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 3208 to 3257 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
401 u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] Rooted Subtracted 55.9231 62.0565 6.1334
402 arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] Measured 6230.94 7168.2 937.26
endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] Squared Divided 39472 48393.1 1.22601
eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] Rooted 50.1918 55.2294 1.10037
gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [swissprot;acc:p09104] Squared Subtracted 28190.4 33984.1 5793.7
highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101] Ranked 231.802 249.983 18.181
leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] Measured Divided 5201.41 4479.76 1.16109
ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] Rooted Subtracted 59.5128 65.604 6.0912
replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927] Ranked Divided 207.908 226.218 1.08807
403 beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [swissprot;acc:p13929] Squared Subtracted 28190.4 33984.1 5793.7
calcyphosine. [swissprot;acc:q13938] Rooted 59.5128 65.604 6.0912
fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] Measured Divided 5201.41 4479.76 1.16109
glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] Squared 39463.9 48362.1 1.22548
microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2] Ranked Subtracted 228.468 246.338 17.87
nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Rooted Divided 59.6834 65.6741 1.10037
phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] Ranked 207.908 226.218 1.08807
ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] Measured Subtracted 6259.3 7190.91 931.61
404 adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520] Squared Divided 26819.1 32855.4 1.22507
alpha enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (non- neural enolase) (nne) (enolase 1) (phosphopyruvate hydratase). [swissprot;acc:p06733] Subtracted 28190.4 33984.1 5793.7
bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [swissprot;acc:q03001] Ranked 228.463 246.33 17.867
crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Rooted 59.5128 65.604 6.0912
dna repair protein rad52 homolog. [swissprot;acc:p43351] Ranked Divided 207.908 226.218 1.08807
importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] Measured Subtracted 7802.31 8731.82 929.51
leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] Divided 5201.41 4479.76 1.16109
nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] Rooted 59.6834 65.6741 1.10037
405 adenylosuccinate synthase-like 1. [refseq;acc:nm_152328] Squared 26822.2 32858.1 1.22503
b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] Rooted 116.576 105.948 1.10031
ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] Subtracted 48.0045 54.0843 6.0798
clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] Ranked Divided 207.931 226.209 1.0879
gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Subtracted 65.4586 83.0461 17.5875
guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] Measured 1836.71 907.546 929.164
laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] Divided 5201.41 4479.76 1.16109
phosphoglycerate kinase 1 (ec 2.7.2.3) (primer recognition protein 2) (prp 2). [swissprot;acc:p00558] Squared Subtracted 28192 33985.3 5793.3
406 60s ribosomal protein l12. [swissprot;acc:p30050] Rooted Divided 49.9858 45.4433 1.09996
guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] Measured Subtracted 1836.71 907.564 929.146
homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] Squared 32208.8 37986.6 5777.8
neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092] Ranked 237.109 254.667 17.558
putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] Rooted 56.2615 62.2958 6.0343
serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [swissprot;acc:o43464] Squared Divided 18995.7 23245.6 1.22373
thymic stromal co-transporter. [refseq;acc:nm_033051] Measured 5201.41 4479.76 1.16109
transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] Ranked 265.634 244.304 1.08731
407 28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] 239.75 260.544 1.08673
60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] Rooted 49.9856 45.4431 1.09996
guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] Measured Subtracted 1836.76 907.741 929.019
nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556] Squared 32193.3 37967.7 5774.4
neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966] Ranked 237.109 254.667 17.558
oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] Rooted 80.2562 86.277 6.0208
probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] Squared Divided 18995.7 23244.9 1.22369
wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516] Measured 6603.41 7664.65 1.16071
408 ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] Ranked 255.112 234.804 1.08649

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/