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 2775 to 2824 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1388 lin-7 homolog b; lin-7b protein; likely ortholog of mouse lin-7b; mammalian lin-7 protein 2; likely orholog of mouse lin 7 homolog b (c. elegans). [refseq;acc:nm_022165] Divided 5743.39 6192.94 1.07827
p protein (melanocyte-specific transporter protein). [swissprot;acc:q04671] Subtracted 5656.8 6111.9 455.1
1389 mitogen-activated protein kinase 1 (ec 2.7.1.37) (extracellular signal-regulated kinase 2) (erk-2) (mitogen-activated protein kinase 2) (map kinase 2) (mapk 2) (p42-mapk) (ert1). [swissprot;acc:p28482] Divided 6079.13 6554.85 1.07825
serine/threonine protein phosphatase 2b catalytic subunit, beta isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, beta isoform) (cam-prp catalytic subunit). [swissprot;acc:p16299] Subtracted 5656.81 6111.84 455.03
1390 receptor protein-tyrosine kinase erbb-4 precursor (ec 2.7.1.112) (p180erbb4) (tyrosine kinase-type cell surface receptor her4). [swissprot;acc:q15303] Divided 5743.36 6192.72 1.07824
serine/threonine protein phosphatase 2b catalytic subunit, gamma isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, gamma isoform) (calcineurin, testis-specific catalytic subunit) (cam-prp catalytic subunit). [swissprot;acc:p48454] Subtracted 5656.82 6111.8 454.98
1391 alpha adducin (erythrocyte adducin alpha subunit). [swissprot;acc:p35611] 5786.71 6241.16 454.45
epidermal growth factor receptor precursor (ec 2.7.1.112) (receptor protein-tyrosine kinase erbb-1). [swissprot;acc:p00533] Divided 5743.36 6192.7 1.07824
1392 dual specificity mitogen-activated protein kinase kinase 1 (ec 2.7.1.-) (map kinase kinase 1) (mapkk 1) (erk activator kinase 1) (mapk/erk kinase 1) (mek1). [swissprot;acc:q02750] Subtracted 5880.37 6334.71 454.34
receptor protein-tyrosine kinase erbb-2 precursor (ec 2.7.1.112) (p185erbb2) (neu proto-oncogene) (c-erbb-2) (tyrosine kinase-type cell surface receptor her2) (mln 19). [swissprot;acc:p04626] Divided 5743.36 6192.7 1.07824
1393 2-hydroxyphytanoyl-coa lyase (ec 4.1.-.-) (2-hpcl) (hspc279). [swissprot;acc:q9uj83] 6192.72
similar to kinase suppressor of ras (fragment). [sptrembl;acc:q8ivt5] Subtracted 5880.37 6334.71 454.34
1394 dual specificity mitogen-activated protein kinase kinase 2 (ec 2.7.1.-) (map kinase kinase 2) (mapkk 2) (erk activator kinase 2) (mapk/erk kinase 2) (mek2). [swissprot;acc:p36507]
receptor protein-tyrosine kinase erbb-3 precursor (ec 2.7.1.112) (c-erbb3) (tyrosine kinase-type cell surface receptor her3). [swissprot;acc:p21860] Divided 5743.36 6192.72 1.07824
1395 lin-7 homolog c; lin-7 protein 3. [refseq;acc:nm_018362] 5743.26 6191.96 1.07813
proteasome subunit beta type 8 precursor (ec 3.4.25.1) (proteasome component c13) (macropain subunit c13) (multicatalytic endopeptidase complex subunit c13). [swissprot;acc:p28062] Subtracted 6351.32 6805.39 454.07
1396 g-rich sequence factor-1 (grsf-1). [swissprot;acc:q12849] Divided 5803.54 6256.54 1.07806
proteasome subunit beta type 9 precursor (ec 3.4.25.1) (proteasome chain 7) (macropain chain 7) (multicatalytic endopeptidase complex chain 7) (ring12 protein) (low molecular mass protein 2). [swissprot;acc:p28065] Subtracted 6257.62 6711.4 453.78
1397 fidgetin-like 1. [refseq;acc:nm_022116] 6057.46 6510.9 453.44
heterogeneous nuclear ribonucleoprotein f (hnrnp f). [swissprot;acc:p52597] Divided 5803.27 6256.23 1.07805
1398 evolutionarily conserved signaling intermediate in toll pathway; ecsit. [refseq;acc:nm_016581] Subtracted 6184.27 6637.44 453.17
heterogeneous nuclear ribonucleoprotein h (hnrnp h). [swissprot;acc:p31943] Divided 5803.12 6256.05 1.07805
1399 g-rich sequence factor-1 (grsf-1). [swissprot;acc:q12849] Subtracted 5803.54 6256.54 453
heterogeneous nuclear ribonucleoprotein h' (hnrnp h') (ftp-3). [swissprot;acc:p55795] Divided 5803.1 6256.03 1.07805
1400 heterogeneous nuclear ribonucleoprotein h3 (hnrnp h3) (hnrnp 2h9). [swissprot;acc:p31942] 5803.45 6256.43
Subtracted 452.98
1401 hepatocyte nuclear factor 3-gamma (hnf-3g) (forkhead box protein a3) (fork head-related protein fkh h3). [swissprot;acc:p55318] Divided 5728.92 6175.99 1.07804
heterogeneous nuclear ribonucleoprotein f (hnrnp f). [swissprot;acc:p52597] Subtracted 5803.27 6256.23 452.96
1402 43 kda receptor-associated protein of the synapse (rapsyn) (acetylcholine receptor-associated 43 kda protein) (43 kda postsynaptic protein). [swissprot;acc:q13702] Divided 6160.06 6640.78 1.07804
heterogeneous nuclear ribonucleoprotein h (hnrnp h). [swissprot;acc:p31943] Subtracted 5803.12 6256.05 452.93
1403 heterogeneous nuclear ribonucleoprotein h' (hnrnp h') (ftp-3). [swissprot;acc:p55795] 5803.1 6256.03
importin 4. [refseq;acc:nm_024658] Divided 5613.16 6050.16 1.07785
1404 14.5 kda translational inhibitor protein (p14.5) (uk114 antigen homolog). [swissprot;acc:p52758] Subtracted 6336.22 6788.96 452.74
mesoderm induction early response 1. [refseq;acc:nm_020948] Divided 6291.89 6781.6 1.07783
1405 glycerol kinase, testis specific 1 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14409] Subtracted 6137.24 6589.72 452.48
proteasome subunit alpha type 3 (ec 3.4.25.1) (proteasome component c8) (macropain subunit c8) (multicatalytic endopeptidase complex subunit c8). [swissprot;acc:p25788] Divided 6291.89 6781.6 1.07783
1406 glycerol kinase (ec 2.7.1.30) (atp:glycerol 3-phosphotransferase) (glycerokinase) (gk). [swissprot;acc:p32189] Subtracted 6137.09 6589.57 452.48
ribokinase (ec 2.7.1.15). [swissprot;acc:q9h477] Divided 6210.51 6693.49 1.07777
1407 glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14410] Subtracted 6137.53 6590.01 452.48
transketolase (ec 2.2.1.1) (tk). [swissprot;acc:p29401] Divided 5692.53 6134.64 1.07766
1408 proteasome subunit beta type 10 precursor (ec 3.4.25.1) (proteasome mecl-1) (macropain subunit mecl-1) (multicatalytic endopeptidase complex subunit mecl-1). [swissprot;acc:p40306] Subtracted 6079.65 6530.82 451.17
serologically defined colon cancer antigen 16. [refseq;acc:nm_006649] Divided 6268.94 6755.57 1.07763
1409 glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 2 (ec 2.6.1.16) (hexosephosphate aminotransferase 2) (d-fructose-6- phosphate amidotransferase 2) (gfat 2) (gfat2). [swissprot;acc:o94808] 5358.19 5773.37 1.07749
proteasome subunit beta type 6 precursor (ec 3.4.25.1) (proteasome delta chain) (macropain delta chain) (multicatalytic endopeptidase complex delta chain) (proteasome subunit y). [swissprot;acc:p28072] Subtracted 6221.35 6672.51 451.16
1410 delta-interacting protein a (hepatitis delta antigen interacting protein a). [swissprot;acc:q15834] Divided 6274.62 6760.78 1.07748
transcriptional adaptor 3-like isoform a. [refseq;acc:nm_006354] Subtracted 7260.23 7711.3 451.07
1411 14-3-3 protein beta/alpha (protein kinase c inhibitor protein-1) (kcip-1) (protein 1054). [swissprot;acc:p31946] Divided 5812.02 6262.07 1.07743
frg1 protein (fshd region gene 1 protein). [swissprot;acc:q14331] Subtracted 7260.23 7711.3 451.07
1412 histone deacetylase 5 (hd5) (antigen ny-co-9). [swissprot;acc:q9uql6] Divided 5813.84 6263.92 1.07742
transcriptional adapter 2-like (ada2-like protein) (kl04p). [swissprot;acc:o75478] Subtracted 7260.23 7711.3 451.07

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/