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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3591 to 3640 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
Network Comparison Type
red
green
network_comparison
449 SHCBP1 likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] Rooted Subtracted 51.8714 46.3281 5.5433
WDR12 wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7] Measured Divided 3761.59 4319.69 1.14837
450 no value microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] Subtracted 5061.11 5950.22 889.11
ACACB acetyl-coa carboxylase 2 (ec 6.4.1.2) (acc-beta) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:o00763] Squared Divided 31646.1 38288.7 1.2099
CMPK ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] Rooted 50.4595 46.0411 1.09597
CSRP2 smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] Subtracted 51.8717 46.3287 5.543
ITM2A integral membrane protein 2a (e25 protein). [swissprot;acc:o43736] Squared 28657.6 34208.6 5551
MYCL1 l-myc-1 proto-oncogene protein. [swissprot;acc:p12524] Measured Divided 4889.21 5610.52 1.14753
NAV3 neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] Ranked Subtracted 223.801 207.549 16.252
SRP9 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Divided 235.94 218.837 1.07815
451 no value small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] Squared 17543.3 21222.5 1.20972
CSRP3 lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] Rooted Subtracted 51.8789 46.3416 5.5373
MRPL17 mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061] Divided 50.268 45.8663 1.09597
MYCN n-myc proto-oncogene protein. [swissprot;acc:p04198] Measured 4889.71 5610.69 1.14745
NAV2 neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [refseq;acc:nm_145117] Ranked Subtracted 223.79 207.539 16.251
NFKBIE nf-kappab inhibitor epsilon (nf-kappa-bie) (i-kappa-b-epsilon) (ikappabepsilon) (ikb-epsilon) (ikbe). [swissprot;acc:o00221] Squared 50724.5 45178.9 5545.6
POLR3C polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468] Ranked Divided 239.092 257.705 1.07785
TOB2 tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] Measured Subtracted 398.5 1281.5 883
452 no value adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] Rooted Divided 50.4595 46.0415 1.09596
ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] Ranked 224.161 207.972 1.07784
BECN1 beclin 1 (coiled-coil myosin-like bcl2-interacting protein) (protein gt197). [swissprot;acc:q14457] Squared Subtracted 59318.4 53788.1 5530.3
CBLB signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] Rooted 66.0911 71.6061 5.515
POLI polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] Ranked 221.522 205.286 16.236
SNRPF small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] Squared Divided 17543.3 21222.5 1.20972
TOB1 tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] Measured Subtracted 398.5 1281.5 883
ZNF622 zinc finger-like protein 9. [refseq;acc:nm_033414] Divided 3760.8 4315.06 1.14738
453 CBL cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] Rooted Subtracted 66.1583 71.6729 5.5146
DAB2IP dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] Measured 398.5 1281.5 883
MED22 surfeit locus protein 5. [swissprot;acc:q15528] Rooted Divided 50.4595 46.0413 1.09596
PPP6C serine/threonine protein phosphatase 6 (ec 3.1.3.16) (pp6). [swissprot;acc:o00743] Squared 31620.5 38250.7 1.20968
PSMC5 26s protease regulatory subunit 8 (proteasome subunit p45) (thyroid hormone receptor interacting protein 1) (trip1) (msug1 protein) (tat-binding protein homolog 10) (tbp10) (p45/sug). [swissprot;acc:p47210] Subtracted 59318.4 53788.1 5530.3
PXN paxillin. [swissprot;acc:p49023] Ranked 221.522 205.286 16.236
SLC45A2 membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9] Measured Divided 3760.8 4315.06 1.14738
SNRPA1 u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] Ranked 224.161 207.972 1.07784
454 no value 40s ribosomal protein s26. [swissprot;acc:p02383] 210.224 226.578 1.07779
guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915] Measured 3760.8 4315.06 1.14738
AK3 gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7] Rooted 50.4595 46.0412 1.09596
BCAS2 breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] Subtracted 61.1902 66.6503 5.4601
BCL3 b-cell lymphoma 3-encoded protein (bcl-3 protein). [swissprot;acc:p20749] Squared 50598.8 45106.3 5492.5
CPEB4 cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] Measured 398.5 1281.5 883
GRAP grb2-related adaptor protein. [swissprot;acc:q13588] Ranked 223.457 207.222 16.235
SAPS3 sporulation-induced transcript 4-associated protein. [refseq;acc:nm_018312] Squared Divided 31620.5 38250.7 1.20968
455 no value ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] Ranked Subtracted 224.161 207.972 16.189
ACACA acetyl-coa carboxylase 1 (ec 6.4.1.2) (acc-alpha) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:q13085] Squared Divided 31597.8 38216.9 1.20948
CDC5L cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253] Rooted Subtracted 61.1902 66.6503 5.4601
CPEB3 cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] Measured 398.5 1281.5 883
GABPA ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] Divided 4890.51 5610.95 1.14731
NFKB1 nuclear factor nf-kappa-b p105 subunit (dna-binding factor kbf1) (ebp- 1) [contains: nuclear factor nf-kappa-b p50 subunit]. [swissprot;acc:p19838] Squared Subtracted 50588.2 45100.2 5488
SCAPER zinc finger protein 291. [swissprot;acc:q9by12] Rooted Divided 50.4595 46.0413 1.09596
TIMM22 mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584] Ranked 210.225 226.578 1.07779

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
- Hugo is the HGNC identifier if it exists
- 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/