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 description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 7412 to 7461 of 66312 in total
Filtered  : 1
Rank
description
Network Comparison Type
Value Type
Interaction Map
red
green
network_comparison
464 homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [swissprot;acc:q03014] Divided Squared High confidence 54726.7 45358.5 1.20654
huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Subtracted Ranked Low confidence 201.418 194.664 6.754
krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887] High confidence 223.648 207.62 16.028
mitochondrial ribosome recycling factor. [refseq;acc:nm_138777] Squared Low confidence 50615.7 47730.3 2885.4
nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] Rooted High confidence 68.8237 74.1484 5.3247
pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] Divided Measured Low confidence 7847.59 8240.61 1.05008
proton/amino acid transporter 4. [refseq;acc:nm_152313] Subtracted Rooted 77.9895 81.2715 3.282
rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [swissprot;acc:q9y243] Divided High confidence 50.2317 55.0025 1.09498
ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] Squared Low confidence 51553.8 54890.2 1.06472
rna polymerase ii elongation factor ell2. [swissprot;acc:o00472] Ranked 198.618 205.369 1.03399
rna-binding protein. [refseq;acc:nm_019027] Rooted 71.0964 74.3634 1.04595
secretory carrier-associated membrane protein 2. [swissprot;acc:o15127] Subtracted Squared High confidence 26865.9 32332.9 5467
u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] Measured Low confidence 7831.81 8229.98 398.17
465 apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] Divided Rooted 71.0968 74.3631 1.04594
apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] Subtracted Squared 48743.4 45860 2883.4
c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] Divided Ranked 207.812 200.994 1.03392
deltex 2. [refseq;acc:nm_020892] Squared 43977.9 41304.5 1.06472
inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [refseq;acc:nm_001564] Subtracted Ranked High confidence 224.662 240.673 16.011
neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] Divided 248.152 267.226 1.07686
ns1-associated protein 1. [refseq;acc:nm_006372] Subtracted Rooted Low confidence 71.089 74.3682 3.2792
nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] High confidence 68.8197 74.1413 5.3216
presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Measured 2353.63 3225.65 872.02
rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [swissprot;acc:p31751] Divided Rooted 50.2317 55.0025 1.09498
rna polymerase ii elongation factor ell2. [swissprot;acc:o00472] Subtracted Ranked Low confidence 198.618 205.369 6.751
secretory carrier-associated membrane protein 3. [swissprot;acc:o14828] Squared High confidence 26865.9 32332.9 5467
serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537] Divided Measured Low confidence 7580.97 7960.37 1.05005
thimet oligopeptidase (ec 3.4.24.15) (endopeptidase 24.15) (mp78). [swissprot;acc:p52888] Subtracted 8651.4 9048.97 397.57
transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094] Divided High confidence 3847.31 4409.22 1.14605
trna isopentenylpyrophosphate transferase. [refseq;acc:nm_017646] Squared 25310.2 30537 1.20651
466 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] Ranked 248.152 267.226 1.07686
aryl-hydrocarbon interacting protein-like 1. [swissprot;acc:q9nzn9] Subtracted Squared Low confidence 49597.9 46718.7 2879.2
chromosome x open reading frame 9; likely ortholog of mouse sh3 gene sly. [refseq;acc:nm_018990] Ranked 204.331 211.075 6.744
cullin homolog 1 (cul-1). [swissprot;acc:q13616] Measured High confidence 2353.63 3225.65 872.02
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] Divided Ranked Low confidence 207.812 200.994 1.03392
lu1 protein. [refseq;acc:nm_032512] Squared 46292.3 43478.2 1.06472
neurolysin, mitochondrial precursor (ec 3.4.24.16) (neurotensin endopeptidase) (mitochondrial oligopeptidase m) (microsomal endopeptidase) (mep). [swissprot;acc:q9byt8] Subtracted Measured 8651.4 9048.97 397.57
phosphatidate cytidylyltransferase 2 (ec 2.7.7.41) (cdp-diglyceride synthetase 2) (cdp-diglyceride pyrophosphorylase 2) (cdp- diacylglycerol synthase 2) (cds 2) (ctp:phosphatidate cytidylyltransferase 2) (cdp-dag synthase 2) (cdp-dg synthetase 2). [swissprot;acc:o95674] Squared High confidence 26859 32321.2 5462.2
pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Ranked 225.661 209.651 16.01
probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] Divided Squared 25513.6 30779.5 1.2064
rna 3'-terminal phosphate cyclase-like protein (hspc338). [swissprot;acc:q9y2p8] Rooted Low confidence 71.0763 74.3418 1.04594
splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] Subtracted 73.2805 76.558 3.2775
suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] High confidence 49.4233 54.7327 5.3094
transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] Divided Measured 3847.31 4409.22 1.14605
vav-3 protein. [swissprot;acc:q9ukw4] Rooted 66.089 72.3555 1.09482
yippee-like protein 2 (digeorge syndrome-related protein fksg4). [swissprot;acc:q96qa6] Measured Low confidence 8941.56 9388.99 1.05004
467 40s ribosomal protein s5. [swissprot;acc:p46782] Rooted High confidence 50.4649 46.1093 1.09446
adapter-related protein complex 1 gamma 2 subunit (gamma2-adaptin) (adaptor protein complex ap-1 gamma-2 subunit) (g2ad). [swissprot;acc:o75843] Low confidence 69.8743 73.0794 1.04587
adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] Ranked High confidence 248.152 267.226 1.07686
ah receptor-interacting protein (aip) (immunophilin homolog ara9) (hbv-x associated protein 2). [swissprot;acc:o00170] Subtracted Squared Low confidence 49588.5 46710.7 2877.8
dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] Ranked High confidence 248.56 232.579 15.981

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/