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 Network Comparison Type Value Type Interaction Map red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 7412 to 7461 of 29840 in total
Interaction Map  : High confidence
Rank
description
Network Comparison Type
Value Type
red
Filtered
green
network_comparison
464 ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] Divided Ranked 10076.4 0 9928.08 1.01494
cullin homolog 2 (cul-2). [swissprot;acc:q13617] Subtracted Measured 2353.63 1 3225.65 872.02
cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452] Squared 0.417515 0 0.742249 0.324734
histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] Divided Measured 4858.96 1 5568.85 1.1461
homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [swissprot;acc:q03014] Squared 54726.7 45358.5 1.20654
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] Subtracted Ranked 223.648 207.62 16.028
maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708] Divided Measured 2290.09 0 2264.37 1.01136
melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Subtracted Rooted 6.9282 7.14143 0.21323
nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] 68.8237 1 74.1484 5.3247
peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521] Divided Squared 18105.2 0 17795.2 1.01742
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] Rooted 50.2317 1 55.0025 1.09498
secretory carrier-associated membrane protein 2. [swissprot;acc:o15127] Subtracted Squared 26865.9 32332.9 5467
ubiquitin-conjugating enzyme e2-17 kda 3 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 3). [swissprot;acc:p47986] Ranked 15920 0 15780.2 139.8
465 alpha-nac protein. [sptrembl;acc:q9h009] Measured 147.221 151.122 3.901
forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] Squared 9.26264 9.58152 0.31888
homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Divided Measured 6323 6254.09 1.01102
inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [refseq;acc:nm_001564] Subtracted Ranked 224.662 1 240.673 16.011
melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Rooted 6.9282 0 7.14143 0.21323
neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] Divided Ranked 248.152 1 267.226 1.07686
nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] Subtracted Rooted 68.8197 74.1413 5.3216
orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466] Divided Squared 79185.5 0 77891.7 1.01661
presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Subtracted Measured 2353.63 1 3225.65 872.02
protein cgi-140 (protein ptd008) (my006 protein). [swissprot;acc:q9y284] Divided Rooted 48.2804 0 48.8876 1.01258
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] 50.2317 1 55.0025 1.09498
secretory carrier-associated membrane protein 3. [swissprot;acc:o14828] Subtracted Squared 26865.9 32332.9 5467
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 Measured 3847.31 4409.22 1.14605
transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724] Ranked 9482.68 0 9620.66 1.01455
Subtracted 137.98
trna isopentenylpyrophosphate transferase. [refseq;acc:nm_017646] Divided Squared 25310.2 1 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
aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448] Subtracted 15155.8 0 15031.7 124.1
aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468] Divided 1543 1521 1.01446
Rooted 78.4729 79.3914 1.0117
cullin homolog 1 (cul-1). [swissprot;acc:q13616] Subtracted Measured 2353.63 1 3225.65 872.02
hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Rooted 6.9282 0 7.14143 0.21323
huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076] Divided Squared 363053 369010 1.01641
interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] Subtracted 9.26264 9.58152 0.31888
ischemia/reperfusion inducible protein. [refseq;acc:nm_024640] Divided Measured 1467.74 1483.62 1.01082
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] Subtracted Squared 26859 1 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
sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] Subtracted Measured 793.778 0 796.85 3.072
suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] Rooted 49.4233 1 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
467 40s ribosomal protein s5. [swissprot;acc:p46782] 50.4649 46.1093 1.09446
adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] Ranked 248.152 267.226 1.07686
adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] Rooted 26.5153 0 26.8089 1.01107
dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] Subtracted Ranked 248.56 1 232.579 15.981
dok-like protein. [refseq;acc:nm_024872] Squared 0.289941 0 0 0.289941

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/