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 description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2001 to 2050 of 66312 in total
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
Value Type
Interaction Map
red
green
network_comparison
126 ADIPOR2 adiponectin receptor 2. [refseq;acc:nm_024551] Divided Rooted Low confidence 66.1599 71.1967 1.07613
AQP2 aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181] Subtracted Squared High confidence 71387.4 96033.4 24646
ARHGEF5 rho guanine nucleotide exchange factor 5 (guanine nucleotide regulatory protein tim) (oncogene tim) (p60 tim) (transforming immortalized mammary oncogene). [swissprot;acc:q12774] Divided Low confidence 58231.9 51117.1 1.13919
ATG4B cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Measured High confidence 24250 18164.9 1.33499
FBXW7 f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] Subtracted Ranked 285.684 252.234 33.45
HMG20A high-mobility group 20a. [refseq;acc:nm_018200] Rooted 60.9353 75.094 14.1587
HMG20B high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] Divided 60.9342 75.1387 1.23311
LASS2 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Ranked Low confidence 191.688 179.639 1.06707
Subtracted Measured 7098.44 7884.98 786.54
MAGEA4 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Divided 11285.3 10318.5 1.0937
NDUFS4 nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] Subtracted Ranked 226.892 213.661 13.231
NEDD8 ubiquitin-like protein nedd8. [swissprot;acc:q15843] Rooted 67.0736 72.4478 5.3742
PCF11 pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] Squared 58331.7 51036 7295.7
PPP1CA serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] Divided High confidence 189976 124480 1.52616
RINT1 rad50-interacting protein 1. [refseq;acc:nm_021930] Subtracted Measured 450.5 2394.5 1944
STAMBPL1 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Divided Ranked 94 114 1.21277
127 no value cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] Squared 88432.6 58423.3 1.51365
melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Measured Low confidence 11285.3 10318.5 1.0937
APC adenomatous polyposis coli protein (apc protein). [swissprot;acc:p25054] Subtracted Ranked 222.31 235.538 13.228
CHMP2A putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Divided High confidence 94 114 1.21277
CPSF3 cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] Subtracted Squared Low confidence 58384.8 51096.7 7288.1
CUL2 cullin homolog 2 (cul-2). [swissprot;acc:q13617] Ranked High confidence 285.684 252.234 33.45
DNASE2B deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Rooted 153.191 166.771 13.58
HMG20A high-mobility group 20a. [refseq;acc:nm_018200] Divided 60.9353 75.094 1.23236
JUND transcription factor jun-d. [swissprot;acc:p17535] Measured 5638.2 7523.39 1.33436
MAN1B1 endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase (ec 3.2.1.113) (er alpha-1,2-mannosidase) (mannosidase alpha class 1b member 1) (man9glcnac2-specific processing alpha-mannosidase). [swissprot;acc:q9ukm7] Subtracted Rooted Low confidence 66.9562 72.3243 5.3681
MIP lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301] Squared High confidence 71386.9 96032.5 24645.6
PBLD mawd binding protein (unknown protein 32 from 2d-page of liver tissue). [swissprot;acc:p30039] Measured Low confidence 10087.8 10870.9 783.1
RHOBTB2 rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] High confidence 450.5 2394.5 1944
SLC16A2 monocarboxylate transporter 8 (mct 8) (x-linked pest-containing transporter) (mct 7). [swissprot;acc:p36021] Divided Squared Low confidence 63904 72791.6 1.13908
VPS33B vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267] Ranked 203.678 190.88 1.06705
VPS41 vacuolar assembly protein vps41 homolog (s53). [swissprot;acc:p49754] Rooted 70.0842 75.3627 1.07532
128 no value pnas-18. [sptrembl;acc:q9bzu3] Squared High confidence 87787.3 58155.8 1.50952
APC2 adenomatous polyposis coli like. [refseq;acc:nm_005883] Subtracted Ranked Low confidence 222.34 235.547 13.207
AQP1 aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972] Squared High confidence 71346.6 95965.1 24618.5
LENG4 malignant cell expression-enhanced gene/tumor progression-enhanc. [refseq;acc:nm_024298] Divided Rooted Low confidence 64.4748 60.0381 1.0739
LUC7L2 luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] Measured High confidence 4355.61 5810.82 1.3341
MAGEA10 melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Low confidence 11285.3 10318.5 1.0937
PBLD mawd binding protein (unknown protein 32 from 2d-page of liver tissue). [swissprot;acc:p30039] Subtracted Squared 60522.9 67721 7198.1
PSEN1 presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Ranked High confidence 285.684 252.234 33.45
PSEN2 presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Rooted Low confidence 66.9562 72.3243 5.3681
PTPRA vacuolar protein sorting 16 (hvps16). [swissprot;acc:q9h269] Measured 7263.76 8046.29 782.53
SLC16A10 solute carrier family 16 (monocarboxylic acid transporters), member 10; t-type amino acid transporter 1. [refseq;acc:nm_018593] Divided Squared 63903.1 72790.2 1.13907
STAMBP associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Ranked High confidence 94 114 1.21277
STRN striatin. [swissprot;acc:o43815] Low confidence 214.085 200.796 1.06618
TARDBP tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] Rooted High confidence 48.0515 39.0445 1.23069
TCP1 t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] Subtracted Measured 11004.2 12944.2 1940
TIA1 nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Rooted 54.6527 67.9743 13.3216
129 COL4A3BP goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4] Divided Ranked Low confidence 220.969 235.572 1.06609
CUL1 cullin homolog 1 (cul-1). [swissprot;acc:q13616] Subtracted High confidence 285.684 252.234 33.45

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/