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 10264 to 10313 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
1283 orphan nuclear receptor nurr1 (immediate-early response protein not) (transcriptionally inducible nuclear receptor). [swissprot;acc:p43354] Measured Divided 6229.16 6742.79 1.08246
1284 5-formyltetrahydrofolate cyclo-ligase (ec 6.3.3.2) (5,10-methenyl- tetrahydrofolate synthetase) (methenyl-thf synthetase) (mthfs). [swissprot;acc:p49914] Squared Subtracted 27290.4 30221.1 2930.7
actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571] Rooted 63.0056 65.7244 2.7188
cda11 protein. [refseq;acc:nm_032026] Squared Divided 24855.8 28097.9 1.13044
cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] Ranked 218.368 213.22 1.02414
glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] Subtracted 228.642 223.726 4.916
mitogen-activated protein kinase 3 (ec 2.7.1.37) (extracellular signal-regulated kinase 1) (erk-1) (insulin-stimulated map2 kinase) (map kinase 1) (mapk 1) (p44-erk1) (ert2) (p44-mapk) (microtubule- associated protein-2 kinase). [swissprot;acc:p27361] Measured 6079.85 6556.07 476.22
trimethyllysine dioxygenase, mitochondrial precursor (ec 1.14.11.8) (epsilon-trimethyllysine 2-oxoglutarate dioxygenase) (tml-alpha- ketoglutarate dioxygenase) (tml hydroxylase) (tml dioxygenase) (tmld). [swissprot;acc:q9nvh6] Rooted Divided 64.9605 67.8088 1.04385
xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736] Measured 6413.32 6941.48 1.08235
1285 adp,atp carrier protein, fibroblast isoform (adp/atp translocase 2) (adenine nucleotide translocator 2) (ant 2). [swissprot;acc:p05141] Subtracted 5322.16 5798.38 476.22
alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652] Rooted 68.5259 71.2383 2.7124
cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329] Ranked Divided 218.368 213.22 1.02414
cytosolic nonspecific dipeptidase (glutamate carboxypeptidase-like protein 1). [swissprot;acc:q96kp4] Measured 6207.57 6718.7 1.08234
dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] Squared 14701.3 16618.9 1.13044
gtp-binding protein era homolog (hera) (fragment). [swissprot;acc:o75616] Rooted 64.9605 67.8088 1.04385
tgf-beta receptor type i precursor (ec 2.7.1.37) (tgfr-1) (tgf-beta type i receptor) (serine/threonine-protein kinase receptor r4) (skr4) (activin receptor-like kinase 5) (alk-5). [swissprot;acc:p36897] Ranked Subtracted 223.89 228.805 4.915
transportin-sr; importin 12. [refseq;acc:nm_012470] Squared 22037.5 24968.1 2930.6
1286 casein kinase i alpha s-like. [refseq;acc:nm_145203] Measured 4906.33 5382.5 476.17
cytochrome p450 4a11 precursor (ec 1.14.15.3) (cypiva11) (fatty acid omega-hydroxylase) (p-450 hk omega) (lauric acid omega-hydroxylase) (cyp4aii) (p450-hl-omega). [swissprot;acc:q02928] Divided 5655.85 6120.64 1.08218
cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] Ranked 218.368 213.22 1.02414
grpe protein homolog 2, mitochondrial precursor (mt-grpe#2). [swissprot;acc:q8taa5] Rooted 53.457 55.8006 1.04384
phenylalanyl-trna synthetase beta chain (ec 6.1.1.20) (phenylalanine-- trna ligase beta chain) (phers) (hspc173). [swissprot;acc:q9nsd9] Squared Subtracted 22287.6 25217.3 2929.7
rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749] Divided 15001.4 16951.5 1.12999
serine/threonine-protein kinase receptor r2 precursor (ec 2.7.1.37) (skr2) (activin receptor-like kinase 4) (alk-4) (actr-ib). [swissprot;acc:p36896] Ranked Subtracted 223.885 228.797 4.912
ubiquitin. [swissprot;acc:p02248] Rooted 68.5562 71.2644 2.7082
1287 casein kinase i, alpha isoform (ec 2.7.1.-) (cki-alpha) (ck1). [swissprot;acc:p48729] Measured 4906.33 5382.5 476.17
cleavage and polyadenylation specific factor 6, 68 kd subunit; pre-mrna cleavage factor im (68kd); cleavage and polyadenylation specific factor 6, 68kd subunit; pre-mrna cleavage factor i, 68kd subunit. [refseq;acc:nm_007007] Rooted 61.662 64.3527 2.6907
cytochrome p450 4f3 (ec 1.14.13.30) (cypivf3) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:q08477] Measured Divided 5655.85 6120.64 1.08218
dj18d14.4 (cytochrome p450, subfamily iva, polypeptide 11). [sptrembl;acc:q9ntl5] Ranked 218.368 213.22 1.02414
grpe protein homolog 1, mitochondrial precursor (mt-grpe#1) (hmge). [swissprot;acc:q9hav7] Rooted 53.457 55.8006 1.04384
neuronal calcium sensor 1 (ncs-1) (frequenin homolog) (frequenin-like protein) (frequenin-like ubiquitous protein). [swissprot;acc:p36610] Ranked Subtracted 223.887 228.799 4.912
rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [swissprot;acc:q9y243] Squared Divided 15001.4 16951.5 1.12999
ubiquitin-like protein sumo-1 conjugating enzyme (ec 6.3.2.19) (sumo- 1-protein ligase) (ubiquitin carrier protein) (ubiquitin-conjugating enzyme ubce2a) (p18). [swissprot;acc:p50550] Subtracted 25840.7 28767.8 2927.1
1288 activin a receptor, type ic; activin receptor-like kinase 7. [refseq;acc:nm_145259] Ranked 223.884 228.795 4.911
alpha-centractin (centractin) (centrosome-associated actin homolog) (actin-rpv) (arp1). [swissprot;acc:p42024] Rooted 59.226 61.9163 2.6903
chromodomain y-like protein 2. [refseq;acc:nm_152342] Measured 7101.7 7577.75 476.05
cytochrome p450 4b1 (ec 1.14.14.1) (cypivb1) (p450-hp). [swissprot;acc:p13584] Ranked Divided 218.368 213.22 1.02414
cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] Measured 5655.85 6120.64 1.08218
rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [swissprot;acc:p31751] Squared 15001.4 16951.5 1.12999
swi/snf-related matrix-associated actin-dependent regulator of chromatin d2; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60b; swp73-like protein; chromatin remodeling complex baf60b subunit; swi/snf complex 60 kda subunit b. [refseq;acc:nm_003077] Rooted 53.457 55.8006 1.04384
synaptotagmin xii (sytxii). [swissprot;acc:q8iv01] Squared Subtracted 22271.6 25198.4 2926.8
1289 beta-centractin (actin-related protein 1b) (arp1b). [swissprot;acc:p42025] Rooted 59.226 61.9163 2.6903
flotillin-1. [swissprot;acc:o75955] Ranked Divided 218.368 213.22 1.02414
likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033] Measured 5655.85 6120.64 1.08218
peroxisomal n1-acetyl-spermine/spermidine oxidase. [refseq;acc:nm_152911] Ranked Subtracted 228.644 223.736 4.908
pescadillo homolog 1. [swissprot;acc:o00541] Squared Divided 14342.2 16206.3 1.12997
ribosomal protein s6 kinase alpha 3 (ec 2.7.1.37) (s6k-alpha 3) (90 kda ribosomal protein s6 kinase 3) (p90-rsk 3) (ribosomal s6 kinase 2) (rsk-2) (pp90rsk2) (insulin-stimulated protein kinase 1) (ispk-1). [swissprot;acc:p51812] Measured Subtracted 6079.45 6555.4 475.95
shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] Squared 30518.9 33445.2 2926.3
swi/snf-related matrix-associated actin-dependent regulator of chromatin d3; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60c; swp73-like protein; chromatin remodeling complex baf60c subunit; swi/snf complex 60 kda subunit c. [refseq;acc:nm_003078] Rooted Divided 53.457 55.8006 1.04384
1290 apical-like protein (apxl protein). [swissprot;acc:q13796] Squared Subtracted 30517.3 33442.4 2925.1

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/