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 Network Type I Analysis

Type 1 network in which we propagated the absolute log regulation ratio abs(log(r/g)). We used the filtered lowest boundary of the confidence interval for the microarray measurement based and used the high confidence interaction map. Because type-I networks tend to favour highly connected proteins we tested a normalisation scheme in which we would run the network once with real values (the measured column) and once with simulated values where each measured point is set to 1 instead of the actual signal (the expected column). Afterwards we divided the measured value by the expected value. This normalisation scheme works to a certain extend but will lead to a variance that is directly related to the connectivity of each protein. In the end we dropped the use of Type-I networks due to the many technical problems they pose.


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final measured Gene Rank expected Hugo description
Results: HTML CSV LaTeX Showing element 551 to 600 of 3206 in total
final
measured
Rank
expected
Hugo
description
0.209942695 0.0466014 2656 0.221972 SCAMP1 SECRETORY CARRIER-ASSOCIATED MEMBRANE PROTEIN 1. [SWISSPROT;Acc:O15126]
0.209942905 0.0366237 2655 0.174446 SCAMP2 SECRETORY CARRIER-ASSOCIATED MEMBRANE PROTEIN 2. [SWISSPROT;Acc:O15127]
0.209943276 0.0359383 2654 0.171181 SCAMP3 SECRETORY CARRIER-ASSOCIATED MEMBRANE PROTEIN 3. [SWISSPROT;Acc:O14828]
0.209961656 0.122765 2653 0.584702 NUMBL NUMB-LIKE PROTEIN (NUMB-R). [SWISSPROT;Acc:Q9Y6R0]
0.209961776 0.130073 2652 0.619508 NUMB NUMB PROTEIN HOMOLOG (H-NUMB) (PROTEIN S171). [SWISSPROT;Acc:P49757]
0.209962091 0.069842 2651 0.332641 TULP3 TUBBY RELATED PROTEIN 3 (TUBBY-LIKE PROTEIN 3). [SWISSPROT;Acc:O75386]
0.209962186 0.0319827 2650 0.152326 VPS35 VACUOLAR PROTEIN SORTING 35 (VESICLE PROTEIN SORTING 35) (HVPS35) (MATERNAL-EMBRYONIC 3). [SWISSPROT;Acc:Q96QK1]
0.209962194 0.0503166 2649 0.239646 PARD6G PARTITIONING DEFECTIVE-6 HOMOLOG GAMMA (PAR-6 GAMMA) (PAR6D). [SWISSPROT;Acc:Q9BYG4]
0.209962302 0.086385 2648 0.411431 PRKCI "PROTEIN KINASE C, IOTA TYPE (EC 2.7.1.37) (NPKC-IOTA) (ATYPICAL PROTEIN KINASE C-LAMDA/IOTA) (APKC-LAMBDA/IOTA). [SWISSPROT;Acc:P41743]"
0.209962366 0.0696821 2647 0.331879 TULP1 TUBBY RELATED PROTEIN 1 (TUBBY-LIKE PROTEIN 1). [SWISSPROT;Acc:O00294]
0.209962525 0.179287 2646 0.8539 VPS29 VACUOLAR PROTEIN SORTING 29 (VESICLE PROTEIN SORTING 29) (HVPS29) (MDS007) (PEP11) (DC7/DC15). [SWISSPROT;Acc:Q9UBQ0]
0.209962554 0.0704817 2645 0.335687 PRKCZ "PROTEIN KINASE C, ZETA TYPE (EC 2.7.1.37) (NPKC-ZETA). [SWISSPROT;Acc:Q05513]"
0.20996256 0.0898392 2644 0.427882 TUB TUBBY PROTEIN HOMOLOG. [SWISSPROT;Acc:P50607]
0.209963302 0.115058 2643 0.547991 TBC1D5 TBC1 DOMAIN FAMILY MEMBER 5. [SWISSPROT;Acc:Q92609]
0.209972651 0.515928 2642 2.45712 CDS2 PHOSPHATIDATE CYTIDYLYLTRANSFERASE 2 (EC 2.7.7.41) (CDP-DIGLYCERIDE SYNTHETASE 2) (CDP-DIGLYCERIDE PYROPHOSPHORYLASE 2) (CDP- DIACYLGLYCEROL SYNTHASE 2) (CDS 2) (CTP:PHOSPHATIDATE CYTIDYLYLTRANSFERASE 2) (CDP-DAG SYNTHASE 2) (CDP-DG SYNTHETASE 2). [Source
0.209997063 0.0214512 2641 0.10215 TST THIOSULFATE SULFURTRANSFERASE (EC 2.8.1.1) (RHODANESE). [SWISSPROT;Acc:Q16762]
0.209997361 0.0246707 2638 0.117481 RHOA TRANSFORMING PROTEIN RHOA (H12). [SWISSPROT;Acc:P06749]
2639 MPST 3-MERCAPTOPYRUVATE SULFURTRANSFERASE (EC 2.8.1.2) (MST). [SWISSPROT;Acc:P25325]
2640 AARSD1
0.209997444 0.262879 2637 1.25182 CBS CYSTATHIONINE BETA-SYNTHASE (EC 4.2.1.22) (SERINE SULFHYDRASE) (BETA-THIONASE). [SWISSPROT;Acc:P35520]
0.209997471 0.0215869 2636 0.102796 RHOC TRANSFORMING PROTEIN RHOC (H9). [SWISSPROT;Acc:P08134]
0.20999872 0.0132921 2635 0.0632961 CHRNA3 "NEURONAL ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-3 CHAIN PRECURSOR. [SWISSPROT;Acc:P32297]"
0.209998739 0.416438 2634 1.98305 ISCU NITROGEN FIXATION CLUSTER-LIKE. [RefSeq;Acc:NM_014301]
0.209998836 0.0189378 2633 0.0901805 STARD8 STAR-RELATED LIPID TRANSFER PROTEIN 8 (STARD8) (START DOMAIN- CONTAINING PROTEIN 8). [SWISSPROT;Acc:Q92502]
0.209998965 0.0186658 2632 0.0888852 CHRNA4 "NEURONAL ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-4 CHAIN PRECURSOR. [SWISSPROT;Acc:P43681]"
0.209999026 0.0131531 2631 0.0626341 CHRNA6 "NEURONAL ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-6 CHAIN PRECURSOR. [SWISSPROT;Acc:Q15825]"
0.209999041 0.0142351 2630 0.0677865 CHRNA2 "NEURONAL ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-2 CHAIN PRECURSOR. [SWISSPROT;Acc:Q15822]"
0.209999127 0.0673673 2629 0.320798 MAPKAPK2 MAP KINASE-ACTIVATED PROTEIN KINASE 2 (EC 2.7.1.-) (MAPK-ACTIVATED PROTEIN KINASE 2) (MAPKAP KINASE 2) (MAPKAPK-2). [SWISSPROT;Acc:P49137]
0.209999227 0.0434669 2628 0.206986 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)
0.209999235 0.0686246 2627 0.326785 DPAGT1 UDP-N-ACETYLGLUCOSAMINE--DOLICHYL-PHOSPHATE N- ACETYLGLUCOSAMINEPHOSPHOTRANSFERASE (EC 2.7.8.15) (GPT) (G1PT) (N-ACETYLGLUCOSAMINE-1-PHOSPHATE TRANSFERASE) (GLCNAC-1-P TRANSFERASE). [SWISSPROT;Acc:Q9H3H5]
0.209999243 0.052697 2626 0.250939 MAPKAPK3 MITOGEN-ACTIVATED PROTEIN KINASE-ACTIVATED PROTEIN KINASE 3; MAPKAP KINASE 3. [RefSeq;Acc:NM_004635]
0.209999404 0.0197176 2625 0.0938936 STARD13 STAR-RELATED LIPID TRANSFER PROTEIN 13 (STARD13) (START DOMAIN- CONTAINING PROTEIN 13) (46H23.2). [SWISSPROT;Acc:Q9Y3M8]
0.209999479 0.0241785 2623 0.115136 SPHK1 SPHINGOSINE KINASE 1 (EC 2.7.1.-) (SK 1) (SPK 1). [SWISSPROT;Acc:Q9NYA1]
2624 SPHK2 SPHINGOSINE KINASE 2 (EC 2.7.1.-) (SK 2) (SPK 2). [SWISSPROT;Acc:Q9NRA0]
0.209999683 0.0331306 2622 0.157765 MAPK11 MITOGEN-ACTIVATED PROTEIN KINASE 12 (EC 2.7.1.37) (EXTRACELLULAR SIGNAL-REGULATED KINASE 6) (ERK-6) (ERK5) (STRESS-ACTIVATED PROTEIN KINASE-3) (MITOGEN-ACTIVATED PROTEIN KINASE P38 GAMMA) (MAP KINASE P38 GAMMA). [SWISSPROT;Acc:P53778]
0.210000261 0.0241725 2621 0.115107 DLC1 RHO-GTPASE-ACTIVATING PROTEIN 7 (RHO-TYPE GTPASE-ACTIVATING PROTEIN 7) (DELETED IN LIVER CANCER 1 PROTEIN) (DLC-1) (HP PROTEIN) (STAR-RELATED LIPID TRANSFER PROTEIN 12) (STARD12) (START DOMAIN-CONTAINING PROTEIN 12). [SWISSPROT;Acc:Q96QB1]
0.210498978 0.025126 2620 0.119364 ESD ESTERASE D (EC 3.1.1.1). [SWISSPROT;Acc:P10768]
0.210499337 0.478004 2619 2.27081 no value ALCOHOL DEHYDROGENASE CLASS III CHI CHAIN (EC 1.1.1.1) (GLUTATHIONE- DEPENDENT FORMALDEHYDE DEHYDROGENASE) (EC 1.2.1.1) (FDH). [SWISSPROT;Acc:P11766]
0.210596477 0.412171 2618 1.95716 CSTF3 "CLEAVAGE STIMULATION FACTOR SUBUNIT 3; CLEAVAGE STIMULATION FACTOR, 3' PRE-RNA, SUBUNIT 3, 77KD. [RefSeq;Acc:NM_001326]"
0.210658617 0.143053 2617 0.679075 MAP2K6 DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 6 (EC 2.7.1.-) (MAP KINASE KINASE 6) (MAPKK 6) (MAPK/ERK KINASE 6) (SAPKK3). [SWISSPROT;Acc:P52564]
0.210745481 0.127536 2616 0.605166 MAP2K3 DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 3 (EC 2.7.1.-) (MAP KINASE KINASE 3) (MAPKK 3) (MAPK/ERK KINASE 3). [SWISSPROT;Acc:P46734]
0.211226711 0.159172 2615 0.75356 XPO1 "EXPORTIN 1; EXPORTIN-1 (REQUIRED FOR CHROMOSOME REGION MAINTENANCE); EXPORTIN 1 (CRM1, YEAST, HOMOLOG); CRM1, YEAST, HOMOLOG. [RefSeq;Acc:NM_003400]"
0.211324157 0.397319 2614 1.88014 KYNU KYNURENINASE (EC 3.7.1.3) (L-KYNURENINE HYDROLASE). [SWISSPROT;Acc:Q16719]
0.211332766 0.0258274 2612 0.122212 ATP5J2 "ATP SYNTHASE F CHAIN, MITOCHONDRIAL (EC 3.6.3.14). [SWISSPROT;Acc:P56134]"
2613 DHX35 PROBABLE ATP-DEPENDENT HELICASE DDX35 (DEAH-BOX PROTEIN 35). [SWISSPROT;Acc:Q9H5Z1]
0.211333709 0.0461407 2611 0.218331 TOPBP1 TOPOISOMERASE (DNA) II BINDING PROTEIN. [RefSeq;Acc:NM_007027]
0.2113339 0.974934 2610 4.61324 ACOX1 "ACYL-COENZYME A OXIDASE 1, PEROXISOMAL (EC 1.3.3.6) (PALMITOYL-COA OXIDASE) (AOX). [SWISSPROT;Acc:Q15067]"
0.21157178 0.503361 2609 2.37915 ACSS2 "ACETYL-COENZYME A SYNTHETASE, CYTOPLASMIC (EC 6.2.1.1) (ACETATE--COA LIGASE) (ACYL-ACTIVATING ENZYME) (ACETYL-COA SYNTHETASE) (ACS) (ACECS). [SWISSPROT;Acc:Q9NR19]"
0.211947145 0.668547 2608 3.15431 ACAA1 "3-KETOACYL-COA THIOLASE, PEROXISOMAL PRECURSOR (EC 2.3.1.16) (BETA- KETOTHIOLASE) (ACETYL-COA ACYLTRANSFERASE) (PEROXISOMAL 3-OXOACYL- COA THIOLASE). [SWISSPROT;Acc:P09110]"
0.211948508 0.0751775 2607 0.354697 HMGCS1 "HYDROXYMETHYLGLUTARYL-COA SYNTHASE, CYTOPLASMIC (EC 2.3.3.10) (HMG-COA SYNTHASE) (3-HYDROXY-3-METHYLGLUTARYL COENZYME A SYNTHASE). [SWISSPROT;Acc:Q01581]"

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 bloody hugo identifier as demanded by the BMC Bioinformatics idiots
- http://analysis.yellowcouch.org/