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.


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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2401 to 2450 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
Network Comparison Type
red
green
network_comparison
301 no value Measured cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] Divided 13768.2 11466 1.20078
Squared proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] 28896.2 36767 1.27238
Rooted mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] 203.673 182.638 1.11517
ALG1 Ranked beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] 150.982 166.372 1.10193
COPZ1 Squared coatomer zeta-1 subunit (zeta-1 coat protein) (zeta-1 cop) (cgi-120) (hspc181). [swissprot;acc:q9y3c3] Subtracted 51527.6 43689.1 7838.5
CUTL1 Rooted ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] 66.1048 74.0977 7.9929
MAGED4 Ranked melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] 88.2482 110.265 22.0168
NOLA1 Measured nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] 4446.72 5553.79 1107.07
302 ARCN1 Squared coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [swissprot;acc:p48444] 51527.6 43689.1 7838.5
CUTL2 Rooted homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] 66.1046 74.0964 7.9918
HCK Squared tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Divided 28896.2 36767 1.27238
MAGEE2 Ranked hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] Subtracted 88.2482 110.265 22.0168
PLDN Measured pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] Divided 5894.75 7073.65 1.19999
PSCD1 Rooted cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 203.673 182.638 1.11517
RPL26 Ranked 60s ribosomal protein l26. [swissprot;acc:q02877] 242.326 267.008 1.10185
RRM2 Measured ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] Subtracted 6704.44 7811.45 1107.01
303 no value Ranked melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] 88.2482 110.265 22.0168
CRKL Squared crk-like protein. [swissprot;acc:p46109] Divided 28896.2 36767 1.27238
PPIE peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [swissprot;acc:q9unp9] Subtracted 51527.6 43689.1 7838.5
PPP1CC Measured serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Divided 22268.8 18560.4 1.1998
PSCD2 Rooted cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 203.673 182.638 1.11517
RPL35 Ranked 60s ribosomal protein l35. [swissprot;acc:p42766] 242.333 266.999 1.10179
RRM2 Rooted ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] Subtracted 62.9007 70.8854 7.9847
TXNL4A Measured spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] 4723.53 5828.46 1104.93
304 no value Ranked 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] Divided 242.339 266.986 1.1017
ABL1 Squared proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] 28896.2 36767 1.27238
COPZ2 coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [swissprot;acc:q9p299] Subtracted 51527.6 43689.1 7838.5
MAGEA11 Ranked melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] 88.2482 110.265 22.0168
POLI Measured polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] 5221.28 6314.35 1093.07
PRPF31 pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Divided 4855.46 5824.52 1.19958
PSCD4 Rooted cytohesin 4. [swissprot;acc:q9uia0] 203.673 182.638 1.11517
SF4 splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Subtracted 53.6107 61.5862 7.9755
305 no value atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 75.6323 67.6572 7.9751
FYN Squared proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] Divided 28896.2 36767 1.27238
MAGEA2B Ranked melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Subtracted 88.2482 110.265 22.0168
MRPL2 mitochondrial ribosomal protein l2. [refseq;acc:nm_015950] Divided 242.339 266.986 1.1017
OSR1 Measured odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] 3856.29 4624.15 1.19912
PSCD3 Rooted cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 203.673 182.638 1.11517
PXN Measured paxillin. [swissprot;acc:p49023] Subtracted 5221.28 6314.35 1093.07
WASL Squared neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] 28918.3 36746 7827.7
306 no value Measured pnas-18. [sptrembl;acc:q9bzu3] Divided 13680.5 11409.6 1.19903
Ranked 60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] 242.153 266.673 1.10126
hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Subtracted 88.2482 110.265 22.0168
FGR Squared proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] Divided 28896.2 36767 1.27238
KYNU Measured kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] Subtracted 8430.03 9518.11 1088.08
ODC1 Squared ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926] 33044.9 40781.4 7736.5
PPP1CC Rooted serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] 127.967 120.003 7.964
RBM39 rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] Divided 56.3935 62.8817 1.11505
307 AASS Squared aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763] Subtracted 33010.8 40732.2 7721.4
AGPAT2 Measured 1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120] 7556.75 8636.87 1080.12

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/