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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Filtered Gene Rank Network Comparison Type description green network_comparison Value Type Interaction Map red
Results: HTML CSV LaTeX Showing element 601 to 650 of 38536 in total
Filtered  : 0
Network Comparison Type  : Divided
Rank
description
green
network_comparison
Value Type
Interaction Map
red
76 cab2. [refseq;acc:nm_033419] 128.776 1.77407 Measured Low confidence 72.5877
dead-box protein. [refseq;acc:nm_018665] 183 1.71403 High confidence 313.667
phosphatase and tensin homolog 2 (fragment). [sptrembl;acc:o43460] 15.6032 1.35616 Rooted Low confidence 11.5054
prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765] 57.5264 2.83112 Squared High confidence 20.3193
protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0] 0.0318343 2.9145 Low confidence 0.092781
spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813] 2695 1.28905 Ranked High confidence 3474
testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [swissprot;acc:p16562] 13.6105 1.35766 Rooted 10.025
ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] 12345.3 1.23945 Ranked Low confidence 9960.27
77 adenosine deaminase (ec 3.5.4.4) (adenosine aminohydrolase). [swissprot;acc:p00813] 13871.6 1.23278 11252.3
amiloride-sensitive cation channel 3 isoform a; testis sodium channel 1; proton-gated cation channel subunit; modulatory subunit of asic2a; amiloride-sensitive cation channel 3, testis. [refseq;acc:nm_004769] 17.0377 2.86254 Squared 5.95196
bromodomain adjacent to zinc finger domain protein 1a (atp-utilizing chromatin assembly and remodeling factor 1) (hacf1) (atp-dependent chromatin remodelling protein) (williams syndrome transcription factor-related chromatin remodeling factor 180) (wcrf180) (hwalp1) (chrac subunit acf1) (hspc317). [swissprot;acc:q9nrl2] 8.62956 1.3559 Rooted 11.7008
dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] 2804 1.7602 Measured 1593
elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897] 917.917 2.79146 Squared High confidence 328.83
inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268] 416.524 1.70956 Measured 712.071
regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754] 11366.5 1.28853 Ranked 8821.32
tigger transposable element derived 6. [refseq;acc:nm_030953] 17.6725 1.35313 Rooted 13.0605
78 amiloride-sensitive sodium channel gamma-subunit (epithelial na+ channel gamma subunit) (gamma enac) (nonvoltage-gated sodium channel 1 gamma subunit) (scneg) (gamma nach). [swissprot;acc:p51170] 17.0364 2.86222 Squared Low confidence 5.95216
histone-lysine n-methyltransferase, h3 lysine-79 specific (ec 2.1.1.43) (histone h3-k79 methyltransferase) (h3-k79-hmtase) (dot1-like protein). [swissprot;acc:q8tek3] 13236 1.23114 Ranked 10751
low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] 95 1.69474 Measured High confidence 161
maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168] 8.89934 1.35589 Rooted Low confidence 12.0665
protein tyrosine phosphatase type iva, member 2 isoform 1; protein tyrosine phosphatase iva2; protein tyrosine phosphatase iva; phosphatase of regenerating liver 2. [refseq;acc:nm_003479] 112.5 1.68 Measured 189
repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] 9706.12 1.27969 Ranked High confidence 7584.72
tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208] 17.6565 1.35273 Rooted 13.0525
transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084] 0.591716 2.77777 Squared 0.213018
79 glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] 572.008 1.67507 Measured Low confidence 341.484
melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] 17020.5 1.23109 Ranked 13825.5
nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] 12106.5 1.27901 High confidence 9465.55
peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] 1088.19 2.74107 Squared 396.995
polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393] 544.991 1.68316 Measured 323.79
tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702] 17.6559 1.35271 Rooted 13.0522
transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084] 0.591716 2.77777 Squared Low confidence 0.213018
wd-repeat protein 5 (wd-repeat protein big-3). [swissprot;acc:q9ugp9] 7.54566 1.35397 Rooted 10.2166
80 abl-philin 2. [refseq;acc:nm_032327] 0.199053 2.7396 Squared 0.545325
acrc protein; putative nuclear protein. [refseq;acc:nm_052957] 32.7593 1.35212 Rooted High confidence 44.2946
alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] 12.3132 1.35362 Low confidence 16.6674
deltex homolog 1; hdx-1. [refseq;acc:nm_004416] 11617.9 1.27636 Ranked High confidence 9102.34
melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] 17020.5 1.23109 Low confidence 13825.5
prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765] 493 1.68259 Measured High confidence 293
rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [swissprot;acc:p31150] 2589.83 2.71164 Squared 955.08
transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084] 50 1.66667 Measured Low confidence 30
81 fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] 40.2058 1.34951 Rooted High confidence 54.2583
melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] 17020.5 1.23109 Ranked Low confidence 13825.5
peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] 925.387 2.739 Squared 337.856
polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393] 123.721 2.69156 High confidence 45.9662
selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] 11356 1.2736 Ranked 14463
tigger transposable element derived 6. [refseq;acc:nm_030953] 17.6725 1.35313 Rooted Low confidence 13.0605
tolloid-like 1. [refseq;acc:nm_012464] 688.237 1.66614 Measured 413.072
transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084] 50 1.66667 High confidence 30
82 60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268] 141.849 2.63788 Squared 374.181
dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] 6058 1.27212 Ranked 7706.5

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/