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 59624 to 59673 of 66312 in total
Interaction Map  : Low confidence
Filtered  : 1
Rank
Hugo
Value Type
description
Network Comparison Type
red
green
network_comparison
4225 TXNDC9 Measured protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530] Subtracted 8007.81 8178.9 171.09
4226 no value Ranked 40s ribosomal protein s3a. [swissprot;acc:p49241] Divided 203.416 201.41 1.00996
pre-b-cell leukemia transcription factor-2 (homeobox protein pbx2) (g17 protein). [swissprot;acc:p40425] Subtracted 202.007 200.008 1.999
ACOT8 Rooted peroxisomal acyl-coenzyme a thioester hydrolase 1 (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 1) (hiv-nef associated acyl coa thioesterase) (thioesterase ii) (hte). [swissprot;acc:o14734] Divided 71.7787 73.5441 1.0246
MRPS9 Measured 28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] Subtracted 7621.65 7792.73 171.08
PSMC1 Squared 26s protease regulatory subunit 4 (p26s4). [swissprot;acc:q03527] 46486 45383.5 1102.5
PSPHL l-3-phosphoserine phosphatase (ec 3.1.3.3) (psp) (o-phosphoserine phosphohydrolase) (pspase). [swissprot;acc:p78330] Divided 48466.6 47270.2 1.02531
UBE2A Measured ubiquitin-conjugating enzyme e2 a (ec 6.3.2.19) (ubiquitin-protein ligase a) (ubiquitin carrier protein a) (hr6a) (hhr6a). [swissprot;acc:p49459] 8277.18 8443.29 1.02007
ZNF45 Rooted zinc finger protein 45 (brc1744). [swissprot;acc:q02386] Subtracted 76.1821 78.0464 1.8643
4227 no value Measured 60s ribosomal protein l12. [swissprot;acc:p30050] 7341.93 7512.99 171.06
Rooted zinc finger protein 83 (zinc finger protein hpf1). [swissprot;acc:p51522] 76.1821 78.0464 1.8643
CPA5 Squared carboxypeptidase a5. [refseq;acc:nm_080385] 47109.8 48210.5 1100.7
NEDD4 ubiquitin-protein ligase nedd-4 (ec 6.3.2.-). [swissprot;acc:p46934] Divided 45822 44692 1.02528
NOSTRIN Measured nostrin. [refseq;acc:nm_052946] 7937.71 8096.9 1.02005
RACGAP1 Ranked rac gtpase activating protein 1; gtpase activating protein. [refseq;acc:nm_013277] 198.195 196.245 1.00994
SAE1 sumo-1 activating enzyme subunit 1; sumo-1 activating enzyme e1 n subunit; sentrin/sumo-activating protein aos1; ubiquitin-like protein sumo-1 activating enzyme. [refseq;acc:nm_005500] Subtracted 203.206 201.215 1.991
XPOT Rooted exportin t (trna exportin) (exportin(trna)). [swissprot;acc:o43592] Divided 73.4308 75.2361 1.02459
4228 no value Ranked 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] Subtracted 207.351 209.342 1.991
HNRNPA1 Measured heterogeneous nuclear ribonucleoprotein a1 (helix-destabilizing protein) (single-strand binding protein) (hnrnp core protein a1). [swissprot;acc:p09651] Divided 7628.52 7781.5 1.02005
LRPPRC 130 kda leucine-rich protein (lrp 130) (gp130) (leucine-rich ppr-motif containing protein). [swissprot;acc:p42704] Subtracted 7896.47 8067.47 171
MYCL1 Ranked l-myc-1 proto-oncogene protein. [swissprot;acc:p12524] Divided 203.653 201.651 1.00993
NPC2 Squared epididymal secretory protein e1 precursor (niemann-pick disease type c2 protein) (epi-1) (he1) (epididymal secretory protein 14.6) (esp14.6). [swissprot;acc:q15668] Subtracted 46061.5 44960.8 1100.7
PDK1 [pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [swissprot;acc:q15118] Divided 43688 42611.4 1.02527
PSMB5 Rooted proteasome subunit beta type 5 precursor (ec 3.4.25.1) (proteasome epsilon chain) (macropain epsilon chain) (multicatalytic endopeptidase complex epsilon chain) (proteasome subunit x) (proteasome chain 6) (proteasome subunit mb1). [swissprot;acc:p28074] 72.2679 74.0397 1.02452
ZSCAN20 zinc finger protein 31. [refseq;acc:nm_145238] Subtracted 76.1821 78.0464 1.8643
4229 ALDH4A1 Ranked delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial precursor (ec 1.5.1.12) (p5c dehydrogenase). [swissprot;acc:p30038] Divided 185.549 183.726 1.00992
EN2 Rooted homeobox protein engrailed-2 (hu-en-2). [swissprot;acc:p19622] 69.0131 70.7049 1.02451
GRB2 Squared growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354] Subtracted 44490.6 43391 1099.6
NEDD4L ubiquitin-protein ligase nedd4-like; neural precursor cell expressed, developmentally down-regulated gene 4-like; potential epithelial sodium channel regulator; homolog of yeast ubiquitin-protein ligase rsp5. [refseq;acc:nm_015277] Divided 45817 44688.2 1.02526
SLC25A1 Measured tricarboxylate transport protein, mitochondrial precursor (citrate transport protein) (ctp) (tricarboxylate carrier protein). [swissprot;acc:p53007] Subtracted 7896.47 8067.47 171
SMARCA5 Ranked swi/snf-related matrix-associated actin-dependent regulator of chromatin a5; sucrose nonfermenting-like 5. [refseq;acc:nm_003601] 205.033 203.046 1.987
SOCS1 Measured suppressor of cytokine signaling 1 (socs-1) (jak-binding protein) (jab) (stat induced stat inhibitor 1) (ssi-1) (tec-interacting protein 3) (tip-3). [swissprot;acc:o15524] Divided 7431.81 7580.36 1.01999
ZNF211 Rooted zinc finger protein 211 (zinc finger protein c2h2-25). [swissprot;acc:q13398] Subtracted 76.1821 78.0464 1.8643
4230 no value zinc finger protein 11b (fragment). [swissprot;acc:q06732]
CAPZB Measured f-actin capping protein beta subunit (capz beta). [swissprot;acc:p47756] 7896.47 8067.47 171
KLF6 Rooted core promoter element-binding protein (kruppel-like factor 6) (b-cell derived protein 1) (proto-oncogene bcd1) (transcription factor zf9) (gc-rich sites binding factor gbf). [swissprot;acc:q99612] Divided 76.1722 78.0392 1.02451
PDK2 Squared [pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [swissprot;acc:q15119] 43687.9 42611.7 1.02526
PI4KA phosphatidylinositol 4-kinase alpha (ec 2.7.1.67) (pi4-kinase) (ptdins-4-kinase) (pi4k-alpha). [swissprot;acc:p42356] Subtracted 47201.3 46101.9 1099.4
PLAA Ranked phospholipase a-2-activating protein (plap) (pla2p). [swissprot;acc:q9y263] Divided 185.549 183.726 1.00992
PTP4A3 Measured protein tyrosine phosphatase type iva, member 3 isoform 2; potentially prenylated protein tyrosine phosphatase. [refseq;acc:nm_007079] 8224.26 8388.41 1.01996
REEP6 Ranked polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393] Subtracted 200.99 199.003 1.987
4231 no value Rooted zinc finger protein 208. [swissprot;acc:o43345] 76.1821 78.0464 1.8643
ACTR1A Squared alpha-centractin (centractin) (centrosome-associated actin homolog) (actin-rpv) (arp1). [swissprot;acc:p42024] Divided 45823 44694.5 1.02525
CNOT6 Ranked kiaa1194. [refseq;acc:nm_015455] 196.794 194.863 1.00991
FBXO32 Measured f-box only protein 32 (muscle atrophy f-box protein) (mafbx) (atrogin- 1). [swissprot;acc:q969p5] Subtracted 7921.78 8092.63 170.85
GABARAP Ranked gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] 190.846 188.86 1.986
NDUFA10 Rooted nadh-ubiquinone oxidoreductase 42 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-42kd) (ci-42kd). [swissprot;acc:o95299] Divided 70.7716 72.5055 1.0245
PTP4A2 Measured protein tyrosine phosphatase type iva, member 2 isoform 1; protein tyrosine phosphatase iva2; protein tyrosine phosphatase iva; phosphatase of regenerating liver 2. [refseq;acc:nm_003479] 8224.26 8388.41 1.01996
PXMP3 Squared peroxisome assembly factor-1 (paf-1) (peroxin-2) (peroxisomal membrane protein 3) (35 kda peroxisomal membrane protein). [swissprot;acc:p28328] Subtracted 42606.3 41507.2 1099.1
4232 CDC20 Rooted cell division cycle 20; cell division cycle 20, s.cerevisiae homolog. [refseq;acc:nm_001255] Divided 74.4869 76.3104 1.02448

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/