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 2408 to 2457 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
301 proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Squared Divided 28896.2 36767 1.27238
302 60s ribosomal protein l26. [swissprot;acc:q02877] Ranked 242.326 267.008 1.10185
coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [swissprot;acc:p48444] Squared Subtracted 51527.6 43689.1 7838.5
cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] Rooted Divided 203.673 182.638 1.11517
hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] Ranked Subtracted 88.2482 110.265 22.0168
homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] Rooted 66.1046 74.0964 7.9918
pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] Measured Divided 5894.75 7073.65 1.19999
ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] Subtracted 6704.44 7811.45 1107.01
tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Squared Divided 28896.2 36767 1.27238
303 60s ribosomal protein l35. [swissprot;acc:p42766] Ranked 242.333 266.999 1.10179
crk-like protein. [swissprot;acc:p46109] Squared 28896.2 36767 1.27238
cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Rooted 203.673 182.638 1.11517
melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Ranked Subtracted 88.2482 110.265 22.0168
peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [swissprot;acc:q9unp9] Squared 51527.6 43689.1 7838.5
ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] Rooted 62.9007 70.8854 7.9847
serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Measured Divided 22268.8 18560.4 1.1998
spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] Subtracted 4723.53 5828.46 1104.93
304 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] Ranked Divided 242.339 266.986 1.1017
coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [swissprot;acc:q9p299] Squared Subtracted 51527.6 43689.1 7838.5
cytohesin 4. [swissprot;acc:q9uia0] Rooted Divided 203.673 182.638 1.11517
melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Ranked Subtracted 88.2482 110.265 22.0168
polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] Measured 5221.28 6314.35 1093.07
pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Divided 4855.46 5824.52 1.19958
proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Squared 28896.2 36767 1.27238
splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Rooted Subtracted 53.6107 61.5862 7.9755
305 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 75.6323 67.6572 7.9751
cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] Divided 203.673 182.638 1.11517
melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Ranked Subtracted 88.2482 110.265 22.0168
mitochondrial ribosomal protein l2. [refseq;acc:nm_015950] Divided 242.339 266.986 1.1017
neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] Squared Subtracted 28918.3 36746 7827.7
odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] Measured Divided 3856.29 4624.15 1.19912
paxillin. [swissprot;acc:p49023] Subtracted 5221.28 6314.35 1093.07
proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] Squared Divided 28896.2 36767 1.27238
306 60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] Ranked 242.153 266.673 1.10126
hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Subtracted 88.2482 110.265 22.0168
kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] Measured 8430.03 9518.11 1088.08
ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926] Squared 33044.9 40781.4 7736.5
pnas-18. [sptrembl;acc:q9bzu3] Measured Divided 13680.5 11409.6 1.19903
proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] Squared 28896.2 36767 1.27238
rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] Rooted 56.3935 62.8817 1.11505
serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Subtracted 127.967 120.003 7.964
307 1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120] Measured 7556.75 8636.87 1080.12
aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763] Squared 33010.8 40732.2 7721.4
grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791] Divided 28896.4 36766.8 1.27237
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Ranked Subtracted 88.2482 110.265 22.0168
neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] Rooted 66.0989 74.0609 7.962
serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] Ranked Divided 242.153 266.673 1.10126
t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] Measured 12365.2 14824.9 1.19892
transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] Rooted 50.4687 45.2733 1.11476
308 1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7] Squared 30596.2 38919.9 1.27205

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/