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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Rank Gene Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1601 to 1650 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
green
network_comparison
401 Measured adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] 5201.41 4479.76 1.16109
Ranked replication protein a 70 kda dna-binding subunit (rp-a) (rf-a) (replication factor-a protein 1) (single-stranded dna-binding protein). [swissprot;acc:p27694] 207.908 226.218 1.08807
Squared axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] 33044.3 40524.8 1.22638
Rooted serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172] 116.707 106.044 1.10055
402 Measured leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] 5201.41 4479.76 1.16109
Ranked replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927] 207.908 226.218 1.08807
Squared endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] 39472 48393.1 1.22601
Rooted eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] 50.1918 55.2294 1.10037
403 Measured fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] 5201.41 4479.76 1.16109
Ranked phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] 207.908 226.218 1.08807
Squared glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] 39463.9 48362.1 1.22548
Rooted nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] 59.6834 65.6741 1.10037
404 Measured leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] 5201.41 4479.76 1.16109
Ranked dna repair protein rad52 homolog. [swissprot;acc:p43351] 207.908 226.218 1.08807
Squared adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520] 26819.1 32855.4 1.22507
Rooted nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] 59.6834 65.6741 1.10037
405 Measured laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] 5201.41 4479.76 1.16109
Ranked clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] 207.931 226.209 1.0879
Squared adenylosuccinate synthase-like 1. [refseq;acc:nm_152328] 26822.2 32858.1 1.22503
Rooted b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] 116.576 105.948 1.10031
406 Measured thymic stromal co-transporter. [refseq;acc:nm_033051] 5201.41 4479.76 1.16109
Ranked transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] 265.634 244.304 1.08731
Squared 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] 18995.7 23245.6 1.22373
Rooted 60s ribosomal protein l12. [swissprot;acc:p30050] 49.9858 45.4433 1.09996
407 Measured wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516] 6603.41 7664.65 1.16071
Ranked 28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] 239.75 260.544 1.08673
Squared probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] 18995.7 23244.9 1.22369
Rooted 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] 49.9856 45.4431 1.09996
408 Measured dok-like protein. [refseq;acc:nm_024872] 6102.59 7081.46 1.1604
Ranked ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] 255.112 234.804 1.08649
Squared probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] 18995.7 23244.7 1.22368
Rooted dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] 49.9856 45.4432 1.09996
409 Measured docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] 6102.59 7081.46 1.1604
Ranked rna polymerase i associated factor 53. [refseq;acc:nm_022490] 241.045 261.874 1.08641
Squared serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] 18995.6 23242.8 1.22359
Rooted mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001] 50.4409 45.8795 1.09942
410 Measured docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] 6102.59 7081.46 1.1604
Ranked tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888] 233.376 253.539 1.0864
Squared crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] 19546.1 23881.6 1.22181
Rooted phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] 55.5489 50.535 1.09922
411 Measured tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] 6102.59 7081.46 1.1604
Ranked tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780] 233.376 253.539 1.0864
Squared small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] 17861.2 21821.8 1.22174
Rooted pp3111 protein. [refseq;acc:nm_022156] 55.5489 50.535 1.09922
412 Measured mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] 3594.31 4169.95 1.16015
Ranked ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985] 240.788 261.416 1.08567
Squared t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] 19556 23891.8 1.22171
Rooted syntaxin 18. [swissprot;acc:q9p2w9] 55.5489 50.535 1.09922
413 Measured vav proto-oncogene. [swissprot;acc:p15498] 6644.99 7707.8 1.15994
Ranked dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160] 240.913 261.45 1.08525

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/