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 green Gene Value Type description Network Comparison Type network_comparison Interaction Map red
Results: HTML CSV LaTeX Showing element 501 to 550 of 77072 in total
Filtered  : 0
Rank
green
Value Type
description
Network Comparison Type
network_comparison
Interaction Map
red
32 11.258 Rooted ubiquitin protein ligase. [refseq;acc:nm_130466] Divided 2.13529 High confidence 24.0391
35.5 Measured melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] 2.97183 Low confidence 105.5
47.9266 Rooted fibrillin 3. [refseq;acc:nm_032447] Subtracted 6.8075 54.7341
58 Measured mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 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
8691.76 Ranked importin 9. [refseq;acc:nm_018085] Divided 1.52929 High confidence 13292.2
14842.4 pnas-129. [sptrembl;acc:q9bxv8] Subtracted 3734.8 Low confidence 11107.6
15983.3 myoglobin. [swissprot;acc:p02144] Divided 1.39162 11485.4
19014.6 syntaxin 10 (syn10). [swissprot;acc:o60499] Subtracted 5130.2 High confidence 13884.4
27221.2 Squared 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] 7328.6 19892.6
48048.2 myosin regulatory light chain 2, nonsarcomeric (myosin rlc). [swissprot;acc:p19105] 6799.3 Low confidence 54847.5
33 0.355148 melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Divided 9.62112 3.41692
4.57302 beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] 16.8159 High confidence 76.8994
5.80678 Rooted melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] 1.69589 Low confidence 9.84765
25.7294 fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] 2.0801 High confidence 12.3693
35.5 Measured melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] 2.97183 Low confidence 105.5
39.8063 lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893] 3.15402 High confidence 12.6208
58.122 Rooted trinucleotide repeat containing 15. [refseq;acc:nm_015575] Subtracted 6.5363 Low confidence 64.6583
70.9983 nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] 9.359 High confidence 61.6393
4245.16 Measured scribble. [refseq;acc:nm_015356] 547.36 Low confidence 3697.8
7867 Ranked cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [swissprot;acc:q9ubr2] 3648 11515
8691.76 nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733] Divided 1.52929 High confidence 13292.2
9192.38 Measured protein cgi-147. [swissprot;acc:q9y3e5] Subtracted 796.26 8396.12
14746.1 Ranked fk506-binding protein 6 (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (36 kda fk506 binding protein) (fkbp- 36) (immunophilin fkbp36). [swissprot;acc:o75344] Divided 1.37827 Low confidence 20324.1
20387 similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517] Subtracted 5123 High confidence 15264
36822.7 Squared ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9] 7010.7 29812
130587 microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] 6603 Low confidence 123984
34 0.355148 melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Divided 9.62112 3.41692
0.697197 lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893] 15.9968 High confidence 0.0435834
5.80678 Rooted melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] 1.69589 Low confidence 9.84765
11.7898 phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086] 2.02503 High confidence 23.8747
12.49 succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521] Subtracted 9.32772 3.16228
14.4058 potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] 6.50517 Low confidence 7.90063
35.5 Measured melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Divided 2.97183 105.5
47 glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] 3.04255 High confidence 143
1361.92 peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] Subtracted 521.18 Low confidence 840.74
3340.03 acrc protein; putative nuclear protein. [refseq;acc:nm_052957] 791.03 High confidence 4131.06
6812 Ranked fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] 4731 11543
7506.66 fibrillin 3. [refseq;acc:nm_032447] Divided 1.37724 Low confidence 5450.5
9520.8 sam-domain protein samsn-1 (sam domain, sh3 domain and nuclear localisation signals protein 1). [swissprot;acc:q9nsi8] Subtracted 3531.9 13052.7
17173.8 microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268] Divided 1.52196 High confidence 11284
72701 Squared coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] Subtracted 6682.4 79383.4
129956 th1-like; th1 drosophila homolog; th1-like (drosophila homolog); negative elongation factor proteins c and d. [refseq;acc:nm_016397] 6596 Low confidence 136552
35 0.355148 melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Divided 9.62112 3.41692
1.18697 Rooted serpin b12. [swissprot;acc:q96p63] Subtracted 9.10583 High confidence 10.2928
5.80678 melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Divided 1.69589 Low confidence 9.84765
8.64796 fk506-binding protein 6 (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (36 kda fk506 binding protein) (fkbp- 36) (immunophilin fkbp36). [swissprot;acc:o75344] Subtracted 6.40139 2.24657
11.7898 beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] Divided 2.02503 High confidence 23.8747
35.5 Measured melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] 2.97183 Low confidence 105.5

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/