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 3808 to 3857 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
476 vav proto-oncogene. [swissprot;acc:p15498] Squared Divided 31223.8 37614.3 1.20467
477 dehydrodolichyl diphosphate synthase. [refseq;acc:nm_024887] Subtracted 27034.1 32301.8 5267.7
inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [refseq;acc:nm_001566] Rooted Divided 62.574 68.4128 1.09331
nitrogen fixation cluster-like. [refseq;acc:nm_014301] Measured 9649.61 11053.5 1.14549
probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] Subtracted 5067 5926.17 859.17
rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] Ranked 220.183 236.015 15.832
saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] Divided 251.926 234.547 1.0741
transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] Rooted Subtracted 93.8375 88.6044 5.2331
vav-3 protein. [swissprot;acc:q9ukw4] Squared Divided 31248.8 37623.4 1.204
478 histone h2b.c (h2b/c). [swissprot;acc:q99880] Rooted 50.6084 55.2961 1.09263
probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] Squared Subtracted 25513.6 30779.5 5265.9
probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] Measured 5066.99 5926.1 859.11
serine/threonine-protein kinase pak 2 (ec 2.7.1.-) (p21-activated kinase 2) (pak-2) (pak65) (gamma-pak) (s6/h4 kinase). [swissprot;acc:q13177] Ranked 220.171 235.979 15.808
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Squared Divided 16318.4 19645.8 1.2039
star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8] Measured 9649.61 11053.5 1.14549
transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994] Ranked 228.051 212.321 1.07409
tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] Rooted Subtracted 93.8375 88.6044 5.2331
479 conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83] Ranked 220.172 235.98 15.808
ferritin heavy chain (ferritin h subunit). [swissprot;acc:p02794] Rooted 62.7397 67.9651 5.2254
histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] Divided 50.6084 55.2961 1.09263
iron-responsive element binding protein 1 (ire-bp 1) (iron regulatory protein 1) (irp1) (ferritin repressor protein) (aconitate hydratase) (ec 4.2.1.3) (citrate hydro-lyase) (aconitase). [swissprot;acc:p21399] Squared Subtracted 49941.4 44680.1 5261.3
nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] Ranked Divided 228.051 212.321 1.07409
ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] Measured Subtracted 7170.83 8029.64 858.81
star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502] Divided 9649.61 11053.5 1.14549
translation initiation factor if-2. [swissprot;acc:o60841] Squared 24031.6 28929.7 1.20382
480 cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] Rooted Subtracted 62.7424 67.9648 5.2224
histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106] Divided 50.6084 55.2961 1.09263
homeobox protein engrailed-2 (hu-en-2). [swissprot;acc:p19622] Squared Subtracted 31406.6 36662.8 5256.2
neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822] Measured Divided 9649.61 11053.5 1.14549
neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092] Ranked 237.109 254.667 1.07405
phosphatidate cytidylyltransferase 1 (ec 2.7.7.41) (cdp-diglyceride synthetase 1) (cdp-diglyceride pyrophosphorylase 1) (cdp- diacylglycerol synthase 1) (cds 1) (ctp:phosphatidate cytidylyltransferase 1) (cdp-dag synthase 1) (cdp-dg synthetase 1). [swissprot;acc:q92903] Squared 26874.6 32347.4 1.20364
serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] Measured Subtracted 5066.93 5925.38 858.45
serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [swissprot;acc:q13153] Ranked 220.172 235.98 15.808
481 breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] Measured 5493.1 6350.19 857.09
cpg binding protein (protein containing phd finger and cxxc domain 1). [swissprot;acc:q9p0u4] Squared 31406.6 36662.8 5256.2
dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] Rooted 62.7424 67.9648 5.2224
histone h2b. [refseq;acc:nm_175055] Divided 50.6084 55.2961 1.09263
mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] Measured 9649.61 11053.5 1.14549
neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966] Ranked 237.109 254.667 1.07405
serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [swissprot;acc:o75914] Subtracted 220.171 235.979 15.808
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Squared Divided 16335.9 19660.7 1.20353
482 activator of basal transcription 1; tata-binding protein-binding protein; basal transcriptional activator. [refseq;acc:nm_013375] Subtracted 31406.6 36662.8 5256.2
cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253] Measured 5493.1 6350.19 857.09
disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [swissprot;acc:o14490] Rooted 62.7424 67.9648 5.2224
heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839] Ranked Divided 237.109 254.667 1.07405
histone h2b.s (h2b/s). [swissprot;acc:p57053] Rooted 50.6084 55.2961 1.09263
mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [swissprot;acc:q16539] Measured 9649.61 11053.5 1.14549
rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] Ranked Subtracted 220.161 235.95 15.789
solute carrier family 13, member 3 (sodium-dependent high-affinity dicarboxylate transporter 2) (na(+)/dicarboxylate cotransporter 3) (nadc-3) (hnadc3). [swissprot;acc:q8wwt9] Squared Divided 26867.3 32335.2 1.20352
483 40s ribosomal protein s28. [swissprot;acc:p25112] Measured Subtracted 7161.14 8015.92 854.78

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/