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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Gene Rank description Value Type Network Comparison Type Filtered Interaction Map green red network_comparison
Results: HTML CSV LaTeX Showing element 551 to 600 of 9634 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Rank
description
Filtered
Interaction Map
green
red
network_comparison
138 transgelin 2 (sm22-alpha homolog). [swissprot;acc:p37802] 1 Low confidence 205.4 218.36 1.0631
zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782] 0 7516 8730 1.16152
139 alpha crystallin a chain. [swissprot;acc:p02489] High confidence 13972.2 16372.4 1.17178
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] 1 225.68 271.752 1.20415
glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] 0 Low confidence 10962.4 12716.5 1.16001
testican-1 precursor (spock protein). [swissprot;acc:q08629] 1 234.111 220.254 1.06291
140 mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] 0 High confidence 14027.1 16411.9 1.17001
ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] 1 49 59 1.20408
spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6] 0 Low confidence 7533.54 6520.34 1.15539
testican-2 precursor. [swissprot;acc:q92563] 1 234.047 220.222 1.06278
141 probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] 0 High confidence 8991.19 7690.02 1.1692
ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] 1 49 59 1.20408
rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] Low confidence 206.52 219.344 1.0621
transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084] 0 15652 18079 1.15506
142 endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase (ec 3.2.1.113) (er alpha-1,2-mannosidase) (mannosidase alpha class 1b member 1) (man9glcnac2-specific processing alpha-mannosidase). [swissprot;acc:q9ukm7] 1 198.732 211.056 1.06201
ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] High confidence 49 59 1.20408
voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] 0 7026.41 8214.41 1.16908
zinc finger protein 183-like 1. [refseq;acc:nm_178861] Low confidence 12382.9 10720.7 1.15505
143 anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] 1 High confidence 49 59 1.20408
dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] 0 Low confidence 16782.2 14529.8 1.15502
dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959] High confidence 13005.3 11124.8 1.16904
presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] 1 Low confidence 198.732 211.056 1.06201
144 dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325] 0 High confidence 13000.1 11123.4 1.16872
f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] 1 Low confidence 198.732 211.056 1.06201
kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] High confidence 319.651 265.686 1.20312
l-lactate dehydrogenase a chain (ec 1.1.1.27) (ldh-a) (ldh muscle subunit) (ldh-m). [swissprot;acc:p00338] 0 Low confidence 16094.8 18586.3 1.1548
145 metaxin 1. [swissprot;acc:q13505] 12622.6 10935 1.15433
potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] 1 High confidence 319.546 265.639 1.20293
presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Low confidence 198.732 211.056 1.06201
sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] 0 High confidence 6817.49 7955.61 1.16694
146 coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] 14662.1 12577.8 1.16571
kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193] 1 319.531 265.632 1.20291
macrophage mannose receptor precursor (mmr) (cd206 antigen). [swissprot;acc:p22897] 0 Low confidence 9167.67 7966.03 1.15085
nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] 1 213.661 226.892 1.06193
147 60s ribosomal protein l7. [swissprot;acc:p18124] 0 High confidence 9505.89 11080.3 1.16562
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 1 42.3003 50.7983 1.2009
pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278] 0 Low confidence 9133.64 7942.9 1.14991
rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] 1 206.507 219.273 1.06182
148 dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] 0 9368.39 10771.7 1.14979
sad1/unc-84 protein-like 1. [swissprot;acc:o94901] 1 High confidence 247.559 296.677 1.19841
sentrin-specific protease 8 (ec 3.4.22.-) (sentrin/sumo-specific protease senp8) (cysteine protease fksg8). [swissprot;acc:q96ld8] Low confidence 198.33 210.579 1.06176
spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6] 0 High confidence 7863.63 6755.71 1.164
149 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 1 170 142 1.19718
block 23. [sptrembl;acc:q8nhw5] 0 13334.8 11469.3 1.16265
sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] Low confidence 8262.77 7190.64 1.1491
ubiquitin-like protein nedd8. [swissprot;acc:q15843] 1 198.33 210.579 1.06176
150 myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] High confidence 46 55 1.19565
serine/threonine-protein kinase plk (ec 2.7.1.-) (plk-1) (serine- threonine protein kinase 13) (stpk13). [swissprot;acc:p53350] Low confidence 194.554 206.516 1.06148
synaptosomal-associated protein 23 (snap-23) (vesicle-membrane fusion protein snap-23). [swissprot;acc:o00161] 0 12769.9 11125.4 1.14781
zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782] High confidence 7516 8730 1.16152

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/