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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 [...,...].
Gene Rank description Value Type Network Comparison Type Interaction Map red Filtered network_comparison green
Results: HTML CSV LaTeX Showing element 3682 to 3731 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
network_comparison
green
461 bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [swissprot;acc:o95817] Rooted Subtracted 55.1867 5.3655 60.5522
grb2-related adaptor protein. [swissprot;acc:q13588] Measured Divided 5986.65 1.14683 6865.68
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] Ranked 223.648 1.0772 207.62
presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Measured Subtracted 2353.63 872.02 3225.65
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] Ranked 186.52 16.1 170.42
solute carrier family 13, member 4 (na+/sulfate cotransporter sut-1). [swissprot;acc:q9ukg4] Squared 26867.2 5467.8 32335
utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] Divided 29544.1 1.20763 35678.3
462 40s ribosomal protein s3. [swissprot;acc:p23396] Rooted 50.6274 1.09498 46.236
dna-directed rna polymerases i, ii, and iii 17.1 kda polypeptide (ec 2.7.7.6) (rpb17) (rpb8) (rpabc3). [swissprot;acc:p52434] Ranked Subtracted 236.662 16.046 252.708
mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] Divided 254.434 1.07709 236.224
nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] Rooted Subtracted 49.0526 5.3255 54.3781
ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858] Measured Divided 11383.2 1.14674 9926.61
s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] Subtracted 2353.63 872.02 3225.65
solute carrier family 13, member 1 (renal sodium/sulfate cotransporter) (na(+)/sulfate cotransporter) (hnasi-1). [swissprot;acc:q9bzw2] Squared 26867.2 5467.8 32335
ubiquitin-conjugating enzyme e2 variant 2; 1 alpha,25-dihydroxyvitamin d3-inducible; enterocyte differentiation promoting factor; methyl methanesulfonate sensitive 2, s. cerevisiae, homolog of. [refseq;acc:nm_003350] Divided 29540.4 1.20759 35672.6
463 atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1] Measured 3720.18 1.1463 4264.46
calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [swissprot;acc:p98194] Squared 25533.3 1.20669 30810.8
dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9] Ranked 238.921 1.07704 257.327
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] Measured Subtracted 2353.63 872.02 3225.65
nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] Rooted 68.8243 5.3253 74.1496
rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749] Divided 50.2317 1.09498 55.0025
secretory carrier-associated membrane protein 1. [swissprot;acc:o15126] Squared Subtracted 26866.1 5467.1 32333.2
splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] Ranked 223.648 16.028 207.62
464 ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6] Divided 210.578 1.07686 226.764
cullin homolog 2 (cul-2). [swissprot;acc:q13617] Measured Subtracted 2353.63 872.02 3225.65
histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] Divided 4858.96 1.1461 5568.85
homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [swissprot;acc:q03014] Squared 54726.7 1.20654 45358.5
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] Ranked Subtracted 223.648 16.028 207.62
nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] Rooted 68.8237 5.3247 74.1484
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 50.2317 1.09498 55.0025
secretory carrier-associated membrane protein 2. [swissprot;acc:o15127] Squared Subtracted 26865.9 5467 32332.9
465 inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [refseq;acc:nm_001564] Ranked 224.662 16.011 240.673
neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] Divided 248.152 1.07686 267.226
nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] Rooted Subtracted 68.8197 5.3216 74.1413
presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Measured 2353.63 872.02 3225.65
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] Rooted Divided 50.2317 1.09498 55.0025
secretory carrier-associated membrane protein 3. [swissprot;acc:o14828] Squared Subtracted 26865.9 5467 32332.9
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] Measured Divided 3847.31 1.14605 4409.22
trna isopentenylpyrophosphate transferase. [refseq;acc:nm_017646] Squared 25310.2 1.20651 30537
466 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] Ranked 248.152 1.07686 267.226
cullin homolog 1 (cul-1). [swissprot;acc:q13616] Measured Subtracted 2353.63 872.02 3225.65
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 26859 5462.2 32321.2
pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Ranked 225.661 16.01 209.651
probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] Squared Divided 25513.6 1.2064 30779.5
suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] Rooted Subtracted 49.4233 5.3094 54.7327
transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] Measured Divided 3847.31 1.14605 4409.22
vav-3 protein. [swissprot;acc:q9ukw4] Rooted 66.089 1.09482 72.3555
467 40s ribosomal protein s5. [swissprot;acc:p46782] 50.4649 1.09446 46.1093
adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] Ranked 248.152 1.07686 267.226
dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] Subtracted 248.56 15.981 232.579

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/