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 2580 to 2629 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
162 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Ranked Subtracted 1 142 170 28
cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Measured Divided 0 5734.28 7252.02 1.26468
dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] Ranked Subtracted 13068 11528 1540
heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] Rooted Divided 1 52.7642 61.9019 1.17318
high-mobility group 20a. [refseq;acc:nm_018200] Measured Subtracted 5140.14 6893.53 1753.39
homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Squared Divided 173408 242989 1.40126
kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193] Rooted Subtracted 43.4554 31.7576 11.6978
lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428] Divided 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
stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975] Squared Subtracted 1 59704 76460.4 16756.4
udp-glucuronosyltransferase 2b15 precursor, microsomal (ec 2.4.1.17) (udpgt) (udpgth-3) (hlug4). [swissprot;acc:p54855] Divided 0 6123.28 3763.18 1.62716
163 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Rooted Subtracted 1 54.935 66.6101 11.6751
beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] Ranked 133 105 28
c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] Squared 59464 76120.8 16656.8
cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Rooted 0 57.5016 60.7262 3.2246
eap30 subunit of ell complex. [refseq;acc:nm_007241] Ranked Divided 1 209.299 249.187 1.19058
elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897] Squared Subtracted 0 328.83 917.917 589.087
eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] Rooted Divided 1 52.7702 61.8915 1.17285
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Squared 173408 242989 1.40126
likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] Measured Subtracted 14976.4 13246.6 1729.8
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Divided 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
rna polymerase i transcription factor rrn3. [refseq;acc:nm_018427] Measured Subtracted 814.485 613.614 200.871
transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] Ranked Divided 8409.21 9668.79 1.14979
ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Subtracted 11613 13133.5 1520.5
zinc finger protein 232. [swissprot;acc:q9uny5] Rooted Divided 17.1325 14.7869 1.15863
164 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Measured Subtracted 1 4489.19 2765.82 1723.37
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] Divided 0 1711.55 1354.26 1.26383
beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Ranked Subtracted 1 133 105 28
daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] Squared Divided 0 145.887 91.0551 1.60218
deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316] Subtracted 1 61733.5 45224.1 16509.4
dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374] Ranked Divided 0 11971.7 10412.4 1.14975
histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106] Squared Subtracted 14421.3 14982.3 561
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Divided 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
musashi 2 isoform a. [refseq;acc:nm_138962] Rooted Subtracted 54.9787 66.2416 11.2629
neurocalcin delta. [swissprot;acc:p29554] Ranked 0 13973.6 15473.5 1499.9
putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] Measured 1475.83 1676.18 200.35
Rooted 22.1344 25.2414 3.107
zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028] Divided 17.1341 14.7892 1.15855
165 dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] Ranked Subtracted 8375.43 9873.58 1498.15
glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] Divided 1 209.299 249.187 1.19058
glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Measured Subtracted 4489.19 2765.82 1723.37
homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Squared Divided 173408 242989 1.40126
integral membrane protein cii-3b. [sptrembl;acc:o75609] Subtracted 0 15669.3 16209.3 540

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/