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 description Gene Network Comparison Type Interaction Map red Value Type network_comparison Filtered green
Results: HTML CSV LaTeX Showing element 3180 to 3229 of 19268 in total
Value Type  : Measured
Rank
description
Network Comparison Type
Interaction Map
red
network_comparison
Filtered
green
398 histone h2b.c (h2b/c). [swissprot;acc:q99880] Divided High confidence 2132.04 1.04078 0 2218.98
interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] Low confidence 135.294 1.10405 149.371
mus81 endonuclease. [refseq;acc:nm_025128] Subtracted 8847.94 431.89 1 9279.83
williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158] High confidence 112.666 29.036 0 141.702
xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] Divided 5084.26 1.16125 1 5904.1
399 dimethylaniline monooxygenase [n-oxide forming] 4 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 4) (fmo 4) (dimethylaniline oxidase 4). [swissprot;acc:p31512] Low confidence 7680.62 1.05272 8085.57
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Subtracted 863.737 118.779 0 744.958
myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] Divided High confidence 548.5 1.03981 527.5
neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] 5201.41 1.16109 1 4479.76
sh2-b homolog; likely ortholog of mouse sh2 domain-containing putative adapter sh2-b; sh2-b gamma signaling protein; sh2-b alpha signaling protein. [refseq;acc:nm_015503] Subtracted 107 29 0 78
similar to hepatocellular carcinoma-associated antigen hca557b. [refseq;acc:nm_145280] Low confidence 8847.94 431.89 1 9279.83
similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517] Divided 250.379 1.10398 0 226.797
u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] Subtracted High confidence 4633.92 938.93 1 5572.85
400 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] Divided 5201.41 1.16109 4479.76
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Subtracted 1834.73 938.837 895.893
hepatocellularcarcinoma-associated antigen hca557a. [refseq;acc:nm_015433] Low confidence 8847.94 431.89 9279.83
hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597] 1940.37 118.76 0 2059.13
mad protein (max dimerizer). [swissprot;acc:q05195] Divided 6970.25 1.05272 1 7337.73
myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] High confidence 548.5 1.03981 0 527.5
protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Subtracted 65.2968 27.6038 37.693
sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] Divided Low confidence 1326.18 1.10389 1201.37
401 adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] High confidence 5201.41 1.16109 1 4479.76
dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] Subtracted Low confidence 7559.1 430.76 7989.86
gdp-mannose pyrophosphorylase a; mannose-1-phosphate guanylyltransferase (gdp). [refseq;acc:nm_013335] Divided 10800.7 1.0527 10260
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Subtracted High confidence 1835.3 938.328 896.972
jm5 protein. [refseq;acc:nm_007075] Low confidence 981.333 118.157 0 1099.49
mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426] High confidence 1549.26 27.2 1522.06
myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Divided 548.5 1.03981 527.5
transcription factor mafg (v-maf musculoaponeurotic fibrosarcoma oncogene homolog g) (hmaf). [swissprot;acc:o15525] Low confidence 1277.86 1.10385 1410.56
402 alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298] Subtracted 8730.02 429.17 1 9159.19
arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] High confidence 6230.94 937.26 7168.2
leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] Divided 5201.41 1.16109 4479.76
lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893] Subtracted 12.6208 27.1855 0 39.8063
myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Divided 548.5 1.03981 527.5
putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] Low confidence 1643.27 1.10305 1812.61
sedlin. [swissprot;acc:o14582] Subtracted 181.896 117.98 299.876
squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] Divided 7934.21 1.05269 1 8352.26
403 fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] High confidence 5201.41 1.16109 4479.76
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Subtracted Low confidence 864.333 117.804 0 746.529
hepatocellularcarcinoma-associated antigen hca557a. [refseq;acc:nm_015433] Divided 2800 1.1028 2539
maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708] Subtracted High confidence 2290.09 25.72 2264.37
myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] Divided 548.5 1.03981 527.5
nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Subtracted Low confidence 7398.26 428.22 1 7826.48
ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] High confidence 6259.3 931.61 7190.91
seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [swissprot;acc:q9np81] Divided Low confidence 8853.13 1.05269 9319.56
404 adiponectin receptor 2. [refseq;acc:nm_024551] Subtracted 7170.39 428.16 7598.55
dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6] 1709.74 117.75 0 1591.99
importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] High confidence 7802.31 929.51 1 8731.82
kinesin-like protein kif23 (mitotic kinesin-like protein-1) (kinesin- like protein 5). [swissprot;acc:q02241] Divided Low confidence 10008.8 1.05265 9508.16
leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] High confidence 5201.41 1.16109 4479.76

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/