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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1282 to 1331 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
Value Type
description
Filtered
red
green
network_comparison
161 Measured melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] 1 23693.7 18263 1.29736
Ranked cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 0 5781.93 6660.63 1.15197
rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] 1 249.663 298.263 1.19466
Squared homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] 173408 242989 1.40126
udp-glucuronosyltransferase 2b10 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:p36537] 0 6123.28 3763.18 1.62716
Rooted adp-ribosylation factor 3. [swissprot;acc:p16587] 14.8377 17.2252 1.16091
ns1-associated protein 1. [refseq;acc:nm_006372] 1 52.7642 61.9019 1.17318
162 Measured cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 0 5734.28 7252.02 1.26468
melanoma antigen, family b, 6. [refseq;acc:nm_173523] 1 23693.7 18263 1.29736
Ranked nostrin. [refseq;acc:nm_052946] 209.299 249.187 1.19058
putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] 0 12301.4 10680.5 1.15176
Squared homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] 1 173408 242989 1.40126
udp-glucuronosyltransferase 2b15 precursor, microsomal (ec 2.4.1.17) (udpgt) (udpgth-3) (hlug4). [swissprot;acc:p54855] 0 6123.28 3763.18 1.62716
Rooted heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] 1 52.7642 61.9019 1.17318
lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428] 0 9.27362 8 1.1592
163 Measured melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] 1 23693.7 18263 1.29736
myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] 0 7830.62 6193.07 1.26442
Ranked eap30 subunit of ell complex. [refseq;acc:nm_007241] 1 209.299 249.187 1.19058
transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] 0 8409.21 9668.79 1.14979
Squared homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 1 173408 242989 1.40126
p28 ing5. [refseq;acc:nm_032329] 0 5071.93 3165.6 1.6022
Rooted eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] 1 52.7702 61.8915 1.17285
zinc finger protein 232. [swissprot;acc:q9uny5] 0 17.1325 14.7869 1.15863
164 Measured aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181] 1711.55 1354.26 1.26383
melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] 1 23693.7 18263 1.29736
Ranked dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374] 0 11971.7 10412.4 1.14975
liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] 1 209.299 249.187 1.19058
Squared daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] 0 145.887 91.0551 1.60218
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] 1 173408 242989 1.40126
Rooted mad protein (max dimerizer). [swissprot;acc:q05195] 55.646 65.1534 1.17086
zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028] 0 17.1341 14.7892 1.15855
165 Measured melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] 1 23693.7 18263 1.29736
mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2] 0 1002.2 793.818 1.26251
Ranked glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] 1 209.299 249.187 1.19058
ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [swissprot;acc:p21108] 0 13255.4 15183.2 1.14544
Squared homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] 1 173408 242989 1.40126
myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] 0 54383.4 34012.2 1.59894
Rooted max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] 1 55.6486 65.1478 1.1707
zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58] 0 17.1346 14.7899 1.15853
166 Measured cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 5629.62 7099.51 1.2611
melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] 1 23693.7 18263 1.29736
Ranked gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] 209.299 249.187 1.19058
my016 protein. [sptrembl;acc:q9h3k6] 0 5561.19 6366.91 1.14488
Squared homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] 1 173408 242989 1.40126
hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543] 0 220.039 350.57 1.59322
Rooted max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] 1 55.6495 65.1458 1.17064
zinc finger imprinted 2. [swissprot;acc:q9nzv7] 0 17.1395 14.7969 1.15832
167 Measured melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] 1 23693.7 18263 1.29736
transcription factor mafk (erythroid transcription factor nf-e2 p18 subunit). [swissprot;acc:o60675] 0 331.61 417.983 1.26047
Ranked glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] 1 209.299 249.187 1.19058

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/