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 2062 to 2111 of 8289 in total
Value Type  : Measured
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
1031 membrane protein expressed in epithelial-like lung adenocarcinoma. [refseq;acc:nm_024792] High confidence 6136.99 6714.98 1.09418
1032 2-oxoglutarate dehydrogenase e1 component, mitochondrial precursor (ec 1.2.4.2) (alpha-ketoglutarate dehydrogenase). [swissprot;acc:q02218] Low confidence 8029.13 8332.97 1.03784
ran binding protein 11. [refseq;acc:nm_016338] High confidence 6138.91 6717.05 1.09418
1033 fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] 6080.91 6653.52 1.09417
inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268] Low confidence 8176.71 8486.04 1.03783
1034 s-adenosylmethionine synthetase alpha and beta forms (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-i/iii). [swissprot;acc:q00266] High confidence 6152.88 6732.12 1.09414
u5 snrnp-associated 102 kda protein (u5-102 kda protein). [swissprot;acc:o94906] Low confidence 7721.24 8013.26 1.03782
1035 casein kinase i, delta isoform (ec 2.7.1.-) (cki-delta) (ckid). [swissprot;acc:p48730] High confidence 5054.73 5530.23 1.09407
vesicle transport-related protein isoform a; vesicle transport-related protein. [refseq;acc:nm_016106] Low confidence 8054.13 8358.75 1.03782
1036 dna polymerase gamma subunit 1 (ec 2.7.7.7) (mitochondrial dna polymerase catalytic subunit) (polg-alpha). [swissprot;acc:p54098] 8023.84 8327.22 1.03781
fructose-1,6-bisphosphatase (ec 3.1.3.11) (d-fructose-1,6-bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:p09467] High confidence 6077.65 6649.22 1.09404
1037 inositol-1(or 4)-monophosphatase (ec 3.1.3.25) (impase) (imp) (inositol monophosphatase) (lithium-sensitive myo-inositol monophosphatase a1). [swissprot;acc:p29218] Low confidence 7811.62 8106.99 1.03781
monoglyceride lipase; lysophospholipase-like. [refseq;acc:nm_007283] High confidence 6544.26 7159.43 1.094
1038 guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] Low confidence 7722.06 8014.04 1.03781
myb proto-oncogene protein (c-myb). [swissprot;acc:p10242] High confidence 5417.95 5924.41 1.09348
1039 guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] Low confidence 7722.06 8014.04 1.03781
myb-related protein b (b-myb). [swissprot;acc:p10244] High confidence 5418.92 5923.09 1.09304
1040 inosine-5'-monophosphate dehydrogenase 1 (ec 1.1.1.205) (imp dehydrogenase 1) (impdh-i) (impd 1). [swissprot;acc:p20839] Low confidence 8176.07 8485.02 1.03779
rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] High confidence 5421.93 5926.08 1.09298
1041 cerebral cell adhesion molecule. [refseq;acc:nm_016174] Low confidence 8151.65 8459.61 1.03778
myb-related protein a (a-myb). [swissprot;acc:p10243] High confidence 5419.18 5922.84 1.09294
1042 pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803] Low confidence 8193.63 8503 1.03776
similar to lim domain only 7 (fragment). [sptrembl;acc:q8n6m2] High confidence 5887.52 6434.32 1.09287
1043 15 kda selenoprotein precursor. [swissprot;acc:o60613] 6344.41 6933.36 1.09283
guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4] Low confidence 8193.38 8502.66 1.03775
1044 mbd2 (methyl-cpg-binding protein)-interacting zinc finger protein. [refseq;acc:nm_015517] High confidence 4757.46 5198.91 1.09279
vesicle trafficking protein sec22b. [refseq;acc:nm_004892] Low confidence 7977.77 8278.9 1.03775
1045 doublesex and mab-3 related transcription factor 3; testis-specific protein; dmrt-like family a3. [refseq;acc:nm_021240] 8193.38 8502.66
immature colon carcinoma transcript 1 (digestion substraction 1) (ds- 1). [swissprot;acc:q14197] High confidence 5364.32 5862.09 1.09279
1046 pyruvate dehydrogenase e1 component alpha subunit, somatic form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type i). [swissprot;acc:p08559] Low confidence 8193.14 8502.35 1.03774
skeletal muscle tropomodulin (sk-tmod) (tropomodulin 4). [swissprot;acc:q9nzq9] High confidence 4757.46 5198.91 1.09279
1047 krueppel-like factor 12 (transcriptional repressor ap-2rep) (hspc122). [swissprot;acc:q9y4x4] Low confidence 8229.78 8540.18 1.03772
ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9] High confidence 4757.46 5198.91 1.09279
1048 adapter-related protein complex 1 beta 1 subunit (beta-adaptin 1) (adaptor protein complex ap-1 beta-1 subunit) (golgi adaptor ha1/ap1 adaptin beta subunit) (clathrin assembly protein complex 1 beta large chain). [swissprot;acc:q10567] Low confidence 7724.96 8016.23 1.03771
tropomodulin 1 (erythrocyte tropomodulin) (e-tmod). [swissprot;acc:p28289] High confidence 4757.46 5198.91 1.09279
1049 anaphase-promoting complex subunit 10; anaphase-promoting complex 10. [refseq;acc:nm_014885] Low confidence 7454.43 7735.48 1.0377
sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1] High confidence 4757.46 5198.91 1.09279
1050 glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [swissprot;acc:p15104] Low confidence 7874.58 8171.49 1.0377
neuronal tropomodulin (n-tmod) (tropomodulin 2). [swissprot;acc:q9nzr1] High confidence 4757.46 5198.91 1.09279
1051 17 beta-hydroxysteroid dehydrogenase. [sptrembl;acc:q13034] Low confidence 8189.31 8498.04 1.0377
homeobox protein dlx-2. [swissprot;acc:q07687] High confidence 4757.46 5198.91 1.09279
1052 estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [swissprot;acc:p14061] Low confidence 8189.19 8497.86 1.03769
homeobox protein dlx-5. [swissprot;acc:p56178] High confidence 4757.46 5198.91 1.09279
1053 fetal brain protein 239 (239fb). [swissprot;acc:q15777]
krueppel-like factor 8 (zinc finger protein 741) (basic kruppel-like factor 3). [swissprot;acc:o95600] Low confidence 8228.43 8538.56 1.03769
1054 homeobox protein dlx-3. [swissprot;acc:o60479] High confidence 4757.46 5198.91 1.09279
speckle-type poz protein. [swissprot;acc:o43791] Low confidence 8125.84 8432 1.03768
1055 activated p21cdc42hs kinase. [refseq;acc:nm_005781] High confidence 4757.46 5198.91 1.09279
kruppel-like factor 3 (basic kruppel-like factor) (caccc-box binding protein bklf) (tef-2). [swissprot;acc:p57682] Low confidence 8228.22 8538.3 1.03768
1056 mitogen-activated protein kinase kinase kinase 7 interacting protein 2 isoform 1; tak1-binding protein 2. [refseq;acc:nm_015093] High confidence 4757.46 5198.91 1.09279

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/