brain 1 (spectrin, non-erythroid beta chain 1) (beta-ii spectrin) (fodrin beta chain). [swissprot;acc:q01082] Subtracted 5232.14 5605.8 373.66
1845 nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] Divided 3591.95 3375.34 1.06417
phosphoacetylglucosamine mutase (ec 5.4.2.3) (pagm) (acetylglucosamine phosphomutase) (n-acetylglucosamine-phosphate mutase) (phosphoglucomutase 3). [swissprot;acc:o95394] Subtracted 5232.14 5605.8 373.66
1846 5'-methylthioadenosine phosphorylase (ec 2.4.2.28) (mta phosphorylase) (mtapase). [swissprot;acc:q13126] 5232.99 5606.53 373.54
cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] Divided 3591.95 3375.34 1.06417
1847 glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [swissprot;acc:p15104] 6215.55 6613.46 1.06402
putative ribosomal rna methyltransferase 1 (ec 2.1.1.-) (rrna (uridine-2'-o-)-methyltransferase) (jm23 protein). [swissprot;acc:q9uet6] Subtracted 5232.99 5606.53 373.54
1848 geranylgeranyl pyrophosphate synthetase (ggpp synthetase) (ggppsase) (geranylgeranyl diphosphate synthase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10); farnesyltranstransferase (ec 2.5.1.29)]. [swissprot;acc:o95749] 4322.65 4696.04 373.39
heat shock protein hsp 90-alpha (hsp 86). [swissprot;acc:p07900] Divided 5746.06 6113.79 1.064
1849 arginase ii, mitochondrial precursor (ec 3.5.3.1) (non-hepatic arginase) (kidney-type arginase). [swissprot;acc:p78540] 6267.93 6668.72 1.06394
mannose-6-phosphate isomerase (ec 5.3.1.8) (phosphomannose isomerase) (pmi) (phosphohexomutase). [swissprot;acc:p34949] Subtracted 5458.12 5830.76 372.64
1850 protein kinase c binding protein 1 (rack7) (cutaneous t-cell lymphoma associated antigen se14-3) (ctcl tumor antigen se14-3) (zinc finger mynd domain containing protein 8). [swissprot;acc:q9ulu4] Divided 6158.6 6551.94 1.06387
putative ankyrin-repeat containing protein. [refseq;acc:nm_025185] Subtracted 5458.12 5830.76 372.64
1851 adenovirus 5 e1a-binding protein (bs69 protein). [swissprot;acc:q15326] Divided 6156.28 6549.03 1.0638
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Subtracted 5458.12 5830.76 372.64
1852 arginase 1 (ec 3.5.3.1) (liver-type arginase). [swissprot;acc:p05089] Divided 6271.17 6670.97 1.06375
protocadherin fat 2 precursor (hfat2) (multiple epidermal growth factor-like domains 1). [swissprot;acc:q9nyq8] Subtracted 5458.12 5830.76 372.64
1853 cadherin-related tumor suppressor homolog precursor (fat protein homolog). [swissprot;acc:q14517]
keratin associated protein 9.2. [refseq;acc:nm_031961] Divided 6076.65 6463.64 1.06368
1854 keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060] 6076.66 6463.14 1.0636
mln64 n-terminal domain homolog (stard3 n-terminal like protein). [swissprot;acc:o95772] Subtracted 5458.12 5830.76 372.64
1855 keratin associated protein 4-2; keratin associated protein 4.2. [refseq;acc:nm_033062] Divided 6076.66 6463.14 1.0636
n-acetylglutamate synthase. [refseq;acc:nm_153006] Subtracted 5162.27 5534.71 372.44
1856 keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4] Divided 6076.66 6463.14 1.0636
trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] Subtracted 4413.55 4784.6 371.05
1857 keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184] Divided 6076.66 6463.15 1.0636
transportin-sr; importin 12. [refseq;acc:nm_012470] Subtracted 5184.94 5555.76 370.82
1858 keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059] Divided 6076.66 6463.13 1.0636
ruvb-like 1 (ec 3.6.1.-) (49-kda tata box-binding protein-interacting protein) (49 kda tbp-interacting protein) (tip49a) (pontin 52) (nuclear matrix protein 238) (nmp 238) (54 kda erythrocyte cytosolic protein) (ecp-54) (tip60-associated protein 54-alpha) (tap54-alpha). [swissprot;acc:q9y265] Subtracted 5882.1 6252.66 370.56
1859 heat shock protein hsp 90-beta (hsp 84) (hsp 90). [swissprot;acc:p08238] 5733.71 6104.26 370.55
keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8] Divided 6076.66 6463.13 1.0636
1860 40s ribosomal protein s24 (s19). [swissprot;acc:p16632] Subtracted 5184.45 5554.97 370.52
keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854] Divided 6076.66 6463.13 1.0636
1861 keratin associated protein 1.5. [refseq;acc:nm_031957] 6463.14
splicing factor 3b subunit 4 (spliceosome associated protein 49) (sap 49) (sf3b50) (pre-mrna splicing factor sf3b 49 kda subunit). [swissprot;acc:q15427] Subtracted 4331.35 4700.91 369.56
1862 26s proteasome non-atpase regulatory subunit 1 (26s proteasome regulatory subunit s1) (26s proteasome subunit p112). [swissprot;acc:q99460] 5826 6195.48 369.48
star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095] Divided 6076.66 6463.13 1.0636
1863 adhesion regulating molecule 1 precursor (110 kda cell membrane glycoprotein) (gp110). [swissprot;acc:q16186] Subtracted 5826 6195.48 369.48
keratin, ultra high-sulfur matrix protein b (uhs keratin b) (uhs kerb). [swissprot;acc:o75690] Divided 6076.66 6463.14 1.0636
1864 keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371]
ubiquitin carboxyl-terminal hydrolase isozyme l5 (ec 3.4.19.12) (uch- l5) (ubiquitin thiolesterase l5) (ubiquitin c-terminal hydrolase uch37) (cgi-70) (ad-019). [swissprot;acc:q9y5k5] Subtracted 5826 6195.48 369.48
1865 rna polymerase ii subunit 5-mediating protein (rpb5-mediating protein). [swissprot;acc:o94763]

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/