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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Gene Rank description Network Comparison Type Value Type Interaction Map Filtered green network_comparison red
Results: HTML CSV LaTeX Showing element 425 to 474 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
Value Type
green
network_comparison
red
54 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Subtracted Ranked 245.247 59.569 185.678
deltex 2. [refseq;acc:nm_020892] Divided Measured 2651.88 1.63814 1618.84
exocyst complex component sec5. [swissprot;acc:q96kp1] Subtracted 19288.8 4027.2 23316
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Squared 242989 69581 173408
melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Divided 129762 1.68808 219048
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Subtracted Rooted 120.823 16.623 137.446
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Divided 58.7986 1.46645 40.0958
transcription factor jun-d. [swissprot;acc:p17535] Ranked 158.941 1.26425 200.941
55 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Measured 2662.12 1.63399 1629.21
glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Subtracted Ranked 245.247 59.569 185.678
hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] Divided Squared 129762 1.68808 219048
homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Subtracted 242989 69581 173408
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Rooted 120.823 16.623 137.446
poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] Measured 19279.5 4023.6 23303.1
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Divided Rooted 28.9323 1.44038 41.6734
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Ranked 254.434 1.26134 320.927
56 cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] Rooted 28.9509 1.43986 41.6851
glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Subtracted Ranked 245.247 59.569 185.678
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] Divided 336.233 1.25998 266.856
homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Subtracted Squared 242989 69581 173408
melanoma antigen, family b, 6. [refseq;acc:nm_173523] Rooted 120.823 16.623 137.446
melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Divided Squared 129762 1.68808 219048
ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Subtracted Measured 24908.5 3997.5 20911
t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] Divided 2664.55 1.63302 1631.67
57 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] Ranked 336.233 1.25998 266.856
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Subtracted Squared 242989 69581 173408
kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Divided Measured 2664.55 1.63302 1631.67
melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Squared 129762 1.68808 219048
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Subtracted Rooted 120.823 16.623 137.446
myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Ranked 245.247 59.569 185.678
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] Divided Rooted 28.9554 1.43973 41.6879
ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] Subtracted Measured 24908.5 3997.5 20911
58 glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Ranked 245.247 59.569 185.678
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Divided 336.191 1.25979 266.863
kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Measured 2664.55 1.63302 1631.67
melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Squared 129762 1.68808 219048
melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Subtracted Rooted 120.823 16.623 137.446
potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Divided 28.9696 1.43933 41.6969
ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Subtracted Measured 24908.5 3997.5 20911
retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Squared 242989 69581 173408
59 anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] Measured 24908.5 3997.5 20911
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] Divided Ranked 336.19 1.25978 266.863
hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Squared 129762 1.68808 219048
kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Measured 2664.55 1.63302 1631.67
melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Subtracted Rooted 120.823 16.623 137.446
nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] Divided 52.2064 1.40262 37.2205
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Subtracted Ranked 327.709 58.431 269.278
serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Squared 130021 69573 199594
60 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Divided Measured 2765.82 1.6231 4489.19
cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] Subtracted Ranked 327.655 58.401 269.254

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/