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 Filtered Interaction Map green red network_comparison
Results: HTML CSV LaTeX Showing element 151 to 200 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
green
red
network_comparison
76 db83 protein. [swissprot;acc:p57088] High confidence 362 288 1.25694
nipsnap1 protein. [swissprot;acc:q9bpw8] Low confidence 226.86 249.584 1.10017
77 putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2] 215.424 195.851 1.09994
voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] High confidence 202.668 254.692 1.2567
78 malignant cell expression-enhanced gene/tumor progression-enhanc. [refseq;acc:nm_024298] Low confidence 231.635 211 1.0978
voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] High confidence 202.668 254.693 1.2567
79 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 208.803 229.144 1.09742
voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] High confidence 202.668 254.693 1.2567
80 rad50-interacting protein 1. [refseq;acc:nm_021930] Low confidence 202.005 221.194 1.09499
voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] High confidence 202.668 254.691 1.25669
81 transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] Low confidence 208.281 227.623 1.09286
voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] High confidence 202.646 254.614 1.25645
82 diacylglycerol kinase, eta isoform 1. [refseq;acc:nm_152910] Low confidence 208.077 226.981 1.09085
guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] High confidence 335.359 267.636 1.25304
83 diacylglycerol kinase, delta (ec 2.7.1.107) (diglyceride kinase) (dgk-delta) (dag kinase delta) (130 kda diacylglycerol kinase) (fragment). [swissprot;acc:q16760] Low confidence 208.077 226.981 1.09085
melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] High confidence 110.265 88.2482 1.24949
84 hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]
transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] Low confidence 207.874 226.338 1.08882
85 melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] High confidence 110.265 88.2482 1.24949
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Low confidence 245.308 225.735 1.08671
86 dna fragmentation factor 40 kda subunit (ec 3.-.-.-) (dff-40) (caspase-activated deoxyribonuclease) (caspase-activated dnase) (cad) (caspase-activated nuclease) (cpan). [swissprot;acc:o76075] 215.309 233.922 1.08645
melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] High confidence 110.265 88.2482 1.24949
87 melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]
potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980] Low confidence 244.933 225.545 1.08596
88 hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] High confidence 110.265 88.2482 1.24949
potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Low confidence 244.701 225.428 1.0855
89 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] High confidence 110.265 88.2482 1.24949
star-related lipid transfer protein 7 (stard7) (start domain- containing protein 7) (gtt1 protein). [swissprot;acc:q9nqz5] Low confidence 210.764 228.743 1.0853
90 necdin. [swissprot;acc:q99608] High confidence 110.265 88.2482 1.24949
tbp-associated factor 2; taf2 rna polymerase ii, tata box binding protein (tbp)-associated factor, 150 kd; tata box binding protein (tbp)-associated factor, rna polymerase ii, b, 150kd; cofactor of initiator function, 150kd subunit. [refseq;acc:nm_003184] Low confidence 219.229 237.567 1.08365
91 melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] High confidence 110.265 88.2482 1.24949
oligophrenin 1. [swissprot;acc:o60890] Low confidence 215.973 233.837 1.08271
92 melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] High confidence 110.265 88.2482 1.24949
oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1] Low confidence 215.846 233.592 1.08222
93 dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] 228.84 247.334 1.08082
melanoma antigen, family b, 6. [refseq;acc:nm_173523] High confidence 110.265 88.2482 1.24949
94 melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]
ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Low confidence 228.693 247.087 1.08043
95 amino acid transporter xat2; likely ortholog of mouse aspartate/glutamate transporter 1 (agt1). [refseq;acc:nm_138817] 185.679 200.497 1.0798
melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] High confidence 110.265 88.2482 1.24949
96 melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]
y+l amino acid transporter 1 (y(+)l-type amino acid transporter 1) (y+lat-1) (y+lat1) (monocyte amino acid permease 2) (mop-2). [swissprot;acc:q9um01] Low confidence 185.679 200.497 1.0798
97 cystine/glutamate transporter (amino acid transport system xc-) (xct) (calcium channel blocker resistance protein ccbr1). [swissprot;acc:q9upy5]
melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] High confidence 110.265 88.2482 1.24949
98 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]
solute carrier family 7 (cationic amino acid transporter, y+ system), member 6. [refseq;acc:nm_003983] Low confidence 185.679 200.497 1.0798
99 eukaryotic translation initiation factor 4b (eif-4b). [swissprot;acc:p23588]
melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] High confidence 110.265 88.2482 1.24949
100 b(0,+)-type amino acid transporter 1 (b(0,+)at) (glycoprotein- associated amino acid transporter b0,+at1). [swissprot;acc:p82251] Low confidence 185.679 200.497 1.0798
melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] High confidence 110.265 88.2482 1.24949

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/