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 Hugo 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
Hugo
description
Value Type
Network Comparison Type
red
green
network_comparison
401 RPA1 replication protein a 70 kda dna-binding subunit (rp-a) (rf-a) (replication factor-a protein 1) (single-stranded dna-binding protein). [swissprot;acc:p27694] Ranked Divided 207.908 226.218 1.08807
402 no value endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] Squared 39472 48393.1 1.22601
EIF6 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
ENO2 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
GULP1 ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] Rooted 59.5128 65.604 6.0912
LRRC15 leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] Measured Divided 5201.41 4479.76 1.16109
NDC80 highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101] Ranked Subtracted 231.802 249.983 18.181
RPA2 replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927] Divided 207.908 226.218 1.08807
SORBS2 arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] Measured Subtracted 6230.94 7168.2 937.26
403 CAPS calcyphosine. [swissprot;acc:q13938] Rooted 59.5128 65.604 6.0912
ENO3 beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [swissprot;acc:p13929] Squared 28190.4 33984.1 5793.7
FEM1B 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
GYS2 glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] Squared 39463.9 48362.1 1.22548
MACF1 microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2] Ranked Subtracted 228.468 246.338 17.87
NUBP1 nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Rooted Divided 59.6834 65.6741 1.10037
PDC phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] Ranked 207.908 226.218 1.08807
SORBS1 ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] Measured Subtracted 6259.3 7190.91 931.61
404 ADSS adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520] Squared Divided 26819.1 32855.4 1.22507
CRNKL1 crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Rooted Subtracted 59.5128 65.604 6.0912
CSE1L importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] Measured 7802.31 8731.82 929.51
DST 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
ENO1 alpha enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (non- neural enolase) (nne) (enolase 1) (phosphopyruvate hydratase). [swissprot;acc:p06733] Squared 28190.4 33984.1 5793.7
LRRC3 leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] Measured Divided 5201.41 4479.76 1.16109
NUBP2 nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] Rooted 59.6834 65.6741 1.10037
RAD52 dna repair protein rad52 homolog. [swissprot;acc:p43351] Ranked 207.908 226.218 1.08807
405 ADSSL1 adenylosuccinate synthase-like 1. [refseq;acc:nm_152328] Squared 26822.2 32858.1 1.22503
BRAF 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
CEBPZ ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] Subtracted 48.0045 54.0843 6.0798
CLTCL1 clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] Ranked Divided 207.931 226.209 1.0879
GABARAP gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Subtracted 65.4586 83.0461 17.5875
GNA11 guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] Measured 1836.71 907.546 929.164
LAMC1 laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] Divided 5201.41 4479.76 1.16109
PGK1 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 no value 60s ribosomal protein l12. [swissprot;acc:p30050] Rooted Divided 49.9858 45.4433 1.09996
transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] Ranked 265.634 244.304 1.08731
DHX15 putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] Rooted Subtracted 56.2615 62.2958 6.0343
GNAQ guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] Measured 1836.71 907.564 929.146
HOXD9 homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] Squared 32208.8 37986.6 5777.8
HTRA2 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] Divided 18995.7 23245.6 1.22373
NETO2 neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092] Ranked Subtracted 237.109 254.667 17.558
SLC46A2 thymic stromal co-transporter. [refseq;acc:nm_033051] Measured Divided 5201.41 4479.76 1.16109
407 no value 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] Rooted 49.9856 45.4431 1.09996
GNAZ 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
HTRA4 probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] Squared Divided 18995.7 23244.9 1.22369
MRPS9 28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] Ranked 239.75 260.544 1.08673
NDUFA6 nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556] Squared Subtracted 32193.3 37967.7 5774.4
NETO1 neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966] Ranked 237.109 254.667 17.558
SLC15A2 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
WIPF1 wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516] Measured Divided 6603.41 7664.65 1.16071
408 no value dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] Rooted 49.9856 45.4432 1.09996

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
- Hugo is the HGNC identifier if it exists
- 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/