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 1273 to 1322 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
Filtered
red
green
network_comparison
160 apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] Rooted 1 52.7642 61.9019 1.17318
ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1] Ranked 0 11732 13530.6 1.15331
e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409] Rooted 34.3021 29.5305 1.16158
glutamyl aminopeptidase (ec 3.4.11.7) (eap) (aminopeptidase a) (apa) (differentiation antigen gp160). [swissprot;acc:q07075] Squared 6123.28 3763.18 1.62716
guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] Ranked 1 249.663 298.263 1.19466
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Squared 173408 242989 1.40126
huntingtin interacting protein c. [refseq;acc:nm_012272] Measured 0 1653.74 1296.38 1.27566
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] 1 23693.7 18263 1.29736
161 adp-ribosylation factor 3. [swissprot;acc:p16587] Rooted 0 14.8377 17.2252 1.16091
cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Ranked 5781.93 6660.63 1.15197
glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434] Measured 903.767 1152.06 1.27473
homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Squared 1 173408 242989 1.40126
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Measured 23693.7 18263 1.29736
ns1-associated protein 1. [refseq;acc:nm_006372] Rooted 52.7642 61.9019 1.17318
rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] Ranked 249.663 298.263 1.19466
udp-glucuronosyltransferase 2b10 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:p36537] Squared 0 6123.28 3763.18 1.62716
162 cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Measured 5734.28 7252.02 1.26468
heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] Rooted 1 52.7642 61.9019 1.17318
homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Squared 173408 242989 1.40126
lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428] Rooted 0 9.27362 8 1.1592
melanoma antigen, family b, 6. [refseq;acc:nm_173523] Measured 1 23693.7 18263 1.29736
nostrin. [refseq;acc:nm_052946] Ranked 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
udp-glucuronosyltransferase 2b15 precursor, microsomal (ec 2.4.1.17) (udpgt) (udpgth-3) (hlug4). [swissprot;acc:p54855] Squared 6123.28 3763.18 1.62716
163 eap30 subunit of ell complex. [refseq;acc:nm_007241] Ranked 1 209.299 249.187 1.19058
eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] Rooted 52.7702 61.8915 1.17285
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Squared 173408 242989 1.40126
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Measured 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
p28 ing5. [refseq;acc:nm_032329] Squared 5071.93 3165.6 1.6022
transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] Ranked 8409.21 9668.79 1.14979
zinc finger protein 232. [swissprot;acc:q9uny5] Rooted 17.1325 14.7869 1.15863
164 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] Measured 1711.55 1354.26 1.26383
daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] Squared 145.887 91.0551 1.60218
dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374] Ranked 11971.7 10412.4 1.14975
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Squared 1 173408 242989 1.40126
liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] Ranked 209.299 249.187 1.19058
mad protein (max dimerizer). [swissprot;acc:q05195] Rooted 55.646 65.1534 1.17086
melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Measured 23693.7 18263 1.29736
zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028] Rooted 0 17.1341 14.7892 1.15855
165 glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] Ranked 1 209.299 249.187 1.19058
homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Squared 173408 242989 1.40126
max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] Rooted 55.6486 65.1478 1.1707
melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Measured 23693.7 18263 1.29736
mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2] 0 1002.2 793.818 1.26251
myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] Squared 54383.4 34012.2 1.59894
ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [swissprot;acc:p21108] Ranked 13255.4 15183.2 1.14544
zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58] Rooted 17.1346 14.7899 1.15853
166 cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Measured 5629.62 7099.51 1.2611
gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] Ranked 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/