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 313 to 362 of 8289 in total
Value Type  : Measured
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
157 hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] High confidence 23693.7 18263 1.29736
vacuolar assembly protein vps41 homolog (s53). [swissprot;acc:p49754] Low confidence 7497.17 8131.56 1.08462
158 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] High confidence 23693.7 18263 1.29736
mitochondrial tumor suppressor gene 1; transcription factor mtsg1; at2 receptor-interacting protein 1; erythroid differentiation-related gene. [refseq;acc:nm_020749] Low confidence 6434.71 6976.28 1.08416
159 brain protein 44. [swissprot;acc:o95563] 10392.1 11259.7 1.08349
necdin. [swissprot;acc:q99608] High confidence 23693.7 18263 1.29736
160 melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]
methylenetetrahydrofolate reductase (ec 1.5.1.20). [swissprot;acc:p42898] Low confidence 10452.8 11320.8 1.08304
161 melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] High confidence 23693.7 18263 1.29736
monocarboxylate transporter 6 (mct 6) (mct 5). [swissprot;acc:o15375] Low confidence 10351.8 11210.8 1.08298
162 cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 12424.3 11472.3
melanoma antigen, family b, 6. [refseq;acc:nm_173523] High confidence 23693.7 18263 1.29736
163 melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]
monocarboxylate transporter 1 (mct 1). [swissprot;acc:p53985] Low confidence 10348.5 11206.7 1.08293
164 melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] High confidence 23693.7 18263 1.29736
monocarboxylate transporter 2 (mct 2). [swissprot;acc:o60669] Low confidence 10346.9 11204.8 1.08291
165 melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] High confidence 23693.7 18263 1.29736
monocarboxylate transporter 3 (mct 3). [swissprot;acc:o95907] Low confidence 10341.7 11198.5 1.08285
166 melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] High confidence 23693.7 18263 1.29736
monocarboxylate transporter 4 (mct 4) (mct 3). [swissprot;acc:o15427] Low confidence 10325 11178.2 1.08263
167 cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 12376.5 11436.5 1.08219
melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] High confidence 23693.7 18263 1.29736
168 mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] Low confidence 12376.4 11436.5 1.08218
melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] High confidence 23693.7 18263 1.29736
169 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] Low confidence 12375.5 11435.8 1.08217
melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] High confidence 23693.7 18263 1.29736
170 amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410] Low confidence 6131.26 6633.65 1.08194
melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] High confidence 23693.7 18263 1.29736
171 melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1]
sentrin-specific protease 8 (ec 3.4.22.-) (sentrin/sumo-specific protease senp8) (cysteine protease fksg8). [swissprot;acc:q96ld8] Low confidence 7012.61 7584.69 1.08158
172 trophinin. [swissprot;acc:q12816] High confidence 23693.7 18263 1.29736
ubiquitin-like protein nedd8. [swissprot;acc:q15843] Low confidence 7012.61 7584.69 1.08158
173 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] High confidence 4579.34 5940.64 1.29727
septin 2 (nedd5 protein homolog). [swissprot;acc:q15019] Low confidence 10168.5 10996.7 1.08145
174 cytohesin 4. [swissprot;acc:q9uia0] 12315 11390.6 1.08115
mad protein (max dimerizer). [swissprot;acc:q05195] High confidence 4455.95 5774.03 1.2958
175 endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase (ec 3.2.1.113) (er alpha-1,2-mannosidase) (mannosidase alpha class 1b member 1) (man9glcnac2-specific processing alpha-mannosidase). [swissprot;acc:q9ukm7] Low confidence 7004.28 7569.94 1.08076
max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] High confidence 4456.67 5773.77 1.29553
176 max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] 4456.93 5773.67 1.29544
presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Low confidence 7004.28 7569.94 1.08076
177 max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] High confidence 4457.06 5773.63 1.29539
rhomboid-related protein 4 (ec 3.4.21.-) (ventrhoid transmembrane protein). [swissprot;acc:p58872] Low confidence 23239.9 21503.3 1.08076
178 bax inhibitor-1 (bi-1) (testis enhanced gene transcript). [swissprot;acc:p55061]
myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] High confidence 21591.5 27904.5 1.29238
179 f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] Low confidence 7004.28 7569.94 1.08076
myosin vc (myosin 5c). [swissprot;acc:q9nqx4] High confidence 21591.5 27904.5 1.29238
180 myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]
rhomboid-related protein 1 (ec 3.4.21.-) (rrp) (rhomboid-like protein 1). [swissprot;acc:o75783] Low confidence 23239.9 21503.3 1.08076
181 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] High confidence 4068.56 5252.6 1.29102
presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Low confidence 7004.28 7569.94 1.08076

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/