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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1562 to 1611 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
Network Comparison Type
red
green
network_comparison
196 AQP4 aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087] Measured Subtracted 10640.2 12117.8 1477.6
CLSTN1 calsyntenin-1 precursor. [swissprot;acc:o94985] Squared Divided 71062.4 95488.9 1.34373
FOXP4 forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Ranked 263.215 231.407 1.13745
GAD2 glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] Rooted 59.6399 51.9242 1.1486
ISCU nitrogen fixation cluster-like. [refseq;acc:nm_014301] Squared Subtracted 42411.6 55802.1 13390.5
PPP2R5A 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] Rooted 116.707 106.044 10.663
PPP2R5E serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537] Measured Divided 17738.5 13995.7 1.26742
197 no value succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521] Squared 71062.4 95488.9 1.34373
AQP5 aquaporin 5. [swissprot;acc:p55064] Measured Subtracted 10640 12117.6 1477.6
FOXP1 forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Ranked Divided 263.215 231.407 1.13745
LUC7L2 luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] Rooted Subtracted 55.2859 65.9288 10.6429
NAPG gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] Divided 59.6399 51.9242 1.1486
PPP2R5A 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] Measured 17738.5 13995.7 1.26742
SNORA7A 60s ribosomal protein l32. [swissprot;acc:p02433] Ranked Subtracted 241.13 266.969 25.839
STARD13 star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8] Squared 42411.6 55802.1 13390.5
198 no value 40s ribosomal protein s29. [swissprot;acc:p30054] Ranked 241.849 267.642 25.793
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] Measured 10639.9 12117.4 1477.5
BRAF b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] Divided 17710.9 13977.7 1.26708
Rooted Subtracted 116.576 105.948 10.628
FOXP3 forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Ranked Divided 263.191 231.394 1.13741
GAD1 glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] Rooted 59.6399 51.9242 1.1486
PTPRB protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] Squared 71062.2 95488.6 1.34373
STARD8 star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502] Subtracted 42411.6 55802.1 13390.5
199 CHRNA2 neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822]
EGFL8 palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] Ranked Divided 242.735 276.059 1.13729
LUC7L luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Rooted Subtracted 55.297 65.9236 10.6266
MIP lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301] Measured 10639.8 12117.3 1477.5
PPP2CA serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] Divided 4916.8 3888.18 1.26455
PRSS16 thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] Squared 71062.2 95488.6 1.34373
RPS11 40s ribosomal protein s11. [swissprot;acc:p04643] Ranked Subtracted 241.399 267.088 25.689
STT3B source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Rooted Divided 61.2893 70.3856 1.14842
200 no value 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] Ranked Subtracted 241.808 267.335 25.527
AQP1 aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972] Measured 10635.3 12111.4 1476.1
BCAR1 crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] Divided 4808.79 6074.21 1.26315
CCDC47 gk001 protein. [refseq;acc:nm_020198] Squared 71062.2 95488.6 1.34373
EGFL7 egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] Ranked 242.718 276.018 1.1372
MAPKAPK3 mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] Squared Subtracted 42411.6 55802.1 13390.5
PPP2CA serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] Rooted 63.5827 53.0856 10.4971
STT3A oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Divided 61.2893 70.3856 1.14842
201 CCT4 t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] Measured 4810.22 6075.04 1.26294
CLSTN2 calsyntenin-2 precursor. [swissprot;acc:q9h4d0] Squared 71033.4 95440.2 1.3436
CPSF4 cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693] Rooted Subtracted 138.375 127.926 10.449
DDOST dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] Divided 61.2893 70.3856 1.14842
MAPK14 mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [swissprot;acc:q16539] Squared Subtracted 42411.6 55802.1 13390.5
RPL11 60s ribosomal protein l11. [swissprot;acc:p39026] Ranked 241.828 267.346 25.518
SF4 splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Divided 240.133 211.382 1.13601
SSR4 translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] Measured Subtracted 10603.5 12069.5 1466
202 no value splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] Rooted Divided 57.3527 65.7973 1.14724
CHRNA4 neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] Squared Subtracted 42411.6 55802.1 13390.5
CLSTN1 calsyntenin-1 precursor. [swissprot;acc:o94985] Measured 10603.5 12069.5 1466

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/