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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expected Gene Rank description measured Hugo final
Results: HTML CSV LaTeX Showing element 1101 to 1150 of 3206 in total
expected
Rank
description
measured
Hugo
final
0.331879 2647 TUBBY RELATED PROTEIN 1 (TUBBY-LIKE PROTEIN 1). [SWISSPROT;Acc:O00294] 0.0696821 TULP1 0.209962366
0.332147 797 ADIPOCYTE PLASMA MEMBRANE-ASSOCIATED PROTEIN (BSCV PROTEIN). [SWISSPROT;Acc:Q9HDC9] 0.0870266 C20orf3 0.262012302
0.332307 1728 0.0787698 C12orf26 0.237039244
0.33238 2831 CALSYNTENIN-3 PRECURSOR. [SWISSPROT;Acc:Q9BQT9] 0.0641829 CLSTN3 0.193100969
0.332615 2190 NUCLEASE SENSITIVE ELEMENT BINDING PROTEIN 1 (Y BOX BINDING PROTEIN-1) (Y-BOX TRANSCRIPTION FACTOR) (YB-1) (CCAAT-BINDING TRANSCRIPTION FACTOR I SUBUNIT A) (CBF-A) (ENHANCER FACTOR I SUBUNIT A) (EFI-A) (DNA-BINDING PROTEIN B) (DBPB). [SWISSPROT;Acc 0.0752905 YBX1 0.226359304
0.332641 2651 TUBBY RELATED PROTEIN 3 (TUBBY-LIKE PROTEIN 3). [SWISSPROT;Acc:O75386] 0.069842 TULP3 0.209962091
0.332683 1532 NIN ONE BINDING PROTEIN; ADENOCARCINOMA ANTIGEN RECOGNIZED BY T LYMPHOCYTES 4. [RefSeq;Acc:NM_014062] 0.0805704 NOB1 0.2421837
0.332958 2907 0.057982 TMEM55A 0.174142084
0.333333 3175 0.0184372 NIPA2 0.055311655
3176 C6orf130
3177 PUTATIVE GLIALBLASTOMA CELL DIFFERENTIATION-RELATED; PUTATIVE GLIALBLASTOMA CELL DIFFERENTIATION-RELATED PROTEIN. [RefSeq;Acc:NM_016172] UBAC1
0.333672 602 0.0897926 ZNF703 0.26910439
0.334101 2354 UPSTREAM STIMULATORY FACTOR 2 (UPSTREAM TRANSCRIPTION FACTOR 2) (FOS-INTERACTING PROTEIN) (FIP) (MAJOR LATE TRANSCRIPTION FACTOR 2). [SWISSPROT;Acc:Q15853] 0.0736246 USF2 0.220366296
0.335124 2425 DNA-REPAIR PROTEIN XRCC3 (X-RAY REPAIR CROSS-COMPLEMENTING PROTEIN 3). [SWISSPROT;Acc:O43542] 0.0730211 XRCC3 0.21789278
0.335687 2645 "PROTEIN KINASE C, ZETA TYPE (EC 2.7.1.37) (NPKC-ZETA). [SWISSPROT;Acc:Q05513]" 0.0704817 PRKCZ 0.209962554
0.33698 32 PROTO-ONCOGENE TYROSINE-PROTEIN KINASE SRC (EC 2.7.1.112) (P60-SRC) (C-SRC). [SWISSPROT;Acc:P12931] 0.141847 no value 0.420935961
33 TYROSINE-PROTEIN KINASE HCK (EC 2.7.1.112) (P59-HCK/P60-HCK) (HEMOPOIETIC CELL KINASE). [SWISSPROT;Acc:P08631] HCK
0.337014 613 ZINC FINGER PROTEIN ZIC 4 (ZINC FINGER PROTEIN OF THE CEREBELLUM 4) (FRAGMENT). [SWISSPROT;Acc:Q8N9L1] 0.0906044 ZIC4 0.268844618
0.337266 1492 EPIDERMAL GROWTH FACTOR RECEPTOR PRECURSOR (EC 2.7.1.112) (RECEPTOR PROTEIN-TYROSINE KINASE ERBB-1). [SWISSPROT;Acc:P00533] 0.0818867 EGFR 0.242795598
0.337351 35 CRK-LIKE PROTEIN. [SWISSPROT;Acc:P46109] 0.142003 CRKL 0.420935465
0.33749 1232 0.0836052 KIAA0859 0.247726451
0.337708 1656 COPPER-TRANSPORTING ATPASE 1 (EC 3.6.3.4) (COPPER PUMP 1) (MENKES DISEASE-ASSOCIATED PROTEIN). [SWISSPROT;Acc:Q04656] 0.0806616 ATP7A 0.238850131
0.337743 332 "NADH-UBIQUINONE OXIDOREDUCTASE 23 KDA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 1.6.5.3) (EC 1.6.99.3) (COMPLEX I-23KD) (CI-23KD) (TYKY SUBUNIT). [SWISSPROT;Acc:O00217]" 0.0963108 NDUFS8 0.285160018
2597 AMYLOID BETA PRECURSOR PROTEIN-BINDING PROTEIN 1; AMYLOID PROTEIN-BINDING PROTEIN 1. [RefSeq;Acc:NM_003905] 0.0719023 APPBP1 0.212890571
0.337971 34 PROTO-ONCOGENE C-CRK (P38) (ADAPTER MOLECULE CRK). [SWISSPROT;Acc:P46108] 0.142264 CRK 0.420935524
0.338193 2832 CALSYNTENIN-2 PRECURSOR. [SWISSPROT;Acc:Q9H4D0] 0.0653044 CLSTN2 0.193098024
0.338281 614 DJ947L8.1.1 (NOVEL CUB AND SUSHI (SCR REPEAT) DOMAIN PROTEIN) (FRAGMENT). [SPTREMBL;Acc:Q9H4V7] 0.090945 no value 0.26884454
0.338342 37 PROTO-ONCOGENE TYROSINE-PROTEIN KINASE FGR (EC 2.7.1.112) (P55-FGR) (C-FGR). [SWISSPROT;Acc:P09769] 0.14242 FGR 0.42093503
0.338961 39 PROTO-ONCOGENE TYROSINE-PROTEIN KINASE FYN (EC 2.7.1.112) (P59-FYN) (SYN) (SLK). [SWISSPROT;Acc:P06241] 0.14268 FYN 0.420933382
0.340529 1580 SQUAMOUS CELL CARCINOMA ANTIGEN 1 (SCCA-1) (PROTEIN T4-A). [SWISSPROT;Acc:P29508] 0.0820308 SERPINB4 0.240892259
0.340556 2468 45 KDA CALCIUM-BINDING PROTEIN PRECURSOR (CAB45) (STROMAL CELL-DERIVED FACTOR 4) (SDF-4). [SWISSPROT;Acc:Q9BRK5] 0.0737619 SDF4 0.216592572
2469 "SPECTRIN BETA CHAIN, BRAIN 4 (SPECTRIN, NON-ERYTHROID BETA CHAIN 4) (BETA-V SPECTRIN) (BSPECV). [SWISSPROT;Acc:Q9NRC6]" SPTBN5
2470 LSM14B
0.340942 38 TYROSINE-PROTEIN KINASE ABL2 (EC 2.7.1.112) (TYROSINE KINASE ARG). [SWISSPROT;Acc:P42684] 0.143514 ABL2 0.420933766
0.341561 36 PROTO-ONCOGENE TYROSINE-PROTEIN KINASE ABL1 (EC 2.7.1.112) (P150) (C-ABL). [SWISSPROT;Acc:P00519] 0.143775 ABL1 0.42093506
0.341646 1366 "TESTIS-SPECIFIC HISTONE H2B; H2B HISTONE FAMILY, MEMBER U, (TESTIS-SPECIFIC). [RefSeq;Acc:NM_170610]" 0.0836563 HIST1H2BA 0.244862519
0.34213 1582 OXYSTEROLS RECEPTOR LXR-BETA (LIVER X RECEPTOR BETA) (NUCLEAR ORPHAN RECEPTOR LXR-BETA) (UBIQUITOUSLY-EXPRESSED NUCLEAR RECEPTOR) (NUCLEAR RECEPTOR NER). [SWISSPROT;Acc:P55055] 0.0824164 NR1H2 0.240892059
0.343091 2252 TRANSKETOLASE-LIKE 1 (EC 2.2.1.1) (TRANSKETOLASE 2) (TK 2) (TRANSKETOLASE RELATED PROTEIN). [SWISSPROT;Acc:P51854] 0.0765571 TKTL1 0.223139342
0.343534 1457 MEGF11 PROTEIN. [RefSeq;Acc:NM_032445] 0.0835145 MEGF11 0.24310403
0.343879 986 0.087747 HECW2 0.255168242
0.344638 568 SIMILAR TO KINASE SUPPRESSOR OF RAS (FRAGMENT). [SPTREMBL;Acc:Q8IVT5] 0.0932883 KSR1 0.270684893
0.345038 2594 "UBIQUITIN-ACTIVATING ENZYME E1C (UBA3 HOMOLOG, YEAST); UBIQUITIN-ACTIVATING ENZYME E1C (HOMOLOGOUS TO YEAST UBA3). [RefSeq;Acc:NM_003968]" 0.0734554 UBE1C 0.212890754
0.345603 2449 6-PHOSPHOGLUCONOLACTONASE (EC 3.1.1.31) (6PGL). [SWISSPROT;Acc:O95336] 0.0750119 PGLS 0.217046438
0.346067 1515 KELCH-LIKE ECH-ASSOCIATED PROTEIN 1 (CYTOSOLIC INHIBITOR OF NRF2). [SWISSPROT;Acc:Q14145] 0.0838767 KEAP1 0.242371275
0.346879 44 HEPATOCYTE NUCLEAR FACTOR 4-ALPHA (HNF-4-ALPHA) (TRANSCRIPTION FACTOR HNF-4) (TRANSCRIPTION FACTOR 14). [SWISSPROT;Acc:P41235] 0.144656 HNF4A 0.417021497
0.348604 1429 "MICROTUBULE-ASSOCIATED PROTEIN, RP/EB FAMILY, MEMBER 2; T-CELL ACTIVATION PROTEIN, EB1 FAMILY; APC-BINDING PROTEIN EB1. [RefSeq;Acc:NM_014268]" 0.0850122 MAPRE2 0.243864672
0.349234 1745 GANGLIOSIDE-INDUCED DIFFERENTIATION-ASSOCIATED PROTEIN 1-LIKE 1. [RefSeq;Acc:NM_024034] 0.0826697 GDAP1L1 0.236717215
0.349357 3018 PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E (EC 5.2.1.8) (PPIASE E) (ROTAMASE E) (CYCLOPHILIN E) (CYCLOPHILIN 33). [SWISSPROT;Acc:Q9UNP9] 0.0424091 PPIE 0.121391871
0.35015 1618 ACID CERAMIDASE PRECURSOR (EC 3.5.1.23) (ACYLSPHINGOSINE DEACYLASE) (N-ACYLSPHINGOSINE AMIDOHYDROLASE) (AC) (PUTATIVE 32 KDA HEART PROTEIN) (PHP32). [SWISSPROT;Acc:Q13510] 0.083902 ASAH1 0.239617307
0.350552 1470 TRANSCRIPTION FACTOR P65 (NUCLEAR FACTOR NF-KAPPA-B P65 SUBUNIT). [SWISSPROT;Acc:Q04206] 0.0851899 RELA 0.243016443

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/