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 12414 to 12463 of 29840 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
1050 microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268] Squared Subtracted 31026.8 34372.7 3345.9
mitochondrial ribosomal protein l22. [refseq;acc:nm_014180] Rooted Divided 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
annexin a11 (annexin xi) (calcyclin-associated annexin 50) (cap-50) (56 kda autoantigen). [swissprot;acc:p50995] Ranked Subtracted 219.673 213.378 6.295
bomapin (protease inhibitor 10) (serpin b10). [swissprot;acc:p48595] Squared Divided 20357.7 23353.8 1.14717
epidermal growth factor receptor pathway substrate 8-like protein 2; eps8-related protein 2; epidermal growth factor receptor pathway substrate 8-related protein 2. [refseq;acc:nm_022772] Rooted Subtracted 60.7905 64.0183 3.2278
homeobox protein dlx-2. [swissprot;acc:q07687] Measured Divided 4757.46 5198.91 1.09279
microtubule-associated protein rp/eb family member 3 (protein eb3). [swissprot;acc:q9upy8] Squared Subtracted 31026.8 34372.6 3345.8
signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240] Measured 5208.27 5737.17 528.9
1052 histidine-rich membrane protein ke4. [swissprot;acc:q92504] Squared 31026.9 34372.4 3345.5
homeobox protein dlx-5. [swissprot;acc:p56178] Measured Divided 4757.46 5198.91 1.09279
kappa b-ras 1. [refseq;acc:nm_020345] Rooted Subtracted 61.2289 64.4564 3.2275
lysyl-trna synthetase (ec 6.1.1.6) (lysine--trna ligase) (lysrs). [swissprot;acc:q15046] Ranked 220.291 226.584 6.293
plasminogen activator inhibitor-2 precursor (pai-2) (placental plasminogen activator inhibitor) (monocyte arg-serpin) (urokinase inhibitor). [swissprot;acc:p05120] Squared Divided 20357.7 23353.8 1.14717
protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031] Measured Subtracted 6278.76 6807.51 528.75
retinol dehydrogenase 8 (all-trans); photoreceptor outer segment all-trans retinol dehydrogenase. [refseq;acc:nm_015725] Ranked Divided 211.449 217.998 1.03097
small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072] Rooted 83.0639 87.321 1.05125
1053 annexin a7 (annexin vii) (synexin). [swissprot;acc:p20073] Ranked Subtracted 219.655 213.385 6.27
fetal brain protein 239 (239fb). [swissprot;acc:q15777] Measured Divided 4757.46 5198.91 1.09279
i-kappa-b-interacting ras-like protein 2. [refseq;acc:nm_017595] Rooted Subtracted 61.2289 64.4564 3.2275
importin beta-3 subunit (karyopherin beta-3 subunit) (ran-binding protein 5). [swissprot;acc:o00410] Divided 62.9727 66.1956 1.05118
microtubule-associated protein rp/eb family member 1 (apc-binding protein eb1). [swissprot;acc:q15691] Squared Subtracted 31026.9 34372.4 3345.5
peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] Measured 5166.04 5694.55 528.51
proteasome subunit alpha type 5 (ec 3.4.25.1) (proteasome zeta chain) (macropain zeta chain) (multicatalytic endopeptidase complex zeta chain). [swissprot;acc:p28066] Ranked Divided 207.04 200.84 1.03087
serpin b11. [swissprot;acc:q96p15] Squared 20357.7 23353.8 1.14717
1054 60s ribosomal protein l21. [swissprot;acc:p46778] Ranked 223.958 217.263 1.03082
heat shock factor binding protein 1. [swissprot;acc:o75506] Measured Subtracted 5915.42 6443.77 528.35
homeobox protein dlx-3. [swissprot;acc:o60479] Divided 4757.46 5198.91 1.09279
placental thrombin inhibitor (cytoplasmic antiproteinase) (cap) (protease inhibitor 6) (pi-6). [swissprot;acc:p35237] Squared 20357.7 23353.8 1.14717
proteasome subunit alpha type 5 (ec 3.4.25.1) (proteasome zeta chain) (macropain zeta chain) (multicatalytic endopeptidase complex zeta chain). [swissprot;acc:p28066] Ranked Subtracted 207.04 200.84 6.2
ran-gtp binding protein (fragment). [sptrembl;acc:o60518] Rooted Divided 62.9646 66.1812 1.05109
snare associated protein snapin. [refseq;acc:nm_012437] Subtracted 61.2289 64.4564 3.2275
u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] Squared 18595.6 21936.3 3340.7
1055 26s proteasome non-atpase regulatory subunit 6 (26s proteasome regulatory subunit s10) (p42a) (proteasome regulatory particle subunit p44s10). [swissprot;acc:q15008] 27408.7 30747.3 3338.6
activated p21cdc42hs kinase. [refseq;acc:nm_005781] Measured Divided 4757.46 5198.91 1.09279
cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452] Squared 20357.7 23353.8 1.14717
hcv ns3-transactivated protein 1. [refseq;acc:nm_019048] Ranked 219.01 212.468 1.03079
hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Subtracted 138.705 132.538 6.167
importin beta-3 subunit (karyopherin beta-3 subunit) (ran-binding protein 5). [swissprot;acc:o00410] Rooted 62.9727 66.1956 3.2229
importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] Divided 74.1383 77.9257 1.05109
mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352] Measured Subtracted 5167.15 5695.44 528.29
1056 kinesin family member c3. [refseq;acc:nm_005550] Rooted Divided 63.3481 66.5681 1.05083
leukocyte elastase inhibitor (lei) (monocyte/neutrophil elastase inhibitor) (m/nei) (ei). [swissprot;acc:p30740] Squared 20357.7 23353.8 1.14717
methyltransferase like 2. [refseq;acc:nm_018396] Ranked Subtracted 147.211 153.371 6.16
mitogen-activated protein kinase kinase kinase 7 interacting protein 2 isoform 1; tak1-binding protein 2. [refseq;acc:nm_015093] Measured Divided 4757.46 5198.91 1.09279
protein bap28. [swissprot;acc:q9h583] Rooted Subtracted 51.1817 54.4034 3.2217
u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] Squared 18960.3 22298 3337.7
vacuolar atp synthase catalytic subunit a, ubiquitous isoform (ec 3.6.3.14) (v-atpase a subunit 1) (vacuolar proton pump alpha subunit 1) (v-atpase 69 kda subunit 1) (isoform va68). [swissprot;acc:p38606] Ranked Divided 219.01 212.468 1.03079

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/