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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Rank Gene Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2958 to 3007 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
Network Comparison Type
red
green
network_comparison
370 Squared protein 4.1 (band 4.1) (p4.1) (epb4.1) (4.1r). [swissprot;acc:p11171] Divided 45986 56776.1 1.23464
Rooted grb2-related adaptor protein. [swissprot;acc:q13588] Subtracted 61.4282 68.0107 6.5825
methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [swissprot;acc:p50579] Divided 49.7435 45.0586 1.10397
371 Measured pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Subtracted 4855.46 5824.52 969.06
serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [swissprot;acc:o43464] Divided 5067.02 5926.46 1.16961
Ranked oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] Subtracted 186.172 166.661 19.511
ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] Divided 186.52 170.42 1.09447
Squared band 4.1-like protein 1 (neuronal protein 4.1) (4.1n). [swissprot;acc:q9h4g0] 45985.9 56776 1.23464
calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] Subtracted 29095.3 35337.6 6242.3
Rooted 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] 61.3383 67.8668 6.5285
zinc finger-like protein 9. [refseq;acc:nm_033414] Divided 49.3451 54.4606 1.10367
372 Measured probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] 5067 5926.17 1.16956
squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] Subtracted 4909.79 5878.79 969
Ranked polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467] 239.709 259.038 19.329
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] Divided 186.52 170.42 1.09447
Squared band 4.1-like protein 3 (4.1b) (differentially expressed in adenocarcinoma of the lung protein 1) (dal-1). [swissprot;acc:q9y2j2] 45986.7 56776.8 1.23464
ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] Subtracted 29335.6 35515.5 6179.9
Rooted membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9] Divided 49.3451 54.4606 1.10367
neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] Subtracted 61.3354 67.8623 6.5269
373 Measured probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] Divided 5066.99 5926.1 1.16955
u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] Subtracted 4682.88 5646.19 963.31
Ranked 60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7] Divided 242.37 265.255 1.09442
dynactin 4. [refseq;acc:nm_032486] Subtracted 233.142 252.253 19.111
Squared arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] 28863.2 35031.5 6168.3
band 4.1-like protein 2 (generally expressed protein 4.1) (4.1g). [swissprot;acc:o43491] Divided 45986 56776.1 1.23464
Rooted guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915] 49.3451 54.4606 1.10367
neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] Subtracted 61.3354 67.8621 6.5267
374 Measured homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] 4246.95 5208.98 962.03
serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] Divided 5066.93 5925.38 1.16942
Ranked neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] Subtracted 248.152 267.226 19.074
transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] Divided 267.208 244.168 1.09436
Squared electron transfer flavoprotein beta-subunit (beta-etf). [swissprot;acc:p38117] Subtracted 31189.6 37352.8 6163.2
spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6] Divided 45987 56777.1 1.23463
Rooted 60s ribosomal protein l26. [swissprot;acc:q02877] 50.2549 45.5599 1.10305
e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] Subtracted 61.3352 67.8618 6.5266
375 Measured u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] Divided 4700.42 5492.63 1.16854
ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] Subtracted 4250.14 5211.25 961.11
Ranked adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] 248.152 267.226 19.074
dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802] Divided 242.686 265.516 1.09407
Squared 45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [swissprot;acc:q9brk5] 45987 56777.1 1.23463
ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [refseq;acc:nm_003349] Subtracted 29547.4 35683.5 6136.1
Rooted 60s ribosomal protein l35. [swissprot;acc:p42766] Divided 50.2545 45.5637 1.10295
rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] Subtracted 56.3935 62.8817 6.4882
376 Measured 44050 protein. [refseq;acc:nm_178832] Divided 17385.9 14889.2 1.16769
homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Subtracted 4251.65 5212.33 960.68
Ranked adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] 248.152 267.226 19.074
probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] Divided 257.017 234.945 1.09395
Squared galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470] 46021.4 56813.2 1.2345
utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] Subtracted 29544.1 35678.3 6134.2
Rooted 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] Divided 50.2554 45.5688 1.10285

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/