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 [...,...].
Rank Gene Value Type description Network Comparison Type Filtered Interaction Map red green network_comparison
Results: HTML CSV LaTeX Showing element 930 to 979 of 12912 in total
Network Comparison Type  : Divided
Filtered  : 1
Interaction Map  : High confidence
Rank
Value Type
description
red
green
network_comparison
233 Ranked lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] 239.32 267.842 1.11918
Squared map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137] 42411.6 55802.1 1.31573
Rooted melanoma antigen, family b, 6. [refseq;acc:nm_173523] 137.446 120.823 1.13758
234 Measured ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] 5181.2 6410.58 1.23728
Ranked chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] 287.41 256.835 1.11905
Squared neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825] 42411.6 55802.1 1.31573
Rooted melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] 137.446 120.823 1.13758
235 Measured ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] 5181.2 6410.58 1.23728
Ranked phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] 227.357 254.15 1.11785
Squared nitrogen fixation cluster-like. [refseq;acc:nm_014301] 42411.6 55802.1 1.31573
Rooted melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] 137.446 120.823 1.13758
236 Measured spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] 4723.53 5828.46 1.23392
Ranked pp3111 protein. [refseq;acc:nm_022156] 227.357 254.15 1.11785
Squared star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8] 42411.6 55802.1 1.31573
Rooted melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] 137.446 120.823 1.13758
237 Measured u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] 4567.04 5631.2 1.23301
Ranked syntaxin 18. [swissprot;acc:q9p2w9] 227.357 254.15 1.11785
Squared star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502] 42411.6 55802.1 1.31573
Rooted melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] 137.446 120.823 1.13758
238 Measured protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] 27642.5 22440.4 1.23182
Ranked rd protein. [swissprot;acc:p18615] 227.357 254.15 1.11785
Squared neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822] 42411.6 55802.1 1.31573
Rooted melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] 137.446 120.823 1.13758
239 Measured carboxypeptidase b precursor. [refseq;acc:nm_020361] 7711.38 6265.8 1.23071
Ranked glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] 227.357 254.15 1.11785
Squared mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] 42411.6 55802.1 1.31573
Rooted melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] 137.446 120.823 1.13758
240 Measured mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] 7711.36 6265.79 1.23071
Ranked androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] 227.357 254.15 1.11785
Squared mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [swissprot;acc:q16539] 42411.6 55802.1 1.31573
Rooted melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] 137.446 120.823 1.13758
241 Measured plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] 7711.31 6265.76 1.23071
Ranked atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] 227.357 254.15 1.11785
Squared neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] 42411.6 55802.1 1.31573
Rooted melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] 137.446 120.823 1.13758
242 Measured max protein. [swissprot;acc:p25912] 4640.26 5704.87 1.22943
Ranked j domain containing protein 1. [swissprot;acc:q9ukb3] 227.357 254.15 1.11785
Squared neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] 42411.6 55802.1 1.31573
Rooted 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] 137.446 120.823 1.13758
243 Measured homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] 4246.95 5208.98 1.22652
Ranked sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] 227.357 254.15 1.11785
Squared sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0] 42411.6 55802.1 1.31573
Rooted trophinin. [swissprot;acc:q12816] 137.446 120.823 1.13758
244 Measured ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] 4250.14 5211.25 1.22614
Ranked ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] 227.357 254.15 1.11785
Squared dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] 14728.8 19330.8 1.31245
Rooted myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] 146.94 167.046 1.13683
245 Measured homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] 4251.65 5212.33 1.22595
Ranked small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] 226.109 202.333 1.11751
Squared 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 8875.01 6768.05 1.31131

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/