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.


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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 1158 to 1207 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
Hugo
description
Interaction Map
red
green
network_comparison
579 ZNF593 zinc finger protein t86. [swissprot;acc:o00488] High confidence 246.805 231.796 1.06475
580 CNN2 calponin h2, smooth muscle (neutral calponin). [swissprot;acc:q99439] Low confidence 202.382 196.334 1.0308
ZNRD1 zinc ribbon domain containing, 1; transcription-associated zinc ribbon protein; rna polymerase i small specific subunit rpa12. [refseq;acc:nm_014596] High confidence 236.751 252.038 1.06457
581 CEBPZ ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] Low confidence 205.428 199.293 1.03078
TLX3 t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711] High confidence 237.28 252.492 1.06411
582 BARX1 homeobox protein barh-like 1. [swissprot;acc:q9hbu1]
CYP4F3 cytochrome p450 4f3 (ec 1.14.13.30) (cypivf3) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:q08477] Low confidence 203.164 197.1 1.03077
583 CYP4F2 cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329] 203.166 197.101
OPN4 opsin 4 (melanopsin). [swissprot;acc:q9uhm6] High confidence 237.28 252.492 1.06411
584 CYP4F11 cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] Low confidence 203.163 197.102 1.03075
TLX2 t-cell leukemia homeobox protein 2 (homeobox protein hox-11l1) (neural crest homeobox protein). [swissprot;acc:o43763] High confidence 237.28 252.492 1.06411
585 SURF6 surfeit locus protein 6. [swissprot;acc:o75683] Low confidence 205.21 199.088 1.03075
TLX1 t-cell leukemia homeobox protein 1 (homeobox protein hox-11) (tcl-3 proto-oncogene). [swissprot;acc:p31314] High confidence 237.28 252.492 1.06411
586 no value enthoprotin; epsin 4; clathrin interacting protein localized in the trans-golgi region. [refseq;acc:nm_014666] Low confidence 205.506 199.406 1.03059
HECTD1 hect domain containing protein 1 (fragment). [swissprot;acc:q9ult8] High confidence 237.28 252.492 1.06411
587 BARX2 homeobox protein barh-like 2. [swissprot;acc:q9umq3]
DDX24 atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] Low confidence 205.461 199.383 1.03048
588 AGPAT4 1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [swissprot;acc:q9nrz5] 191.507 185.859 1.03039
SBDS shwachman-bodian-diamond syndrome protein (cgi-97). [swissprot;acc:q9y3a5] High confidence 216.557 230.362 1.06375
589 no value u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] 228.215 214.546 1.06371
NAV2 neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [refseq;acc:nm_145117] Low confidence 204.056 198.046 1.03035
590 AP2M1 clathrin coat assembly protein ap50 (clathrin coat associated protein ap50) (plasma membrane adaptor ap-2 50 kda protein) (ha2 50 kda subunit) (clathrin assembly protein complex 2 medium chain) (ap-2 mu 2 chain). [swissprot;acc:p20172] 211.788 218.216
RRM1 ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] High confidence 217.215 204.279 1.06333
591 BUD31 g10 protein homolog (edg-2). [swissprot;acc:p41223] Low confidence 201.67 195.729 1.03035
RPP30 ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [swissprot;acc:p78346] High confidence 216.72 230.439 1.0633
592 ERGIC2 cda14. [refseq;acc:nm_016570] Low confidence 211.525 205.3 1.03032
PPP1R7 protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] High confidence 91.63 97.4011 1.06298
593 DR1 tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658] 232.118 218.406 1.06278
NAV1 neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] Low confidence 204.074 198.071 1.03031
594 CDC40 pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] High confidence 223.282 210.136 1.06256
NAV3 neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] Low confidence 204.073 198.07 1.03031
595 ABTB1 ankyrin repeat and btb (poz) domain containing 1 isoform 1; elongation factor 1a binding protein. [refseq;acc:nm_032548] 205.485 199.453 1.03024
VAV1 vav proto-oncogene. [swissprot;acc:p15498] High confidence 212.2 199.849 1.0618
596 RBX1 ring-box 1; ring box protein 1; regulator of cullins 1; ring finger protein; zyp protein. [refseq;acc:nm_014248] Low confidence 205.485 199.453 1.03024
VAV3 vav-3 protein. [swissprot;acc:q9ukw4] High confidence 212.253 199.908 1.06175
597 ARID1B brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] Low confidence 204.856 198.854 1.03018
VAV2 vav-2 protein. [swissprot;acc:p52735] High confidence 212.526 200.212 1.0615
598 AKT1 rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749] 248.463 234.095 1.06138
ARID1A swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497] Low confidence 204.843 198.851 1.03013
599 AKT3 rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [swissprot;acc:q9y243] High confidence 248.463 234.095 1.06138
SFRS3 splicing factor, arginine/serine-rich 3 (pre-mrna splicing factor srp20) (x16 protein). [swissprot;acc:p23152] Low confidence 208.383 202.291 1.03012
600 AKT2 rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [swissprot;acc:p31751] High confidence 248.463 234.095 1.06138
ING3 inhibitor of growth family, member 3. [refseq;acc:nm_019071] Low confidence 210.546 204.42 1.02997
601 CROT peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9] 208.67 202.603 1.02995
VPS39 vam6/vps39-like protein (hvam6p). [swissprot;acc:q96jc1] High confidence 206.274 218.792 1.06069
602 MAP4 microtubule-associated protein 4 (map 4). [swissprot;acc:p27816]
SH2D3C sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489] Low confidence 201.426 195.579 1.0299
603 BCAR3 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] 201.427 195.587 1.02986
LEF1 lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2] High confidence 225.829 212.945 1.0605
604 RPL15 60s ribosomal protein l15. [swissprot;acc:p39030] 217.862 230.978 1.0602

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/