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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Filtered Rank Value Type green Gene description Network Comparison Type network_comparison Interaction Map red
Results: HTML CSV LaTeX Showing element 451 to 500 of 77072 in total
Filtered  : 0
Rank
Value Type
green
description
Network Comparison Type
network_comparison
Interaction Map
red
29 Measured 2399.76 regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754] Subtracted 849.19 High confidence 3248.95
21088.5 cytochrome c oxidase polypeptide viic, mitochondrial precursor (ec 1.9.3.1). [swissprot;acc:p15954] 582.8 Low confidence 20505.7
Ranked 8257 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 5473.5 High confidence 13730.5
8687.07 solute carrier family 12 (potassium/chloride transporters), member 9; cation-chloride cotransporter-interacting protein. [refseq;acc:nm_020246] Divided 1.39628 Low confidence 12129.6
11625 phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086] 1.57201 High confidence 7395
15924 glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] Subtracted 4163 Low confidence 11761
Squared 0.355148 hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Divided 9.62112 3.41692
141.427 potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] 27.2794 High confidence 5.18438
15317.3 sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] Subtracted 7115.03 Low confidence 8202.27
64272.5 galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470] 7856.1 High confidence 72128.6
Rooted 1.80368 cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] 9.57372 11.3774
6.85565 glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] Divided 1.7443 Low confidence 11.9583
7.34614 microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268] 2.42243 High confidence 17.7955
9.246 pnas-129. [sptrembl;acc:q9bxv8] Subtracted 7.1816 Low confidence 16.4276
30 Measured 35.5 melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Divided 2.97183 105.5
111.739 dystrophin. [swissprot;acc:p11532] 3.82335 High confidence 427.217
704.5 protein kinase, lysine deficient 3. [refseq;acc:nm_020922] Subtracted 579.5 Low confidence 125
4102.97 cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] 837.72 High confidence 3265.25
Ranked 8257 lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] 5473.5 13730.5
11625 beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] Divided 1.57201 7395
13210.4 synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] Subtracted 4151.3 Low confidence 17361.7
15987.1 alpha 2 globin. [refseq;acc:nm_000517] Divided 1.39185 11486.2
Squared 0.355148 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] 9.62112 3.41692
141.944 potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] 22.6931 High confidence 6.25494
7964.87 lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] Subtracted 6882.39 Low confidence 1082.48
31089.6 segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] 7779.1 High confidence 23310.5
Rooted 7.5 protein tyrosine phosphatase type iva, member 2 isoform 1; protein tyrosine phosphatase iva2; protein tyrosine phosphatase iva; phosphatase of regenerating liver 2. [refseq;acc:nm_003479] Divided 1.74163 Low confidence 13.0622
9.43398 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Subtracted 9.43398 High confidence 0
12.5698 ptd016 protein. [refseq;acc:nm_016125] Divided 2.29492 5.47723
Subtracted 7.09257 Low confidence
31 Measured 0.00001 dok-like protein. [refseq;acc:nm_024872] Divided 3500000 High confidence 35
35.5 hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] 2.97183 Low confidence 105.5
2637 spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813] Subtracted 804 High confidence 1833
3114.19 adenomatous polyposis coli like. [refseq;acc:nm_005883] 570 Low confidence 2544.19
Ranked 5266.67 leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735] Divided 1.53462 High confidence 8082.33
6248 potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] Subtracted 5379 11627
9583.37 trinucleotide repeat containing 15. [refseq;acc:nm_015575] 4007.66 Low confidence 5575.71
15984.3 hemoglobin gamma-a and gamma-g chains. [swissprot;acc:p02096] Divided 1.39168 11485.6
Squared 0.355148 melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] 9.62112 3.41692
103.726 fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] 18.7211 High confidence 5.54059
26377.5 scribble. [refseq;acc:nm_015356] Subtracted 6838.2 Low confidence 19539.3
27772 fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] 7674.2 High confidence 35446.2
Rooted 9.43398 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 9.43398 0
12.7411 synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] Divided 1.73139 Low confidence 7.3589
27.8029 potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] 2.28539 High confidence 12.1655
51.8401 segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Subtracted 6.8546 Low confidence 58.6947
32 Measured 35.5 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Divided 2.97183 105.5
58 mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Subtracted 801 High confidence 859
184 cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336] Divided 3.25 598
3026.64 dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] Subtracted 550.54 Low confidence 2476.1

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/