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 Value Type Hugo description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1901 to 1950 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
Hugo
description
red
green
network_comparison
476 Measured CHRNA6 neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825] 9649.61 11053.5 1.14549
Ranked KCNA4 potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459] 226.681 210.814 1.07527
Squared VAV1 vav proto-oncogene. [swissprot;acc:p15498] 31223.8 37614.3 1.20467
Rooted SEPHS1 selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903] 62.574 68.4128 1.09331
477 Measured ISCU nitrogen fixation cluster-like. [refseq;acc:nm_014301] 9649.61 11053.5 1.14549
Ranked NIP7 saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] 251.926 234.547 1.0741
Squared VAV3 vav-3 protein. [swissprot;acc:q9ukw4] 31248.8 37623.4 1.204
Rooted INPP4A inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [refseq;acc:nm_001566] 62.574 68.4128 1.09331
478 Measured STARD13 star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8] 9649.61 11053.5 1.14549
Ranked BRF1 transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994] 228.051 212.321 1.07409
Squared SRP9 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 16318.4 19645.8 1.2039
Rooted HIST1H2BL histone h2b.c (h2b/c). [swissprot;acc:q99880] 50.6084 55.2961 1.09263
479 Measured STARD8 star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502] 9649.61 11053.5 1.14549
Ranked NOLA1 nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] 228.051 212.321 1.07409
Squared EIF5B translation initiation factor if-2. [swissprot;acc:o60841] 24031.6 28929.7 1.20382
Rooted HIST2H2BA histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] 50.6084 55.2961 1.09263
480 Measured CHRNA2 neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822] 9649.61 11053.5 1.14549
Ranked NETO2 neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092] 237.109 254.667 1.07405
Squared CDS1 phosphatidate cytidylyltransferase 1 (ec 2.7.7.41) (cdp-diglyceride synthetase 1) (cdp-diglyceride pyrophosphorylase 1) (cdp- diacylglycerol synthase 1) (cds 1) (ctp:phosphatidate cytidylyltransferase 1) (cdp-dag synthase 1) (cdp-dg synthetase 1). [swissprot;acc:q92903] 26874.6 32347.4 1.20364
Rooted no value histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106] 50.6084 55.2961 1.09263
481 Measured MAPKAPK3 mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] 9649.61 11053.5 1.14549
Ranked NETO1 neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966] 237.109 254.667 1.07405
Squared SRP9 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 16335.9 19660.7 1.20353
Rooted no value histone h2b. [refseq;acc:nm_175055] 50.6084 55.2961 1.09263
482 Measured 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] 9649.61 11053.5 1.14549
Ranked HNRNPU heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839] 237.109 254.667 1.07405
Squared SLC13A3 solute carrier family 13, member 3 (sodium-dependent high-affinity dicarboxylate transporter 2) (na(+)/dicarboxylate cotransporter 3) (nadc-3) (hnadc3). [swissprot;acc:q8wwt9] 26867.3 32335.2 1.20352
Rooted no value histone h2b.s (h2b/s). [swissprot;acc:p57053] 50.6084 55.2961 1.09263
483 Measured CHRNA4 neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] 9649.61 11053.5 1.14549
Ranked RUNX2 runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [swissprot;acc:q13950] 237.109 254.667 1.07405
Squared SLC13A2 solute carrier family 13, member 2 (renal sodium/dicarboxylate cotransporter) (na(+)/dicarboxylate cotransporter 1) (nadc-1). [swissprot;acc:q13183] 26867.3 32335.2 1.20352
Rooted no value histone h2b.d (h2b/d). [swissprot;acc:q99877] 50.6084 55.2961 1.09263
484 Measured CHRNA3 neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] 9649.61 11053.5 1.14549
Ranked HNRPUL1 e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040] 237.109 254.667 1.07405
Squared SLC13A4 solute carrier family 13, member 4 (na+/sulfate cotransporter sut-1). [swissprot;acc:q9ukg4] 26867.2 32335 1.20351
Rooted HIST3H3 histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695] 50.6084 55.2961 1.09263
485 Measured SPHK2 sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0] 9649.61 11053.5 1.14549
Ranked RPL18 60s ribosomal protein l18. [swissprot;acc:q07020] 237.109 254.667 1.07405
Squared SLC13A1 solute carrier family 13, member 1 (renal sodium/sulfate cotransporter) (na(+)/sulfate cotransporter) (hnasi-1). [swissprot;acc:q9bzw2] 26867.2 32335 1.20351
Rooted HIST1H2BA testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610] 50.6084 55.2961 1.09263
486 Measured CLEC11A stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975] 10908.6 12491.8 1.14513
Ranked MCTS1 mct-1 protein. [refseq;acc:nm_014060] 226.313 243.03 1.07387
Squared SCAMP2 secretory carrier-associated membrane protein 2. [swissprot;acc:o15127] 26865.9 32332.9 1.20349
Rooted no value histone h2b.e (h2b/e). [swissprot;acc:q99879] 50.6084 55.2961 1.09263
487 Measured PYCR2 pyrroline 5-carboxylate reductase isoform. [refseq;acc:nm_013328] 5277.4 6042.88 1.14505
Ranked MRPL22 mitochondrial ribosomal protein l22. [refseq;acc:nm_014180] 226.313 243.03 1.07387
Squared SCAMP3 secretory carrier-associated membrane protein 3. [swissprot;acc:o14828] 26865.9 32332.9 1.20349
Rooted no value tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886] 50.0015 54.627 1.09251
488 Measured CLEC3A c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] 10872.4 12447 1.14483
Ranked SART1 squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] 225.026 209.798 1.07258

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/